4AG8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH AXITINIB (AG-013736) (N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL-VINYL)-1H- INDAZOL-6-YLSULFANYL)-BENZAMIDE)

Authors :   M. Mctigue, J. Wickersham, C. Pinko, R. S. Kania, S. Bender

Date :   24 Jan 12 (Deposition) - 26 Sep 12 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Angiogenesis, Nucleotide-Binding, Inhibitor, Phosphorylation, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Mctigue, B. W. Murray, J. H. Chen, Y. Deng, J. Solowiej, R. S. Kania
Molecular Conformations, Interactions, And Properties Associated With Drug Efficiency And Clinical Performance Among Vegfr Tk Inhibitors.
Proc. Natl. Acad. Sci. Usa V. 109 18281 2012
PubMed-ID: 22988103 | Reference-DOI: 10.1073/PNAS.1207759109

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
	Chains	:	A
	EC Number	:	2.7.10.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PACSG2
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	KINASE DOMAIN, RESIDUES 806-940,990-1171
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN RECEPTOR, KDR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1, CD309

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	AXI	1	Ligand/Ion	AXITINIB

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:848 , ALA A:866 , LYS A:868 , GLU A:885 , VAL A:899 , VAL A:914 , VAL A:916 , GLU A:917 , PHE A:918 , CYS A:919 , LYS A:920 , GLY A:922 , LEU A:1035 , CYS A:1045 , ASP A:1046 , PHE A:1047 , HOH A:2085	BINDING SITE FOR RESIDUE AXI A 2000

(no "SS Bond" information available for 4AG8)

(no "Cis Peptide Bond" information available for 4AG8)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046679	V	848	E	VGFR2_HUMAN	Polymorphism	1139776	A	V	848	E
2	UniProt	VAR_036127	G	873	R	VGFR2_HUMAN	Unclassified	---	A	G	873	R
3	CancerSNP	VAR_VGFR2_HUMAN_CCDS3497_1_02 *	G	873	R	VGFR2_HUMAN	Disease (Colorectal cancer)	---	A	G	873	R
4	UniProt	VAR_042061	A	1065	T	VGFR2_HUMAN	Polymorphism	56302315	A	A	1065	T
5	UniProt	VAR_063147	P	1147	S	VGFR2_HUMAN	Disease (HCI)	121917766	A	P	1147	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	VGFR2_HUMAN	840-868	1	A:840-868
2	RECEPTOR_TYR_KIN_III	PS00240	Receptor tyrosine kinase class III signature.	VGFR2_HUMAN	893-906	1	A:893-906
3	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	VGFR2_HUMAN	1024-1036	1	A:1024-1036

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000263923	1a	ENSE00001171700	chr4:55991756-55991394	363	VGFR2_HUMAN	1-23	23	0	-	-
1.2	ENST00000263923	2	ENSE00000716050	chr4:55987357-55987264	94	VGFR2_HUMAN	23-54	32	0	-	-
1.3	ENST00000263923	3	ENSE00000716047	chr4:55984967-55984771	197	VGFR2_HUMAN	54-120	67	0	-	-
1.4	ENST00000263923	4	ENSE00000716045	chr4:55981578-55981448	131	VGFR2_HUMAN	120-163	44	0	-	-
1.5	ENST00000263923	5	ENSE00000716043	chr4:55981209-55981041	169	VGFR2_HUMAN	164-220	57	0	-	-
1.6	ENST00000263923	6	ENSE00000716040	chr4:55980432-55980293	140	VGFR2_HUMAN	220-266	47	0	-	-
1.7	ENST00000263923	7	ENSE00000716038	chr4:55979648-55979471	178	VGFR2_HUMAN	267-326	60	0	-	-
1.8	ENST00000263923	8	ENSE00000716036	chr4:55976935-55976821	115	VGFR2_HUMAN	326-364	39	0	-	-
1.9	ENST00000263923	9	ENSE00000580228	chr4:55976733-55976570	164	VGFR2_HUMAN	364-419	56	0	-	-
1.10	ENST00000263923	10	ENSE00000716032	chr4:55974060-55973904	157	VGFR2_HUMAN	419-471	53	0	-	-
1.11	ENST00000263923	11	ENSE00000716030	chr4:55972977-55972854	124	VGFR2_HUMAN	471-512	42	0	-	-
1.12	ENST00000263923	12	ENSE00000716029	chr4:55972107-55971999	109	VGFR2_HUMAN	513-549	37	0	-	-
1.13a	ENST00000263923	13a	ENSE00001074496	chr4:55971151-55970810	342	VGFR2_HUMAN	549-663	115	0	-	-
1.14	ENST00000263923	14	ENSE00000716025	chr4:55968675-55968529	147	VGFR2_HUMAN	663-712	50	0	-	-
1.15	ENST00000263923	15	ENSE00000716023	chr4:55968195-55968064	132	VGFR2_HUMAN	712-756	45	0	-	-
1.16	ENST00000263923	16	ENSE00000716022	chr4:55964970-55964864	107	VGFR2_HUMAN	756-791	36	0	-	-
1.17	ENST00000263923	17	ENSE00000716020	chr4:55964439-55964304	136	VGFR2_HUMAN	792-837	46	1	A:816-837	22
1.18	ENST00000263923	18	ENSE00000716018	chr4:55963933-55963829	105	VGFR2_HUMAN	837-872	36	1	A:837-872	36
1.19b	ENST00000263923	19b	ENSE00001312000	chr4:55962509-55962396	114	VGFR2_HUMAN	872-910	39	1	A:872-910	39
1.20	ENST00000263923	20	ENSE00000716016	chr4:55961832-55961744	89	VGFR2_HUMAN	910-939	30	1	A:910-938	29
1.21b	ENST00000263923	21b	ENSE00000716015	chr4:55961122-55960969	154	VGFR2_HUMAN	940-991	52	0	-	-
1.22	ENST00000263923	22	ENSE00000877921	chr4:55958881-55958784	98	VGFR2_HUMAN	991-1023	33	1	A:996-1023	28
1.23	ENST00000263923	23	ENSE00001608690	chr4:55956245-55956123	123	VGFR2_HUMAN	1024-1064	41	1	A:1024-1064	41
1.24	ENST00000263923	24	ENSE00000877919	chr4:55955969-55955858	112	VGFR2_HUMAN	1065-1102	38	1	A:1065-1102	38
1.25	ENST00000263923	25	ENSE00000877918	chr4:55955640-55955541	100	VGFR2_HUMAN	1102-1135	34	1	A:1102-1135	34
1.26	ENST00000263923	26	ENSE00000877917	chr4:55955140-55955035	106	VGFR2_HUMAN	1135-1170	36	1	A:1135-1168	34
1.27	ENST00000263923	27	ENSE00000877916	chr4:55953925-55953774	152	VGFR2_HUMAN	1171-1221	51	0	-	-
1.28	ENST00000263923	28	ENSE00000877915	chr4:55948802-55948703	100	VGFR2_HUMAN	1221-1254	34	0	-	-
1.29	ENST00000263923	29	ENSE00001148006	chr4:55948208-55948123	86	VGFR2_HUMAN	1255-1283	29	0	-	-
1.30	ENST00000263923	30	ENSE00001171693	chr4:55946330-55944644	1687	VGFR2_HUMAN	1283-1356	74	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:296
 aligned with VGFR2_HUMAN | P35968 from UniProtKB/Swiss-Prot  Length:1356

    Alignment length:353
                                   825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165   
         VGFR2_HUMAN    816 HCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKTKGARFRQGKDYVGAIPVDLKRRLDSITSSQSSASSGFVEEKSLSDVEEEEAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA 1168
               SCOP domains d4ag8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhh.hhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee.......eeeee....eehhhhhhh....ee..---------------------------------------------------------....eehhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee..hhhhh........eee..eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------E------------------------R-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------S--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------PROTEIN_KINASE_ATP           ------------------------RECEPTOR_TYR_K---------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.17 [INCOMPLETE]----------------------------------Exon 1.19b  PDB: A:872-910             -----------------------------Exon 1.21b  PDB: - UniProt: 940-991                 --------------------------------Exon 1.23  PDB: A:1024-1064              Exon 1.24  PDB: A:1065-1102           --------------------------------Exon 1.26  PDB: A:1135-1168        Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.18  PDB: A:837-872           -------------------------------------Exon 1.20  PDB: A:910-938     ---------------------------------------------------Exon 1.22  PDB: A:996-1023       ------------------------------------------------------------------------------Exon 1.25  PDB: A:1102-1135       --------------------------------- Transcript 1 (2)
                4ag8 A  816 HCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPY---------------------------------------------------------YKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA 1168
                                   825       835       845       855       865       875       885       895       905       915       925       935  |      -         -         -         -         -         -|     1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165   
                                                                                                                                                    938                                                       996

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: automated matches (542)

Human (Homo sapiens) [TaxId: 9606] (452)

d4ag8a_

(no "CATH Domain" information available for 4AG8)

(no "Pfam Domain" information available for 4AG8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VGFR2_HUMAN | P35968)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051879	Hsp90 protein binding	Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
	GO:0019838	growth factor binding	Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0004716	signal transducer, downstream of receptor, with protein tyrosine kinase activity	Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0004714	transmembrane receptor protein tyrosine kinase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
	GO:0038085	vascular endothelial growth factor binding	Interacting selectively and non-covalently with a vascular endothelial growth factor.
	GO:0005021	vascular endothelial growth factor-activated receptor activity	Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0035584	calcium-mediated signaling using intracellular calcium source	A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0002042	cell migration involved in sprouting angiogenesis	The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
	GO:0035924	cellular response to vascular endothelial growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vascular endothelial growth factor stimulus.
	GO:0035162	embryonic hemopoiesis	The stages of blood cell formation that take place within the embryo.
	GO:0003158	endothelium development	The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2000352	negative regulation of endothelial cell apoptotic process	Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0038033	positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway	A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
	GO:0010595	positive regulation of endothelial cell migration	Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0051894	positive regulation of focal adhesion assembly	Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
	GO:0016239	positive regulation of macroautophagy	Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
	GO:0051901	positive regulation of mitochondrial depolarization	Any process that activates, maintains or increases the frequency, rate or extent of the change in the membrane potential of the mitochondria from negative to positive.
	GO:0090141	positive regulation of mitochondrial fission	Any process that increases the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
	GO:0051770	positive regulation of nitric-oxide synthase biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0050927	positive regulation of positive chemotaxis	Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:2001214	positive regulation of vasculogenesis	Any process that activates or increases the frequency, rate or extent of vasculogenesis.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0001570	vasculogenesis	The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0097443	sorting endosome	A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ag8)

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	4ag8
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		Orientation in Membranes	:	OPM
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	VGFR2_HUMAN \| P35968
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	2.7.10.1
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	602089
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	VGFR2_HUMAN \| P35968
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1vr2	HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE DOMAIN
1y6a	CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2- ANILINO-5-ARYL- OXAZOLE INHIBITOR
1y6b	CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2- ANILINO-5-ARYL- OXAZOLE INHIBITOR
1ywn	VEGFR2 IN COMPLEX WITH A NOVEL 4-AMINO-FURO[2,3-D] PYRIMIDINE
2x1w	CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2
2x1x	CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM
2xir	CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH PF- 00337210 (N,2-DIMETHYL-6-(7-(2- MORPHOLINOETHOXY)QUINOLIN-4-YLOXY) BENZOFURAN-3-CARBOXAMIDE)
4agc	CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH AXITINIB (AG-013736) (N- METHYL-2-(3-((E)-2-PYRIDIN-2- YL-VINYL)-1H-INDAZOL -6-YLSULFANYL)-BENZAMIDE)
4agd	CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH SUNITINIB (SU11248) (N-2- DIETHYLAMINOETHYL)-5-((Z)-(5- FLUORO-2-OXO-1H-INDOL-3 -YLIDENE)METHYL)-2,4-DIMETHYL-1H-PYRROLE-3- CARBOXAMIDE)
4asd	CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH SORAFENIB (BAY 43-9006)
4ase	CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH TIVOZANIB (AV-951)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (3, 3)

Exons (9, 9)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (68, 68)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File