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(-) Description

Title :  HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE DOMAIN IN COMPLEX WITH AAL993
 
Authors :  W. Stark, A. Goepfert
Date :  20 Nov 15  (Deposition) - 16 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kdr, Kinase Domain, Atp-Binding Site, Vegfr2 Inhibitors, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Bold, C. Schnell, P. Furet, P. Mcsheehy, J. Bruggen, J. Mestan, P. W. Manley, P. Druckes, M. Burglin, U. Durler, J. Loretan, R. Reuter, M. Wartmann, A. Theuer, B. Bauer-Probst, G. Martiny-Baron, P. Allegrini, A. Goepfert, J. Wood, A. Littlewood-Evans
A Novel Potent Oral Series Of Vegfr2 Inhibitors Abrogate Tumor Growth By Inhibiting Angiogenesis.
J. Med. Chem. V. 59 132 2016
PubMed-ID: 26629594  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01582
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
    Chains: A, B
    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: PVL1393
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: KINASE DOMAIN, RESIDUES 806-1171
    Gene: KDR, FLK1, VEGFR2
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15T22Ligand/Ion2-(PYRIDIN-4-YLMETHYLAMINO)-~{N}-[3-(TRIFLUOROMETHYL)PHENYL]BENZAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15T21Ligand/Ion2-(PYRIDIN-4-YLMETHYLAMINO)-~{N}-[3-(TRIFLUOROMETHYL)PHENYL]BENZAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15T21Ligand/Ion2-(PYRIDIN-4-YLMETHYLAMINO)-~{N}-[3-(TRIFLUOROMETHYL)PHENYL]BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:848 , ALA A:866 , LYS A:868 , GLU A:885 , VAL A:898 , VAL A:899 , VAL A:914 , VAL A:916 , GLU A:917 , CYS A:919 , LEU A:1019 , HIS A:1026 , LEU A:1035 , ILE A:1044 , CYS A:1045 , ASP A:1046 , PHE A:1047binding site for residue 5T2 A 1201
2AC2SOFTWAREALA B:866 , LYS B:868 , GLU B:885 , ILE B:892 , VAL B:898 , VAL B:899 , VAL B:914 , VAL B:916 , GLU B:917 , CYS B:919 , LEU B:1019 , HIS B:1026 , LEU B:1035 , ILE B:1044 , CYS B:1045 , ASP B:1046binding site for residue 5T2 B 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EW3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EW3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EW3)

(-) Exons   (0, 0)

(no "Exon" information available for 5EW3)

(-) Sequences/Alignments

Asymmetric 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:274
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee.......eeeee.....hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..........hhhhhhh...hhhhhhhhhhhhhhhhh............hhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ew3 A  821 PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKVKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA 1168
                                   830       840       850       860       870       880       890       900       910       920       930       940|     1006      1016      1026      1036      1046 ||   1074      1084      1094      1104      1114      1124      1134      1144      1154      1164    
                                                                                                                                                 940|                                               1048|                                                                                                     
                                                                                                                                                  997                                                1067                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.hhh.eeeeeeee.eeeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee.......eeeee.....hhhhhhhhhhh.ee.....eehhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee..........hhhhhhh...hhhhhhhhhhhhhhhhh...............hhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ew3 B  820 LPYDASKWEFPRDRLKLGKPLGGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQ 1165
                                   829       839 ||    853       863       873       883       893       903       913       923       933     |1001      1011      1021      1031      1041      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      
                                               841|                                                                                          939|                                              1048|                                                                                                  
                                                846                                                                                           998                                               1067
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EW3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EW3)

(-) Gene Ontology  (68, 68)

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  5ew3
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  VGFR2_HUMAN | P35968
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  2.7.10.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VGFR2_HUMAN | P35968: 1vr2 1y6a 1y6b 1ywn 2m59 2met 2meu 2oh4 2p2h 2p2i 2qu5 2qu6 2rl5 2x1w 2x1x 2xir 3b8q 3b8r 3be2 3c7q 3cjf 3cjg 3cp9 3cpb 3cpc 3dtw 3efl 3ewh 3kvq 3s35 3s36 3s37 3u6j 3v2a 3v6b 3vhe 3vhk 3vid 3vnt 3vo3 3wzd 3wze 4ag8 4agc 4agd 4asd 4ase

(-) Related Entries Specified in the PDB File

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