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Asym./Biol. Unit (Jmol Viewer)

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

Title :   PHOSPHOINOSITIDE-DEPENDENT KINASE-1 (PDK1) KINASE DOMAIN WITH 1,1-DIMETHYLETHYL {(3R,6S)-1-[2-AMINO-6-(3-AMINO-1H-INDAZOL-6-YL)-4-PYRIMIDINYL]-6-METHYL-3-PIPERIDINYL}CARBAMATE

Authors :   J. R. Medina, C. J. Becker, C. W. Blackledge, C. Duquenne, Y. Feng, S. W. G D. Heerding, W. H. Li, W. H. Miller, S. P. Romeril, D. Scherzer, A. Shu, M A. R. Chadderton, M. Dumble, C. M. Gradiner, S. Gilbert, Q. Liu, S. K. Ra V. Sudakin, H. Xiang, P. G. Brady, N. Campobasso, P. Ward, J. M. Axten

Date :   17 Jan 11 (Deposition) - 09 Mar 11 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Kinase Domain, Agc Kinase, Signal Tranduction, Atp & Phosphoinositide, Phosphorylation On S241, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Medina, C. J. Becker, C. W. Blackledge, C. Duquenne, Y. Feng, S. W. Grant, D. Heerding, W. H. Li, W. H. Miller, S. P. Romeril, D. Scherzer, A. Shu, M. A. Bobko, A. R. Chadderton, M. Dumble, C. M. Gardiner, S. Gilbert, Q. Liu, S. K. Rabindran, V. Sudakin, H. Xiang, P. G. Brady, N. Campobasso, P. Ward, J. M. Axten
Structure-Based Design Of Potent And Selective 3-Phosphoinositide-Dependent Kinase-1 (Pdk1) Inhibitors.
J. Med. Chem. V. 54 1871 2011
PubMed-ID: 21341675 | Reference-DOI: 10.1021/JM101527U
(for further references see the PDB file header)

Molecule 1 - 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	KINASE DOMAIN, RESIDUES 48-359
	Gene	:	PDK1, PDPK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HPDK1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	3Q5	1	Ligand/Ion	TERT-BUTYL {(3R,6S)-1-[2-AMINO-6-(3-AMINO-2H-INDAZOL-6-YL)PYRIMIDIN-4-YL]-6-METHYLPIPERIDIN-3-YL}CARBAMATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:31 , GLU A:90 , SER A:94 , VAL A:96 , ALA A:109 , LYS A:111 , GLU A:130 , MET A:134 , LEU A:159 , SER A:160 , TYR A:161 , ALA A:162 , LEU A:212 , THR A:222 , ASP A:223 , HOH A:389	BINDING SITE FOR RESIDUE 3Q5 A 360
2	AC2	SOFTWARE	ARG A:106 , HIS A:351 , GOL A:362	BINDING SITE FOR RESIDUE SO4 A 1
3	AC3	SOFTWARE	ALA A:103 , THR A:104 , SER A:105 , HIS A:139 , SER A:191 , TRP A:347 , GLU A:348 , ASN A:349 , LEU A:350 , HIS A:351	BINDING SITE FOR RESIDUE GOL A 361
4	AC4	SOFTWARE	SO4 A:1 , HOH A:4 , GLU A:107 , SER A:160 , TYR A:161	BINDING SITE FOR RESIDUE GOL A 362

(no "SS Bond" information available for 3QD3)

(no "Cis Peptide Bond" information available for 3QD3)

(no "SAP(SNP)/Variant" information available for 3QD3)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	PDPK1_HUMAN	88-111	1	A:88-111
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	PDPK1_HUMAN	201-213	1	A:201-213

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	ENST00000342085	1a	ENSE00001944688	chr16:2587965-2588137	173	PDPK1_HUMAN	1-8	8	0	-	-
1.6c	ENST00000342085	6c	ENSE00001640744	chr16:2607704-2607964	261	PDPK1_HUMAN	9-95	87	1	A:71-95	25
1.7	ENST00000342085	7	ENSE00001620065	chr16:2611481-2611523	43	PDPK1_HUMAN	96-110	15	1	A:96-110	15
1.8b	ENST00000342085	8b	ENSE00001694535	chr16:2611772-2611909	138	PDPK1_HUMAN	110-156	47	1	A:110-156	47
1.9b	ENST00000342085	9b	ENSE00001744256	chr16:2615554-2615698	145	PDPK1_HUMAN	156-204	49	1	A:156-204	49
1.10a	ENST00000342085	10a	ENSE00001705748	chr16:2616357-2616454	98	PDPK1_HUMAN	204-237	34	1	A:204-231	28
1.13	ENST00000342085	13	ENSE00001704745	chr16:2627426-2627501	76	PDPK1_HUMAN	237-262	26	1	A:241-262	22
1.14	ENST00000342085	14	ENSE00001686272	chr16:2631296-2631364	69	PDPK1_HUMAN	262-285	24	1	A:262-285	24
1.15b	ENST00000342085	15b	ENSE00001743545	chr16:2631608-2631704	97	PDPK1_HUMAN	285-317	33	1	A:285-317	33
1.16a	ENST00000342085	16a	ENSE00001314244	chr16:2633413-2633586	174	PDPK1_HUMAN	318-375	58	1	A:318-358	41
1.17	ENST00000342085	17	ENSE00000946017	chr16:2636677-2636894	218	PDPK1_HUMAN	376-448	73	0	-	-
1.18	ENST00000342085	18	ENSE00000946018	chr16:2645794-2645851	58	PDPK1_HUMAN	448-467	20	0	-	-
1.19	ENST00000342085	19	ENSE00000946019	chr16:2647124-2647276	153	PDPK1_HUMAN	468-518	51	0	-	-
1.20b	ENST00000342085	20b	ENSE00001505218	chr16:2647652-2653189	5538	PDPK1_HUMAN	519-556	38	0	-	-

Asymmetric/Biological Unit

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

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Chain A from PDB  Type:PROTEIN  Length:279
 aligned with PDPK1_HUMAN | O15530 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:288
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
          PDPK1_HUMAN    71 PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKL 358
               SCOP domains d3qd3a_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------Pkinase-3qd3A01 A:82-341                                                                                                                                                                                                                                            ----------------- Pfam domains
         Sec.struct. author .......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee..---------....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: A:71-95  Exon 1.7       ---------------------------------------------------------------------------------------------Exon 1.10a  PDB: A:204-231        ------------------------Exon 1.14  PDB: A:262-28--------------------------------Exon 1.16a  PDB: A:318-358 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.8b  PDB: A:110-156 UniProt: 110-156     --------------------------------------------------------------------------------Exon 1.13  PDB: A:241-262 ----------------------Exon 1.15b  PDB: A:285-317       ----------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------Exon 1.9b  PDB: A:156-204 UniProt: 156-204       ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3qd3 A  71 PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS---------sFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKL 358
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|        -|      250       260       270       280       290       300       310       320       330       340       350        
                                                                                                                                                                                          231       241-SEP

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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

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

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

Family: automated matches (529)

Protein domain: automated matches (529)

Human (Homo sapiens) [TaxId: 9606] (438)

d3qd3a_

(no "CATH Domain" information available for 3QD3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Homo sapiens (Human) (521)

Pkinase-3qd3A01

A:82-341

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDPK1_HUMAN | O15530)

molecular function
	GO:0004676	3-phosphoinositide-dependent protein kinase activity	Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of a phosphatidylinositol-3-phosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005158	insulin receptor binding	Interacting selectively and non-covalently with the insulin receptor.
	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:0016004	phospholipase activator activity	Increases the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a glycerophospholipid.
	GO:0043274	phospholipase binding	Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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.
biological process
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0032148	activation of protein kinase B activity	Any process that initiates the activity of the inactive enzyme protein kinase B.
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0071364	cellular response to epidermal 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 an epidermal growth factor stimulus.
	GO:0032869	cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0007173	epidermal growth factor receptor signaling pathway	A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0097191	extrinsic apoptotic signaling pathway	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
	GO:0048041	focal adhesion assembly	The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
	GO:0006972	hyperosmotic response	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0010667	negative regulation of cardiac muscle cell apoptotic process	Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0034122	negative regulation of toll-like receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway.
	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	GO:0018107	peptidyl-threonine phosphorylation	The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0090004	positive regulation of establishment of protein localization to plasma membrane	Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
	GO:0010518	positive regulation of phospholipase activity	Any process that increases the frequency, rate or extent of phospholipase activity, the hydrolysis of a phospholipid.
	GO:0051281	positive regulation of release of sequestered calcium ion into cytosol	Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
	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:0043122	regulation of I-kappaB kinase/NF-kappaB signaling	Any process that modulates I-kappaB kinase/NF-kappaB signaling.
	GO:0010594	regulation of endothelial cell migration	Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0043304	regulation of mast cell degranulation	Any process that modulates the frequency, rate, or extent of mast cell degranulation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0003323	type B pancreatic cell development	The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
cellular component
	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:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 3qd3)

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	3qd3
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	2.7.11.1
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (9, 9)

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