Structure of PDB 5dey Chain A Binding Site BS01

Receptor Information
>5dey Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIK
QMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAG
GSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGM
DGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWS
LGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLN
RCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNN
Ligand information
Ligand ID59T
InChIInChI=1S/C25H25ClN6O3/c1-14-4-3-5-21(30-14)15-6-7-18(20(26)9-15)19-8-16-10-29-25(28-2)31-23(16)32(24(19)33)11-22-34-12-17(27)13-35-22/h3-10,17,22H,11-13,27H2,1-2H3,(H,28,29,31)/t17-,22-
InChIKeyZBCMHWUFWQFPLV-VVOJOOEHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1ncc2C=C(C(=O)N(C[C@H]3OC[C@H](N)CO3)c2n1)c4ccc(cc4Cl)c5cccc(C)n5
ACDLabs 12.01n1c(cccc1C)c2ccc(c(c2)Cl)C=3C(=O)N(c4nc(ncc4C=3)NC)CC5OCC(CO5)N
OpenEye OEToolkits 1.9.2Cc1cccc(n1)c2ccc(c(c2)Cl)C3=Cc4cnc(nc4N(C3=O)CC5OCC(CO5)N)NC
CACTVS 3.385CNc1ncc2C=C(C(=O)N(C[CH]3OC[CH](N)CO3)c2n1)c4ccc(cc4Cl)c5cccc(C)n5
FormulaC25 H25 Cl N6 O3
Name8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
ChEMBLCHEMBL3770443
DrugBank
ZINC
PDB chain5dey Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dey Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pK a Polar Moiety.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		A297 K299 E315 V342 M344 Y346 L347 D393 L396
Binding residue
(residue number reindexed from 1)		A48 K50 E66 V93 M95 Y97 L98 D144 L147
Annotation score1
Binding affinityMOAD: Ki=3.7nM
PDBbind-CN: -logKd/Ki=8.43,Ki=3.7nM
BindingDB: Ki=3.7nM,IC50=69nM
Enzymatic activity
Catalytic site (original residue number in PDB) N389 K391 D393 N394 D407 P416 T427
Catalytic site (residue number reindexed from 1) N140 K142 D144 N145 D158 P167 T178
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dey, PDBe:5dey, PDBj:5dey
PDBsum5dey
PubMed26713112
UniProtQ13153|PAK1_HUMAN Serine/threonine-protein kinase PAK 1 (Gene Name=PAK1)

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