Structure of PDB 4zjj Chain D Binding Site BS01

Receptor Information
>4zjj Chain D (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EILEKLRSIVSVKKKYTRFEKIGQGASGTVYTAMDVEVAIKQMNLPKKEL
IINEILVMRENKNPNIVNYLDSYGDELWVVMEYLAGGSLTDVVTETCMDE
GQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCPE
QSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNE
NPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQ
HQFLKIAKPLSSLTPLIAAAKEAT
Ligand information
Ligand ID4OR
InChIInChI=1S/C24H29ClFN5O/c1-5-31-20-8-6-15(25)12-18(20)22(28-19-13-16(26)7-9-21(19)31)27-17-10-11-30(14-17)23(32)29-24(2,3)4/h6-9,12-13,17H,5,10-11,14H2,1-4H3,(H,27,28)(H,29,32)/t17-/m0/s1
InChIKeyNIVBGOGCJSMNMG-KRWDZBQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCN1c2ccc(cc2C(=Nc3c1ccc(c3)F)N[C@H]4CCN(C4)C(=O)NC(C)(C)C)Cl
ACDLabs 12.01C(C)N3c1ccc(cc1N=C(c2c3ccc(c2)Cl)NC4CN(CC4)C(=O)NC(C)(C)C)F
OpenEye OEToolkits 1.9.2CCN1c2ccc(cc2C(=Nc3c1ccc(c3)F)NC4CCN(C4)C(=O)NC(C)(C)C)Cl
CACTVS 3.385CCN1c2ccc(F)cc2N=C(N[CH]3CCN(C3)C(=O)NC(C)(C)C)c4cc(Cl)ccc14
CACTVS 3.385CCN1c2ccc(F)cc2N=C(N[C@H]3CCN(C3)C(=O)NC(C)(C)C)c4cc(Cl)ccc14
FormulaC24 H29 Cl F N5 O
Name(S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide
ChEMBLCHEMBL3609371
DrugBank
ZINCZINC000263620793
PDB chain4zjj Chain D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4zjj Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		M301 E315 M319 N322 I327 V328 M344 F379 N383 H387 L405 T406 D407 F410
Binding residue
(residue number reindexed from 1)		M43 E54 M58 N61 I66 V67 M81 F116 N120 H124 L142 T143 D144 F147
Annotation score1
Binding affinityMOAD: Kd=9.9nM
BindingDB: IC50=18nM,Kd=9.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D389 K391 D393 N394 D407 P416 T427
Catalytic site (residue number reindexed from 1) D126 K128 D130 N131 D144 P149 T160
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:4zjj, PDBe:4zjj, PDBj:4zjj
PDBsum4zjj
PubMed26191365
UniProtQ13153|PAK1_HUMAN Serine/threonine-protein kinase PAK 1 (Gene Name=PAK1)

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