Structure of PDB 6c4d Chain A Binding Site BS01

Receptor Information
>6c4d Chain A (length=267) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVIKMKSSDFLEGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEA
KMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSV
KGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKM
WSKLNNEEHNGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEP
YENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPT
FPGIEEKFRPFYLSQLE
Ligand information
Ligand IDEJP
InChIInChI=1S/C24H20ClN5O3/c1-28-18-8-7-16(12-26)11-20(18)33-14-19(23(28)31)29-10-9-17-21(24(29)32)27-30(22(17)25)13-15-5-3-2-4-6-15/h2-8,11,19H,9-10,13-14H2,1H3/t19-/m0/s1
InChIKeyJWKONLKXWPCOJF-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)[CH](COc2cc(ccc12)C#N)N3CCc4c(Cl)n(Cc5ccccc5)nc4C3=O
ACDLabs 12.01N#Cc2ccc1N(C(C(COc1c2)N3C(c5c(CC3)c(n(Cc4ccccc4)n5)Cl)=O)=O)C
OpenEye OEToolkits 2.0.6CN1c2ccc(cc2OCC(C1=O)N3CCc4c(nn(c4Cl)Cc5ccccc5)C3=O)C#N
OpenEye OEToolkits 2.0.6CN1c2ccc(cc2OC[C@@H](C1=O)N3CCc4c(nn(c4Cl)Cc5ccccc5)C3=O)C#N
CACTVS 3.385CN1C(=O)[C@H](COc2cc(ccc12)C#N)N3CCc4c(Cl)n(Cc5ccccc5)nc4C3=O
FormulaC24 H20 Cl N5 O3
Name(3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile
ChEMBLCHEMBL4100398
DrugBank
ZINC
PDB chain6c4d Chain A Residue 1100 [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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PDB6c4d Discovery of 7-Oxo-2,4,5,7-tetrahydro-6 H-pyrazolo[3,4- c]pyridine Derivatives as Potent, Orally Available, and Brain-Penetrating Receptor Interacting Protein 1 (RIP1) Kinase Inhibitors: Analysis of Structure-Kinetic Relationships.
Resolution2.52 Å
Binding residue
(original residue number in PDB)		K45 L70 V76 L78 L90 M92 V134 A155 D156 L157 L159 S161 F162
Binding residue
(residue number reindexed from 1)		K31 L56 V62 L64 L76 M78 V120 A141 D142 L143 L145 S147 F148
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.04,Ki=0.912nM
BindingDB: IC50=1.3nM,Ki=0.912011nM
Enzymatic activity
Catalytic site (original residue number in PDB) D138 K140 E142 N143 D156 T189
Catalytic site (residue number reindexed from 1) D124 K126 E128 N129 D142 T162
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6c4d, PDBe:6c4d, PDBj:6c4d
PDBsum6c4d
PubMed29485864
UniProtQ13546|RIPK1_HUMAN Receptor-interacting serine/threonine-protein kinase 1 (Gene Name=RIPK1)

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