Structure of PDB 6c3e Chain A Binding Site BS01

Receptor Information
>6c3e Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKIEHNEALLE
EAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPL
SVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASF
KMWSKLNNGTLYYMAPEHLPTEKSDVYSFAVVLWAIFANKEPYENAIAEQ
QLIMAIKSGNRPDVDDLTEYCPREIISLMKLCWEANPEARPTFPGIEEKF
RPFYLSQL
Ligand information
Ligand IDEJY
InChIInChI=1S/C14H11N3O2/c18-17(19)11-6-7-12-13(9-11)16-14(15-12)8-10-4-2-1-3-5-10/h1-7,9H,8H2,(H,15,16)
InChIKeyUMWIVOZCYNITGG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)Cc2[nH]c3ccc(cc3n2)[N+](=O)[O-]
ACDLabs 12.01c1(cc2c(cc1)nc(n2)Cc3ccccc3)[N+](=O)[O-]
CACTVS 3.385[O-][N+](=O)c1ccc2[nH]c(Cc3ccccc3)nc2c1
FormulaC14 H11 N3 O2
Name2-benzyl-5-nitro-1H-benzimidazole
ChEMBLCHEMBL4077039
DrugBank
ZINCZINC000005425467
PDB chain6c3e Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6c3e 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.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K45 L78 M92 L129 H136 A155 D156 S161 F162
Binding residue
(residue number reindexed from 1)		K37 L66 M80 L117 H124 A143 D144 S149 F150
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.20,Ki=63.1nM
BindingDB: Ki=63nM
Enzymatic activity
Catalytic site (original residue number in PDB) D138 K140 E142 N143 D156 T189
Catalytic site (residue number reindexed from 1) D126 K128 E130 N131 D144 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

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Molecular Function
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Biological Process
External links
PDB RCSB:6c3e, PDBe:6c3e, PDBj:6c3e
PDBsum6c3e
PubMed29485864
UniProtQ13546|RIPK1_HUMAN Receptor-interacting serine/threonine-protein kinase 1 (Gene Name=RIPK1)

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