Structure of PDB 4ith Chain A Binding Site BS01

Receptor Information
>4ith Chain A (length=247) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVIKMKSSDFLVSLAFHRTQGLMIMKTVNEALLEEAKMMNRLRHSRVVKL
LGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAY
LHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLGTLYYMAPEH
LNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRP
DVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Ligand information
Ligand IDRCM
InChIInChI=1S/C13H12ClN3O2/c1-17-12(18)10(16-13(17)19)5-7-6-15-11-8(7)3-2-4-9(11)14/h2-4,6,10,15H,5H2,1H3,(H,16,19)/t10-/m1/s1
InChIKeyWIKGAEMMNQTUGL-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1C(=O)N[CH](Cc2c[nH]c3c(Cl)cccc23)C1=O
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=O)Cc2c[nH]c3c2cccc3Cl
OpenEye OEToolkits 1.7.6CN1C(=O)[C@H](NC1=O)Cc2c[nH]c3c2cccc3Cl
CACTVS 3.370CN1C(=O)N[C@H](Cc2c[nH]c3c(Cl)cccc23)C1=O
ACDLabs 12.01O=C1NC(C(=O)N1C)Cc3c2cccc(Cl)c2nc3
FormulaC13 H12 Cl N3 O2
Name(5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione
ChEMBLCHEMBL370438
DrugBank
ZINCZINC000013983453
PDB chain4ith Chain A Residue 307 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ith Structural Basis of RIP1 Inhibition by Necrostatins.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		M67 L70 V75 V76 M92 H136 I154 A155 D156 S161 F162
Binding residue
(residue number reindexed from 1)		M39 L42 V47 V48 M64 H108 I126 A127 D128 S133 F134
Annotation score1
Binding affinityMOAD: ic50=0.3169uM
PDBbind-CN: -logKd/Ki=6.50,IC50=316.9nM
BindingDB: IC50=200nM,EC50=18nM
Enzymatic activity
Catalytic site (original residue number in PDB) D138 K140 E142 N143 D156 T189
Catalytic site (residue number reindexed from 1) D110 K112 E114 N115 D128 T142
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:4ith, PDBe:4ith, PDBj:4ith
PDBsum4ith
PubMed23473668
UniProtQ13546|RIPK1_HUMAN Receptor-interacting serine/threonine-protein kinase 1 (Gene Name=RIPK1)

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