Structure of PDB 3r7o Chain A Binding Site BS01

Receptor Information
>3r7o Chain A (length=301) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTL
LDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICL
RSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLAS
KKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKLPVKWMA
LESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRR
LLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHHHH
H
Ligand information
Ligand IDM61
InChIInChI=1S/C28H32N6O5S/c1-33(17-24-18-38-10-11-39-24)40(36,37)32-22-4-2-19-3-5-27-26(28(35)25(19)13-22)12-20(14-30-27)21-15-31-34(16-21)23-6-8-29-9-7-23/h2-5,12-16,23-24,29,32H,6-11,17-18H2,1H3/t24-/m1/s1
InChIKeyIVWIPVHBADPMSP-XMMPIXPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CN(CC1COCCO1)S(=O)(=O)Nc2ccc3c(c2)C(=O)c4cc(cnc4C=C3)c5cnn(c5)C6CCNCC6
CACTVS 3.370CN(C[CH]1COCCO1)[S](=O)(=O)Nc2ccc3C=Cc4ncc(cc4C(=O)c3c2)c5cnn(c5)C6CCNCC6
OpenEye OEToolkits 1.7.6CN(C[C@@H]1COCCO1)S(=O)(=O)Nc2ccc3c(c2)C(=O)c4cc(cnc4C=C3)c5cnn(c5)C6CCNCC6
CACTVS 3.370CN(C[C@@H]1COCCO1)[S](=O)(=O)Nc2ccc3C=Cc4ncc(cc4C(=O)c3c2)c5cnn(c5)C6CCNCC6
ACDLabs 12.01O=C4c1cc(ccc1C=Cc5ncc(c2cn(nc2)C3CCNCC3)cc45)NS(=O)(=O)N(CC6OCCOC6)C
FormulaC28 H32 N6 O5 S
NameN-[(2R)-1,4-dioxan-2-ylmethyl]-N-methyl-N'-{5-oxo-3-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-5H-benzo[4,5]cyclohepta[1,2-b]pyridin-7-yl}sulfuric diamide
ChEMBLCHEMBL1802917
DrugBank
ZINCZINC000072139828
PDB chain3r7o Chain A Residue 1 [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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PDB3r7o Structural basis for selective small molecule kinase inhibition of activated c-Met.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I1084 G1085 R1086 V1092 A1108 Y1159 M1160 K1161 G1163 D1164 R1208 M1211 D1222
Binding residue
(residue number reindexed from 1)		I37 G38 R39 V45 A61 Y112 M113 K114 G116 D117 R161 M164 D175
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.36,Kd=4.4nM
BindingDB: IC50=3.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1204 A1206 R1208 N1209 D1222
Catalytic site (residue number reindexed from 1) D157 A159 R161 N162 D175
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine 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:3r7o, PDBe:3r7o, PDBj:3r7o
PDBsum3r7o
PubMed21247903
UniProtP08581|MET_HUMAN Hepatocyte growth factor receptor (Gene Name=MET)

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