Structure of PDB 2rfn Chain A Binding Site BS01

Receptor Information
>2rfn Chain A (length=268) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALNPELVQAVQHVVIGPSSLIVHFNEVIFGCVYHGTLLDNDGKKIHCAVK
SLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYM
KHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNC
MLDEKFTVKVADPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPP
YPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSEL
VSRISAIFSTFIGEHYVH
Ligand information
Ligand IDAM7
InChIInChI=1S/C35H35FN4O5/c1-39-34(19-24-7-4-3-5-8-24)38-23-27(35(39)41)25-9-10-31(28(36)20-25)45-30-11-12-37-29-22-33(32(42-2)21-26(29)30)44-16-6-13-40-14-17-43-18-15-40/h3-5,7-12,20-23H,6,13-19H2,1-2H3
InChIKeyPEGWVOKOYYAQEV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN1C(=NC=C(C1=O)c2ccc(c(c2)F)Oc3ccnc4c3cc(c(c4)OCCCN5CCOCC5)OC)Cc6ccccc6
CACTVS 3.341COc1cc2c(Oc3ccc(cc3F)C4=CN=C(Cc5ccccc5)N(C)C4=O)ccnc2cc1OCCCN6CCOCC6
ACDLabs 10.04O=C1N(C(=NC=C1c5ccc(Oc4ccnc3cc(OCCCN2CCOCC2)c(OC)cc34)c(F)c5)Cc6ccccc6)C
FormulaC35 H35 F N4 O5
Name2-benzyl-5-(3-fluoro-4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinolin-4-yl]oxy}phenyl)-3-methylpyrimidin-4(3H)-one
ChEMBLCHEMBL505896
DrugBank
ZINC
PDB chain2rfn 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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PDB2rfn c-Met inhibitors with novel binding mode show activity against several hereditary papillary renal cell carcinoma-related mutations.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I1084 F1089 V1092 A1108 K1110 F1124 E1127 G1128 M1131 L1140 L1142 V1155 L1157 Y1159 M1160 K1161 G1163 M1211
Binding residue
(residue number reindexed from 1)		I28 F29 V32 A48 K50 F64 E67 G68 M71 L80 L82 V95 L97 Y99 M100 K101 G103 M151
Annotation score1
Binding affinityMOAD: ic50=5nM
PDBbind-CN: -logKd/Ki=8.30,IC50=5nM
BindingDB: IC50=8.9nM,Ki=8.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1204 A1206 R1208 N1209 D1222
Catalytic site (residue number reindexed from 1) D144 A146 R148 N149 D162
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
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Biological Process
External links
PDB RCSB:2rfn, PDBe:2rfn, PDBj:2rfn
PDBsum2rfn
PubMed18055465
UniProtP08581|MET_HUMAN Hepatocyte growth factor receptor (Gene Name=MET)

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