Structure of PDB 3v5q Chain B Binding Site BS01

Receptor Information
>3v5q Chain B (length=265) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIHVQHIKRRDIVLKRELGFKVFLAECYNLSPTKDKMLVAVKALKDPTLA
ARKDFQREAELLTNLQHEHIVKFYGVCGDPLIMVFEYMKHGDLNKFLRAH
GPELGLSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGD
FGMDVYSTDYYRTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYG
KQPWFQLSNTEVIECITQGRVLERPRVCPKEVYDVMLGCWQREPQQRLNI
KEIYKILHALGKATP
Ligand information
Ligand ID0F4
InChIInChI=1S/C27H20F3N5O2/c28-27(29,30)16-4-1-5-18(12-16)33-26(37)34-20-7-2-6-19(13-20)32-21-9-10-22-23(14-17-8-3-11-31-17)25(36)35-24(22)15-21/h1-15,31-32H,(H,35,36)(H2,33,34,37)/b23-14-
InChIKeyJCRUDKWPDBIGME-UCQKPKSFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370FC(F)(F)c1cccc(NC(=O)Nc2cccc(Nc3ccc4c(NC(=O)C4=Cc5[nH]ccc5)c3)c2)c1
OpenEye OEToolkits 1.7.6c1cc(cc(c1)NC(=O)Nc2cccc(c2)Nc3ccc4c(c3)NC(=O)C4=Cc5ccc[nH]5)C(F)(F)F
OpenEye OEToolkits 1.7.6c1cc(cc(c1)NC(=O)Nc2cccc(c2)Nc3ccc\4c(c3)NC(=O)/C4=C\c5ccc[nH]5)C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cc(ccc1)NC(=O)Nc2cccc(c2)Nc3ccc\4c(c3)NC(=O)C/4=C/c5cccn5
CACTVS 3.370FC(F)(F)c1cccc(NC(=O)Nc2cccc(Nc3ccc\4c(NC(=O)C\4=C\c5[nH]ccc5)c3)c2)c1
FormulaC27 H20 F3 N5 O2
Name1-(3-{[(3Z)-2-oxo-3-(1H-pyrrol-2-ylmethylidene)-2,3-dihydro-1H-indol-6-yl]amino}phenyl)-3-[3-(trifluoromethyl)phenyl]urea
ChEMBLCHEMBL2037224
DrugBank
ZINCZINC000084705661
PDB chain3v5q Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3v5q Discovery of GNF-5837, a Selective TRK Inhibitor with Efficacy in Rodent Cancer Tumor Models.
Resolution2.2001 Å
Binding residue
(original residue number in PDB)		L544 A570 K572 E588 L592 L595 F617 Y619 M620 G623 F675 H677 L686 I695 G696 D697 F698
Binding residue
(residue number reindexed from 1)		L18 A40 K42 E58 L62 L65 F85 Y87 M88 G91 F128 H130 L139 I148 G149 D150 F151
Annotation score1
Binding affinityBindingDB: IC50=40nM
Enzymatic activity
Catalytic site (original residue number in PDB) D679 R683 N684 D697 S706
Catalytic site (residue number reindexed from 1) D132 R136 N137 D150 S157
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:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3v5q, PDBe:3v5q, PDBj:3v5q
PDBsum3v5q
PubMed24900443
UniProtQ16288|NTRK3_HUMAN NT-3 growth factor receptor (Gene Name=NTRK3)

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