Structure of PDB 3v5q Chain A Binding Site BS01

Receptor Information
>3v5q Chain A (length=263) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIHVQHIKRRDIVLKRELKVFLAECYNLSPTKDKMLVAVKALPTLAARKD
FQREAELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNKFLRAHGP
ELGLSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFG
MDVYSTDYYRTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQ
PWFQLSNTEVIECITQGRVLERPRVCPKEVYDVMLGCWQREPQQRLNIKE
IYKILHALGKATP
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 A Residue 902 [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)		A570 K572 E588 L592 F617 E618 Y619 M620 K621 G623 F675 H677 L686 I695 G696 D697 F698
Binding residue
(residue number reindexed from 1)		A38 K40 E54 L58 F83 E84 Y85 M86 K87 G89 F126 H128 L137 I146 G147 D148 F149
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.40,IC50=0.04uM
BindingDB: IC50=40nM
Enzymatic activity
Catalytic site (original residue number in PDB) D679 R683 N684 D697 S706
Catalytic site (residue number reindexed from 1) D130 R134 N135 D148 S155
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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