Structure of PDB 4pmp Chain A Binding Site BS01

Receptor Information
>4pmp Chain A (length=280) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLKMLVAVKALKSARQDFQ
REAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDA
KLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLV
GQGLVVKIGDFGMSRIYSTDYYRVGTMLPIRWMPPESILYRKFTTESDVW
SFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMR
GCWQREPQQRHSIKDVHARLQALAQAHHHH
Ligand information
Ligand ID31W
InChIInChI=1S/C21H18F3N3O2S/c22-21(23,24)29-18-8-4-16(5-9-18)26-20(28)27(17-6-7-17)13-14-2-1-3-15(12-14)19-25-10-11-30-19/h1-5,8-12,17H,6-7,13H2,(H,26,28)
InChIKeyVXBUABPTAFKXED-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(cc(c1)c2nccs2)CN(C3CC3)C(=O)Nc4ccc(cc4)OC(F)(F)F
ACDLabs 12.01FC(F)(F)Oc1ccc(cc1)NC(=O)N(C2CC2)Cc3cccc(c3)c4nccs4
CACTVS 3.385FC(F)(F)Oc1ccc(NC(=O)N(Cc2cccc(c2)c3sccn3)C4CC4)cc1
FormulaC21 H18 F3 N3 O2 S
Name1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea
ChEMBLCHEMBL3298269
DrugBank
ZINCZINC000098208378
PDB chain4pmp Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pmp Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		A542 L564 V573 F589 E590 Y591 M592 L657 G667 D668 F669
Binding residue
(residue number reindexed from 1)		A38 L56 V65 F81 E82 Y83 M84 L149 G159 D160 F161
Annotation score1
Binding affinityMOAD: Kd~400nM
PDBbind-CN: -logKd/Ki=6.40,Kd~400nM
BindingDB: Kd=400nM,IC50=549nM
Enzymatic activity
Catalytic site (original residue number in PDB) D650 A652 R654 N655 D668 S677 L689
Catalytic site (residue number reindexed from 1) D142 A144 R146 N147 D160 S168 L178
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:4pmp, PDBe:4pmp, PDBj:4pmp
PDBsum4pmp
PubMed24914455
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

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