Structure of PDB 5kmm Chain A Binding Site BS01

Receptor Information
>5kmm 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]
SGLQGHIIACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLV
AVKALKESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRH
GDLNRFLRSHGPDAKLGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHF
VHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPP
ESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGREL
ERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
H
Ligand information
Ligand ID6UJ
InChIInChI=1S/C22H18N4O/c1-15-23-14-20(21(24-15)17-9-3-2-4-10-17)26-22(27)25-19-13-7-11-16-8-5-6-12-18(16)19/h2-14H,1H3,(H2,25,26,27)
InChIKeyQTGKTWMSCVUXHK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5Cc1ncc(c(n1)c2ccccc2)NC(=O)Nc3cccc4c3cccc4
CACTVS 3.385Cc1ncc(NC(=O)Nc2cccc3ccccc23)c(n1)c4ccccc4
FormulaC22 H18 N4 O
Name1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea
ChEMBLCHEMBL4584074
DrugBank
ZINCZINC000584646195
PDB chain5kmm Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5kmm Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		L486 F521 E560 L564 M587 F646 H648 D668 G670
Binding residue
(residue number reindexed from 1)		L3 F30 E66 L70 M93 F150 H152 D172 G174
Annotation score1
Binding affinityBindingDB: IC50=4100nM
Enzymatic activity
Catalytic site (original residue number in PDB) D650 A652 R654 N655 D668 S677 L689
Catalytic site (residue number reindexed from 1) D154 A156 R158 N159 D172 S181 L193
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:5kmm, PDBe:5kmm, PDBj:5kmm
PDBsum5kmm
PubMed28039433
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

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