Structure of PDB 5h3q Chain A Binding Site BS01

Receptor Information
>5h3q Chain A (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNKM
LVAVKALKEARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMR
HGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAG
LHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRW
MPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQG
RELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLD
VL
Ligand information
Ligand ID7HF
InChIInChI=1S/C26H31F2N5O3/c1-4-36-25-17(2)24(33(31-25)19-8-6-5-7-9-19)30-26(34)29-23-16-32(12-13-35-3)15-20(23)18-10-11-21(27)22(28)14-18/h5-11,14,20,23H,4,12-13,15-16H2,1-3H3,(H2,29,30,34)/t20-,23+/m0/s1
InChIKeySQGLEZDWHPDRDX-NZQKXSOJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCOc1c(c(n(n1)c2ccccc2)NC(=O)NC3CN(CC3c4ccc(c(c4)F)F)CCOC)C
CACTVS 3.385CCOc1nn(c2ccccc2)c(NC(=O)N[CH]3CN(CCOC)C[CH]3c4ccc(F)c(F)c4)c1C
CACTVS 3.385CCOc1nn(c2ccccc2)c(NC(=O)N[C@@H]3CN(CCOC)C[C@H]3c4ccc(F)c(F)c4)c1C
OpenEye OEToolkits 2.0.6CCOc1c(c(n(n1)c2ccccc2)NC(=O)N[C@@H]3CN(C[C@H]3c4ccc(c(c4)F)F)CCOC)C
FormulaC26 H31 F2 N5 O3
Name1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea
ChEMBLCHEMBL4090531
DrugBank
ZINCZINC000584905438
PDB chain5h3q Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5h3q The juxtamembrane region of TrkA kinase is critical for inhibitor selectivity
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L486 G488 H489 I490 F521 K544 E560 V573 M587 F589 L641 V647 H648 G667 D668 F669 G670 L795
Binding residue
(residue number reindexed from 1)		L3 G5 H6 I7 F38 K55 E67 V80 M94 F96 L148 V154 H155 G174 D175 F176 G177 L302
Annotation score1
Binding affinityMOAD: ic50=6nM
PDBbind-CN: -logKd/Ki=8.22,IC50=6nM
BindingDB: IC50=6.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) D650 A652 R654 N655 D668 S677 L689
Catalytic site (residue number reindexed from 1) D157 A159 R161 N162 D175 S184 L196
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:5h3q, PDBe:5h3q, PDBj:5h3q
PDBsum5h3q
PubMed28159414
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

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