Structure of PDB 5kmi Chain A Binding Site BS01

Receptor Information
>5kmi Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQGHIIENPQCVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKML
VAVKALKESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMR
HGDLNRFLRSHGPDAKLGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHF
VHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPP
ESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGREL
ERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Ligand information
Ligand ID6UE
InChIInChI=1S/C25H20N4O/c1-16-26-15-22(23(27-16)17-9-3-2-4-10-17)28-25(30)29-24-20-13-7-5-11-18(20)19-12-6-8-14-21(19)24/h2-15,24H,1H3,(H2,28,29,30)
InChIKeyPKOROKYRNIDSPX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(NC(=O)N[CH]2c3ccccc3c4ccccc24)c(n1)c5ccccc5
OpenEye OEToolkits 2.0.5Cc1ncc(c(n1)c2ccccc2)NC(=O)NC3c4ccccc4-c5c3cccc5
CACTVS 3.385Cc1ncc(NC(=O)N[C@H]2c3ccccc3c4ccccc24)c(n1)c5ccccc5
FormulaC25 H20 N4 O
Name1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea
ChEMBLCHEMBL4468886
DrugBank
ZINCZINC000584646161
PDB chain5kmi Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5kmi Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		G488 H489 I490 F521 K544 E560 L564 M587 H648 G667 D668 G670
Binding residue
(residue number reindexed from 1)		G3 H4 I5 F31 K54 E67 L71 M94 H152 G171 D172 G174
Annotation score1
Binding affinityBindingDB: IC50=99nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5kmi, PDBe:5kmi, PDBj:5kmi
PDBsum5kmi
PubMed28039433
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

[Back to BioLiP]