Structure of PDB 5c9c Chain A Binding Site BS01

Receptor Information
>5c9c Chain A (length=254) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNAPTPQQLQAFKN
EVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEM
IKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATS
ILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQII
FMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIEL
LARS
Ligand information
Ligand ID4Z5
InChIInChI=1S/C23H29FN6O/c1-13-9-18(24)19(29-22(31)26-8-7-23(3,4)5)11-16(13)17-10-15-12-27-21(25-6)30-20(15)28-14(17)2/h9-12H,7-8H2,1-6H3,(H2,26,29,31)(H,25,27,28,30)
InChIKeyHHCBMISMPSAZBF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1cc(c(cc1F)C)c2c(nc3c(c2)cnc(n3)NC)C)NCCC(C)(C)C
OpenEye OEToolkits 1.9.2Cc1cc(c(cc1c2cc3cnc(nc3nc2C)NC)NC(=O)NCCC(C)(C)C)F
CACTVS 3.385CNc1ncc2cc(c(C)nc2n1)c3cc(NC(=O)NCCC(C)(C)C)c(F)cc3C
FormulaC23 H29 F N6 O
Name1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea;
LY3009120
ChEMBLCHEMBL3577124
DrugBank
ZINCZINC000205861291
PDB chain5c9c Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5c9c Inhibition of RAF Isoforms and Active Dimers by LY3009120 Leads to Anti-tumor Activities in RAS or BRAF Mutant Cancers.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A480 K482 E500 L504 L513 I526 T528 C531 G592 D593 F594
Binding residue
(residue number reindexed from 1)		A33 K35 E51 L55 L64 I77 T79 C82 G143 D144 F145
Annotation score1
Binding affinityBindingDB: IC50=31nM
Enzymatic activity
Catalytic site (original residue number in PDB) D575 K577 N579 N580 D593 S615
Catalytic site (residue number reindexed from 1) D126 K128 N130 N131 D144 S150
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5c9c, PDBe:5c9c, PDBj:5c9c
PDBsum5c9c
PubMed26343583
UniProtP15056|BRAF_HUMAN Serine/threonine-protein kinase B-raf (Gene Name=BRAF)

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