Structure of PDB 4dbn Chain B Binding Site BS01

Receptor Information
>4dbn Chain B (length=263) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQA
FKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETK
FEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGL
ATVKSRWGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYS
NINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLF
PQILASIELLARS
Ligand information
Ligand ID0JA
InChIInChI=1S/C27H19ClFN5O3S/c28-22-16(2-1-3-17(22)27(13-30)10-11-27)24(36)31-20-12-15(6-7-18(20)29)37-21-9-8-19-25(33-21)38-26(32-19)34-23(35)14-4-5-14/h1-3,6-9,12,14H,4-5,10-11H2,(H,31,36)(H,32,34,35)
InChIKeyMDPMAXSABUPRJI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Fc1ccc(Oc2ccc3nc(NC(=O)C4CC4)sc3n2)cc1NC(=O)c5cccc(c5Cl)C6(CC6)C#N
ACDLabs 12.01N#CC6(c1cccc(c1Cl)C(=O)Nc5c(F)ccc(Oc2nc3sc(nc3cc2)NC(=O)C4CC4)c5)CC6
OpenEye OEToolkits 1.7.6c1cc(c(c(c1)C2(CC2)C#N)Cl)C(=O)Nc3cc(ccc3F)Oc4ccc5c(n4)sc(n5)NC(=O)C6CC6
FormulaC27 H19 Cl F N5 O3 S
Name2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]benzamide
ChEMBLCHEMBL2063743
DrugBank
ZINCZINC000059083294
PDB chain4dbn Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dbn Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors. 1. Exploration of [5,6]-fused bicyclic scaffolds.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		A480 K482 E500 V503 L504 L513 I526 T528 W530 C531 F582 G592 D593 F594
Binding residue
(residue number reindexed from 1)		A34 K36 E54 V57 L58 L67 I80 T82 W84 C85 F136 G146 D147 F148
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,IC50=7.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) D575 K577 N579 N580 D593 W603 S615
Catalytic site (residue number reindexed from 1) D129 K131 N133 N134 D147 W157 S159
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:4dbn, PDBe:4dbn, PDBj:4dbn
PDBsum4dbn
PubMed22376051
UniProtP15056|BRAF_HUMAN Serine/threonine-protein kinase B-raf (Gene Name=BRAF)

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