Structure of PDB 3rcd Chain A Binding Site BS01

Receptor Information
>3rcd Chain A (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALLRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRPKA
NKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVREN
RGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITD
FGLVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPARE
IPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMA
RDPQRFVVIQNLDSTFYRSLLEDDDLVDAEE
Ligand information
Ligand ID03P
InChIInChI=1S/C26H25ClF3N5O3/c1-25(2,37)14-22(36)31-9-11-35-10-8-20-23(35)24(33-15-32-20)34-17-6-7-21(19(27)13-17)38-18-5-3-4-16(12-18)26(28,29)30/h3-8,10,12-13,15,37H,9,11,14H2,1-2H3,(H,31,36)(H,32,33,34)
InChIKeyZYQXEVJIFYIBHZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)c4cc(Oc1ccc(cc1Cl)Nc2ncnc3c2n(cc3)CCNC(=O)CC(O)(C)C)ccc4
OpenEye OEToolkits 1.7.2CC(C)(CC(=O)NCCn1ccc2c1c(ncn2)Nc3ccc(c(c3)Cl)Oc4cccc(c4)C(F)(F)F)O
CACTVS 3.370CC(C)(O)CC(=O)NCCn1ccc2ncnc(Nc3ccc(Oc4cccc(c4)C(F)(F)F)c(Cl)c3)c12
FormulaC26 H25 Cl F3 N5 O3
NameN-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide;
TAK-285
ChEMBLCHEMBL1614725
DrugBank
ZINCZINC000064746555
PDB chain3rcd Chain A Residue 9001 [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]
PDB3rcd Design and Synthesis of Novel Human Epidermal Growth Factor Receptor 2 (HER2)/Epidermal Growth Factor Receptor (EGFR) Dual Inhibitors Bearing a Pyrrolo[3,2-d]pyrimidine Scaffold.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		G727 V734 A751 K753 S783 L785 T798 L800 M801 G804 L852 T862 D863
Binding residue
(residue number reindexed from 1)		G18 V25 A42 K44 S70 L72 T85 L87 M88 G91 L139 T149 D150
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.77,IC50=17nM
BindingDB: IC50=17nM
Enzymatic activity
Catalytic site (original residue number in PDB) D845 A847 R849 N850 D863
Catalytic site (residue number reindexed from 1) D132 A134 R136 N137 D150
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:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3rcd, PDBe:3rcd, PDBj:3rcd
PDBsum3rcd
PubMed22003817
UniProtP04626|ERBB2_HUMAN Receptor tyrosine-protein kinase erbB-2 (Gene Name=ERBB2)

[Back to BioLiP]