Structure of PDB 5wf7 Chain B Binding Site BS09

Receptor Information
>5wf7 Chain B (length=765) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTVDKIASALSVLAEEVPQNHSRLVNFLLEETEKRAPQPRHLSKTDPFAH
MKSKAIDAPEGVPTMDVKFKQHSGEYGKSRNSGRRFQYPVVCIKPDREPV
PPYRFHHAEIRKNILALNSQLNFVPPRSQKIAKRAQAEYAATLAPYLEPW
LRKLNIEGCTKSNLIRFMASDMSPQAVRNASMFTEAWDRVFNDQSKLRRV
ALRDILMLDKNVEPIFDNKRAKALMQKVIDALGSYTTLGCLICFSHDCEH
GEIERDNQKRCFSLEEIGGLMPSLRRKWAAQIEQHPPCRNECYRIHGPPW
SENEVGTLEWMFATIGYSQTLRPECFVGAILGRPCWDVHRKLQELDLPPV
EIPKQKSLPWYDRRKKQLMSDWADATITHEHAVRELFAPCHHDGPCTAAN
GCPCASAGTHPVLCERFCLCTAEECPLKFTGCACHSSGKTCLQRQGRPCI
CVQLNRECDPTLCKGCGARERADPENAYDEVLHSTGCQNVALQRGAAKAV
VLGKSQLEACGYGLFAAEDIEEGEFVIEYTGELISHDEGVRREHRRGDVN
KVSYLFTLLEQEGIWVDAAIYGNLSRYINHATDGNIMPKIMYVNHEWRIK
FTAIKDIKAGEELFFNYGDNFPNLTKKLVEPLLVPKTTQPLFDPLSKVQL
LPGQPLPQHPIDDSWLLLKHRDNLQDFIDLRPEEKEFLQEWDAFILRRHI
SSEQYLPRYFLRFVREKADWLVSKRSRGEEFSKLVATLLARRVLPERVVI
EATQVLNDARGRLRE
Ligand information
Ligand IDA9G
InChIInChI=1S/C31H38N6O2/c1-6-22(5)37-18-20(3)29-25(30(38)34-17-26-19(2)13-21(4)35-31(26)39)14-24(15-27(29)37)23-7-8-28(33-16-23)36-11-9-32-10-12-36/h7-8,13-16,18,22,32H,6,9-12,17H2,1-5H3,(H,34,38)(H,35,39)/t22-/m0/s1
InChIKeyFKSFKBQGSFSOSM-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC[C@H](C)n1cc(c2c1cc(cc2C(=O)NCC3=C(C=C(NC3=O)C)C)c4ccc(nc4)N5CCNCC5)C
ACDLabs 12.01c3c(c1cnc(cc1)N2CCNCC2)cc5c(c3C(NCC=4C(=O)NC(C)=CC=4C)=O)c(cn5C(CC)C)C
OpenEye OEToolkits 2.0.6CCC(C)n1cc(c2c1cc(cc2C(=O)NCC3=C(C=C(NC3=O)C)C)c4ccc(nc4)N5CCNCC5)C
CACTVS 3.385CC[CH](C)n1cc(C)c2c1cc(cc2C(=O)NCC3=C(C)C=C(C)NC3=O)c4ccc(nc4)N5CCNCC5
CACTVS 3.385CC[C@H](C)n1cc(C)c2c1cc(cc2C(=O)NCC3=C(C)C=C(C)NC3=O)c4ccc(nc4)N5CCNCC5
FormulaC31 H38 N6 O2
Name1-[(2S)-butan-2-yl]-N-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indole-4-carboxamide
ChEMBLCHEMBL3287735
DrugBank
ZINCZINC000072318146
PDB chain5wf7 Chain B Residue 8009 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5wf7 An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y303 R304 G808 Y809 R843 V853 Y878
Binding residue
(residue number reindexed from 1)		Y103 R104 G511 Y512 R546 V552 Y577
Annotation score1
Binding affinityMOAD: ic50=98.5uM
PDBbind-CN: -logKd/Ki=4.01,IC50=98.5uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042054 histone methyltransferase activity
Biological Process
GO:0006338 chromatin remodeling

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5wf7, PDBe:5wf7, PDBj:5wf7
PDBsum5wf7
PubMed29904056
UniProtG0RYC6;
G0SDW4

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