Structure of PDB 5u62 Chain A Binding Site BS02

Receptor Information

>5u62 Chain A (length=349) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHS
QGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPI
TMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAI
FGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESY
DYRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPG
KMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVG
KLYVWDLEVCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL

Ligand information

Ligand ID

7WD

InChI

InChI=1S/C15H17N3O2/c16-15-17-7-12-5-4-10(8-18(12)15)6-11-2-1-3-13-14(11)20-9-19-13/h1-3,7,10H,4-6,8-9H2,(H2,16,17)/t10-/m0/s1

InChIKey

GXMMFNNBTMLUSG-JTQLQIEISA-N

SMILES

Software	SMILES
CACTVS 3.385	Nc1ncc2CC[CH](Cn12)Cc3cccc4OCOc34
CACTVS 3.385	Nc1ncc2CC[C@H](Cn12)Cc3cccc4OCOc34
OpenEye OEToolkits 2.0.6	c1cc(c2c(c1)OCO2)CC3CCc4cnc(n4C3)N
OpenEye OEToolkits 2.0.6	c1cc(c2c(c1)OCO2)C[C@@H]3CCc4cnc(n4C3)N
ACDLabs 12.01	c14OCOc1c(CC3CCc2cnc(n2C3)N)ccc4

Formula

C15 H17 N3 O2

Name

(6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine

PDB chain

5u62 Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5u62 Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.
Resolution	1.9 Å
Binding residue (original residue number in PDB)	F97 Y148 D310 Y365 R367
Binding residue (residue number reindexed from 1)	F19 Y70 D226 Y281 R283
Annotation score	1
Binding affinity	MOAD: ic50=1.3uM PDBbind-CN: -logKd/Ki=5.89,IC50=1.3uM BindingDB: IC50=1300nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5u62, PDBe:5u62, PDBj:5u62
PDBsum	5u62
PubMed	27992714
UniProt	O75530\|EED_HUMAN Polycomb protein EED (Gene Name=EED)

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