Structure of PDB 5oy3 Chain A Binding Site BS04

Receptor Information

>5oy3 Chain A (length=450) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCT
DPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDEN
WDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESHIIKFGTNIDLSDAK
RWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTP
GHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWW
PILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPL
TAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKF
CLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFV
TSEGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAPA

Ligand information

Ligand ID

AKG

InChI

InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)

InChIKey

KPGXRSRHYNQIFN-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04	O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6	C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385	OC(=O)CCC(=O)C(O)=O

Formula

C5 H6 O5

Name

2-OXOGLUTARIC ACID

PDB chain

5oy3 Chain A Residue 1703 [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	5oy3 Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity.
Resolution	2.136 Å
Binding residue (original residue number in PDB)	K1381 T1387 H1390 S1398 N1400 H1470
Binding residue (residue number reindexed from 1)	K193 T199 H202 S210 N212 H282
Annotation score	5

Enzymatic activity

Enzyme Commision number

1.14.11.68: [histone H3]-trimethyl-L-lysine(27) demethylase.

External links

PDB	RCSB:5oy3, PDBe:5oy3, PDBj:5oy3
PDBsum	5oy3
PubMed	29220567
UniProt	O15054\|KDM6B_HUMAN Lysine-specific demethylase 6B (Gene Name=KDM6B)

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