Structure of PDB 6dq7 Chain A Binding Site BS01

Receptor Information
>6dq7 Chain A (length=294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTVREYTLQSFGEMADNFKSDYFNMPVH
MVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILP
EEEEYALSGWNLNNMPVLEQSVKVPWLYVGMCFSSFCWHIEDHWSYSINY
LHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNV
LMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDH6M
InChIInChI=1S/C19H24N6O4/c26-13-17(27)25-9-3-8-24(10-11-25)16-12-15(21-7-5-18(28)29)22-19(23-16)14-4-1-2-6-20-14/h1-2,4,6,12,26H,3,5,7-11,13H2,(H,28,29)(H,21,22,23)
InChIKeyBFXYLSMGFITUJF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OCC(=O)N1CCCN(CC1)c2cc(NCCC(O)=O)nc(n2)c3ccccn3
ACDLabs 12.01C(=O)(O)CCNc2cc(N1CCCN(C(=O)CO)CC1)nc(n2)c3ccccn3
OpenEye OEToolkits 2.0.6c1ccnc(c1)c2nc(cc(n2)N3CCCN(CC3)C(=O)CO)NCCC(=O)O
FormulaC19 H24 N6 O4
NameN-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine;
hydrolysis product of 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6dq7 Chain A Residue 601 [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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PDB6dq7 Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution1.852 Å
Binding residue
(original residue number in PDB)		Y409 Y472 F480 C481 H483 E485 K501
Binding residue
(residue number reindexed from 1)		Y126 Y178 F186 C187 H189 E191 K207
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y178 H189 E191 H277 A289
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dq7, PDBe:6dq7, PDBj:6dq7
PDBsum6dq7
PubMed
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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