Structure of PDB 6dq6 Chain A Binding Site BS01

Receptor Information
>6dq6 Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRREYTLQSFGEMADNFKSDYFNMPVHM
VPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPE
EEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSSFCWHIEDHWSY
SINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIM
NPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDH6J
InChIInChI=1S/C19H24N6O4S/c1-2-30(28,29)25-11-5-10-24(12-13-25)17-14-16(21-9-7-18(26)27)22-19(23-17)15-6-3-4-8-20-15/h2-4,6,8,14H,1,5,7,9-13H2,(H,26,27)(H,21,22,23)
InChIKeyCPNWZGJHUIZVEZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C=CS(=O)(=O)N1CCCN(CC1)c2cc(nc(n2)c3ccccn3)NCCC(=O)O
CACTVS 3.385OC(=O)CCNc1cc(nc(n1)c2ccccn2)N3CCCN(CC3)[S](=O)(=O)C=C
ACDLabs 12.01C1CCN(CCN1S([C@H]=C)(=O)=O)c3cc(NCCC(=O)O)nc(c2ccccn2)n3
FormulaC19 H24 N6 O4 S
NameN-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine
ChEMBLCHEMBL4294426
DrugBank
ZINC
PDB chain6dq6 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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PDB6dq6 Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Resolution1.587 Å
Binding residue
(original residue number in PDB)		R73 Y409 D412 Y472 F480 C481 H483 E485 K501 L536
Binding residue
(residue number reindexed from 1)		R62 Y125 D128 Y182 F190 C191 H193 E195 K211 L246
Annotation score1
Binding affinityMOAD: Kd=8.5uM
PDBbind-CN: -logKd/Ki=5.07,Kd=8.5uM
BindingDB: Kd=9000nM,IC50=83000nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y182 H193 E195 H281 A293
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dq6, PDBe:6dq6, PDBj:6dq6
PDBsum6dq6
PubMed30392349
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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