Structure of PDB 5isl Chain A Binding Site BS01

Receptor Information
>5isl Chain A (length=306) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRPREAFGFEQAVREYTLQSFGEMADNF
KSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFP
VKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLMKVPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDL
LHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAE
AVNFCT
Ligand information
Ligand IDMMK
InChIInChI=1S/C15H22N4O3/c1-4-19(8-7-18(2)3)14(20)11-16-10-13-9-12(15(21)22)5-6-17-13/h5-9,16H,4,10-11H2,1-3H3,(H,21,22)/b8-7+
InChIKeyRTKGUAPXWDCFNW-BQYQJAHWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN(C=CN(C)C)C(=O)CNCc1cc(ccn1)C(O)=O
CACTVS 3.385CCN(\C=C\N(C)C)C(=O)CNCc1cc(ccn1)C(O)=O
OpenEye OEToolkits 1.7.6CCN(/C=C/N(C)C)C(=O)CNCc1cc(ccn1)C(=O)O
OpenEye OEToolkits 1.7.6CCN(C=CN(C)C)C(=O)CNCc1cc(ccn1)C(=O)O
ACDLabs 12.01O=C(O)c1ccnc(c1)CNCC(=O)N(\C=C\N(C)C)CC
FormulaC15 H22 N4 O3
Name2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000263620993
PDB chain5isl 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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PDB5isl Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution1.694 Å
Binding residue
(original residue number in PDB)		Y409 W470 Y472 F480 H483 E485 K501 W503 H571 V584 N585
Binding residue
(residue number reindexed from 1)		Y136 W188 Y190 F198 H201 E203 K219 W221 H289 V302 N303
Annotation score1
Binding affinityMOAD: Kd=0.052uM
PDBbind-CN: -logKd/Ki=7.28,Kd=0.052uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y190 H201 E203 H289 A301
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:5isl, PDBe:5isl, PDBj:5isl
PDBsum5isl
PubMed27427228
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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