Structure of PDB 5iwf Chain A Binding Site BS01

Receptor Information
>5iwf 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]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMGFEQAVREYTLQSFGEMADNFKSDYFN
MPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRR
KILPEEEEYALSGWNLNNMPVLEQSVKVPWLYVGMCFSSFCWHIEDHWSY
SINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIM
NPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDLQT
InChIInChI=1S/C15H25N5O2/c1-4-20(8-7-19(2)3)14(21)11-17-10-13-9-12(15(16)22)5-6-18-13/h5-6,9,17H,4,7-8,10-11H2,1-3H3,(H2,16,22)
InChIKeyPNFMVADNCOGWME-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN(CCN(C)C)C(=O)CNCc1cc(ccn1)C(N)=O
OpenEye OEToolkits 1.7.6CCN(CCN(C)C)C(=O)CNCc1cc(ccn1)C(=O)N
FormulaC15 H25 N5 O2
Name2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide;
KDOAM25A
ChEMBLCHEMBL4078388
DrugBank
ZINCZINC000263620895
PDB chain5iwf 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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PDB5iwf Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution2.289 Å
Binding residue
(original residue number in PDB)		Y409 W470 Y472 F480 H483 E485 D486 K501 W503 V584 N585
Binding residue
(residue number reindexed from 1)		Y130 W180 Y182 F190 H193 E195 D196 K211 W213 V294 N295
Annotation score1
Binding affinityBindingDB: IC50=8e+1nM,Kd=2700nM
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:5iwf, PDBe:5iwf, PDBj:5iwf
PDBsum5iwf
PubMed27427228
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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