Structure of PDB 5ivv Chain A Binding Site BS01

Receptor Information
>5ivv Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMAFGFEQAVREYTLQSFGEMADNFKSDYF
NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGR
RKILPEEEEYALSGWNLNNMPVLEQSVLKVPWLYVGMCFSSFCWHIEDHW
SYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVT
IMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand ID6EN
InChIInChI=1S/C14H12N4O2/c1-18-8-12(9-3-2-5-16-13(9)18)17-11-7-15-6-4-10(11)14(19)20/h2-8,17H,1H3,(H,19,20)
InChIKeyRBGNHCYGFBRIRO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1cc(Nc2cnccc2C(O)=O)c3cccnc13
OpenEye OEToolkits 2.0.4Cn1cc(c2c1nccc2)Nc3cnccc3C(=O)O
ACDLabs 12.01c13ncccc1c(Nc2c(C(O)=O)ccnc2)cn3C
FormulaC14 H12 N4 O2
Name3-[(1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)amino]pyridine-4-carboxylic acid
ChEMBLCHEMBL5277662
DrugBank
ZINCZINC000149571461
PDB chain5ivv Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ivv Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution1.848 Å
Binding residue
(original residue number in PDB)		R73 Y409 A411 D412 Y472 F480 H483 K501 W503 H571
Binding residue
(residue number reindexed from 1)		R62 Y131 A133 D134 Y184 F192 H195 K213 W215 H283
Annotation score1
Binding affinityMOAD: Kd=0.45uM
PDBbind-CN: -logKd/Ki=6.35,Kd=0.45uM
BindingDB: IC50=<100nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y184 H195 E197 H283 A295
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:5ivv, PDBe:5ivv, PDBj:5ivv
PDBsum5ivv
PubMed27427228
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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