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BioLiP

Structure of PDB 5a3w Chain A Binding Site BS03

Receptor Information
>5a3w Chain A (length=455) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAE
Ligand information
Ligand IDPD2
InChIInChI=1S/C7H5NO4/c9-6(10)4-1-2-8-5(3-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
InChIKeyMJIVRKPEXXHNJT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)c1ccnc(c1)C(O)=O
ACDLabs 10.04O=C(O)c1nccc(C(=O)O)c1
OpenEye OEToolkits 1.5.0c1cnc(cc1C(=O)O)C(=O)O
FormulaC7 H5 N O4
NamePYRIDINE-2,4-DICARBOXYLIC ACID
ChEMBLCHEMBL316034
DrugBank
ZINCZINC000000391915
PDB chain5a3w Chain A Residue 1757 [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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PDB5a3w Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y425 Y488 F496 H499 E501 K517 W519 H587
Binding residue
(residue number reindexed from 1)		Y129 Y190 F198 H201 E203 K219 W221 H289
Annotation score1
Binding affinityMOAD: Ki=0.39uM
PDBbind-CN: -logKd/Ki=5.82,IC50=1.5uM
BindingDB: IC50=3000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G183 Y190 H201 E203 H289 A301
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:5a3w, PDBe:5a3w, PDBj:5a3w
PDBsum5a3w
PubMed27214403
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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