Structure of PDB 5a3t Chain A Binding Site BS02

Receptor Information
>5a3t Chain A (length=454) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSP
EEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWH
IEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLL
HQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEA
VNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVAS
TVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTC
FMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALK
LRAE
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 chain5a3t Chain A Residue 1756 [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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PDB5a3t Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y425 W486 Y488 F496 H499 E501 K517 W519 H587 V600 N601
Binding residue
(residue number reindexed from 1)		Y128 W187 Y189 F197 H200 E202 K218 W220 H288 V301 N302
Annotation score1
Binding affinityMOAD: Ki=0.001uM
PDBbind-CN: -logKd/Ki=8.40,IC50=0.004uM
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G182 Y189 H200 E202 H288 A300
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:5a3t, PDBe:5a3t, PDBj:5a3t
PDBsum5a3t
PubMed27214403
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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