Structure of PDB 5fpv Chain B Binding Site BS02

Receptor Information
>5fpv Chain B (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVP
PEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQ
EAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDM
VKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK
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 chain5fpv Chain B Residue 1358 [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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PDB5fpv Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Resolution2.44 Å
Binding residue
(original residue number in PDB)		Y133 Y176 Y178 F186 H189 E191 K207 W209 H277 T290 N291
Binding residue
(residue number reindexed from 1)		Y125 Y163 Y165 F173 H176 E178 K194 W196 H264 T277 N278
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G171 Y178 H189 E191 H277 S289
Catalytic site (residue number reindexed from 1) G158 Y165 H176 E178 H264 S276
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
External links
PDB RCSB:5fpv, PDBe:5fpv, PDBj:5fpv
PDBsum5fpv
PubMed27214403
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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