Structure of PDB 5vgi Chain B Binding Site BS02

Receptor Information
>5vgi Chain B (length=345) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSC
RKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
Ligand information
Ligand ID9DJ
InChIInChI=1S/C24H25N3O2/c1-27(19-8-3-2-4-9-19)20-10-11-21-17(14-20)6-5-7-18(21)15-26-23-16-25-13-12-22(23)24(28)29/h2-4,8-14,16,18,26H,5-7,15H2,1H3,(H,28,29)/t18-/m0/s1
InChIKeyXSMABFRQESMONQ-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(c1ccccc1)c2ccc3[CH](CCCc3c2)CNc4cnccc4C(O)=O
OpenEye OEToolkits 2.0.6CN(c1ccccc1)c2ccc3c(c2)CCCC3CNc4cnccc4C(=O)O
CACTVS 3.385CN(c1ccccc1)c2ccc3[C@@H](CCCc3c2)CNc4cnccc4C(O)=O
ACDLabs 12.01c1cc(C(O)=O)c(cn1)NCC2CCCc3c2ccc(c3)N(c4ccccc4)C
OpenEye OEToolkits 2.0.6CN(c1ccccc1)c2ccc3c(c2)CCC[C@H]3CNc4cnccc4C(=O)O
FormulaC24 H25 N3 O2
Name3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid
ChEMBLCHEMBL4216044
DrugBank
ZINC
PDB chain5vgi Chain B Residue 503 [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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PDB5vgi Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		N86 Y132 F185 H188 K206 W208 H240 K241 H276
Binding residue
(residue number reindexed from 1)		N78 Y124 F177 H180 K198 W200 H232 K233 H268
Annotation score1
Binding affinityBindingDB: IC50=104nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G162 Y169 H180 E182 H268 S280
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:5vgi, PDBe:5vgi, PDBj:5vgi
PDBsum5vgi
PubMed28835804
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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