Structure of PDB 5vmp Chain B Binding Site BS02

Receptor Information
>5vmp Chain B (length=347) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWK
PRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSD
KYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLR
TILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGE
PKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYG
IPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAV
LCSCRVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand ID9FJ
InChIInChI=1S/C18H20N2O3/c1-23-14-5-6-15-12(9-14)3-2-4-13(15)10-20-17-11-19-8-7-16(17)18(21)22/h5-9,11,13,20H,2-4,10H2,1H3,(H,21,22)/t13-/m0/s1
InChIKeyNXQKMWGCRMQRSS-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1ccc2c(c1)CCCC2CNc3cnccc3C(=O)O
OpenEye OEToolkits 2.0.6COc1ccc2c(c1)CCC[C@H]2CNc3cnccc3C(=O)O
CACTVS 3.385COc1ccc2[C@@H](CCCc2c1)CNc3cnccc3C(O)=O
ACDLabs 12.01O=C(O)c1ccncc1NCC2CCCc3c2ccc(c3)OC
CACTVS 3.385COc1ccc2[CH](CCCc2c1)CNc3cnccc3C(O)=O
FormulaC18 H20 N2 O3
Name3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid
ChEMBLCHEMBL4211946
DrugBank
ZINC
PDB chain5vmp 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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PDB5vmp Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models.
Resolution2.48 Å
Binding residue
(original residue number in PDB)		Y132 F185 H188 K206 W208 H240 K241 H276
Binding residue
(residue number reindexed from 1)		Y128 F181 H184 K202 W204 H236 K237 H272
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G166 Y173 H184 E186 H272 S284
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:5vmp, PDBe:5vmp, PDBj:5vmp
PDBsum5vmp
PubMed28835804
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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