Structure of PDB 5fy8 Chain B Binding Site BS02

Receptor Information
>5fy8 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]
TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPK
SWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIP
FDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLC
SCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
Ligand information
Ligand IDN81
InChIInChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4-/m0/s1
InChIKeyODBLHEXUDAPZAU-OKKQSCSOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C([C@@H]([C@@H](C(=O)O)O)C(=O)O)C(=O)O
ACDLabs 12.01OC(C(CC(O)=O)C(O)=O)C(O)=O
CACTVS 3.385O[C@@H]([C@H](CC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C(C(C(C(=O)O)O)C(=O)O)C(=O)O
CACTVS 3.385O[CH]([CH](CC(O)=O)C(O)=O)C(O)=O
FormulaC6 H8 O7
Name3-carboxy-2,3-dideoxy-D-erythro-pentaric acid
ChEMBL
DrugBankDB01727
ZINCZINC000000895175
PDB chain5fy8 Chain B Residue 1354 [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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PDB5fy8 Crystal Structure of Human Jmjd2A in Complex with D-Threo-Isocitrate
Resolution2.343 Å
Binding residue
(original residue number in PDB)		Y132 F185 H188 S196 N198 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y126 F179 H182 S190 N192 K200 W202 H270
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G164 Y171 H182 E184 H270 S282
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:5fy8, PDBe:5fy8, PDBj:5fy8
PDBsum5fy8
PubMed
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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