Structure of PDB 5a7p Chain B Binding Site BS03

Receptor Information

>5a7p Chain B (length=346) Species: 9606 (Homo sapiens)

LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKS
WYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPF
DKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCS
CRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF

Ligand information

• Ligand ID: 6Z1
• InChI: InChI=1S/C17H13N3O5/c1-9-6-14(20-25-9)16(22)19-11-2-3-15(21)12(8-11)13-7-10(17(23)24)4-5-18-13/h2-8,21H,1H3,(H,19,22)(H,23,24)
• InChIKey: SXVDKQLIPBWXCB-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc(no1)C(=O)Nc2ccc(c(c2)c3cc(ccn3)C(=O)O)O
  CACTVS 3.385: Cc1onc(c1)C(=O)Nc2ccc(O)c(c2)c3cc(ccn3)C(O)=O
• Formula: C17 H13 N3 O5
• Name: 2-[5-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
• ChEMBL: CHEMBL3775867
• ZINC: ZINC000263621063
• PDB chain: 5a7p Chain B Residue 1361

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a7p Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
• Resolution: 2.28 Å
• Binding residue (original residue number in PDB): N86 Y132 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): N79 Y125 F178 H181 E183 K199 W201 K234 H269
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G163 Y170 H181 E183 H269 S281
• 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:5a7p, PDBe:5a7p, PDBj:5a7p
• PDBsum: 5a7p
• PubMed: 26699912
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)