Structure of PDB 6h4w Chain A Binding Site BS01

Receptor Information

>6h4w Chain A (length=337) Species: 9606 (Homo sapiens)

NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEH
GKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAG
EFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRVKISMD
VFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 6h4w Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6h4w C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.
• Resolution: 2.81 Å
• Binding residue (original residue number in PDB): H188 E190 H276
• Binding residue (residue number reindexed from 1): H173 E175 H261
• 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): G155 Y162 H173 E175 H261 S273
• 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:6h4w, PDBe:6h4w, PDBj:6h4w
• PDBsum: 6h4w
• PubMed: 31158747
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)