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Linked KDM5A jmj domain bound to the inhibitor (R)-2-((2- CHLOROPHENYL)(2-(piperidin-1-YL)ETHOXY)METHYL)-1L2-PYRROLO[3,2- B]PYRIDINE-7-carboxylic acid (compound N51)

Analyse Linked KDM5A jmj domain bound to the inhibitor (R)-2-((2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6BH0
Type
protein
Length
291 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lysine-specific demethylase 5A, linked KDM5A jmj domain
EC
1.14.11.-
UniProt
P29375
Ligands
DO1, MN
Pockets
1 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALysine-specific demethylase 5A, linked KDM5A jmj domain (EC 1.14.11.-)protein29132% helix, 24% strandP29375

Ligands and binding sites

  • DO1 · 2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl) ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
  • MN · Manganese (II) ion · metal · chains A
  • DMS · Dimethyl sulfoxide · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15020.690.7958DO1, MN

Compared structures

  • 6BH0 · LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR… · the same entry in another collection · chain A against A, TM-score 1.00
  • P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.96

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