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Linked KDM5A jmj domain bound to the inhibitor 2-(((2-((2- (DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL) isonicotinamid

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

PDB
5IWF
Type
protein
Length
298 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lysine-specific demethylase 5A,LYSINE-specific demethylase 5A
EC
1.14.11.-
UniProt
P29375
Ligands
LQT, MN
Pockets
2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALysine-specific demethylase 5A,LYSINE-specific demethylase 5A (EC 1.14.11.-)protein29832% helix, 22% strandP29375

Ligands and binding sites

  • LQT · 2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide · ligand · chains A
  • MN · Manganese (II) ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14930.700.8068LQT, MN
2550.320.7717empty

Compared structures

  • 5IWF · 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 0.95

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