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MolNFT v1 · #122551 · protein

Linked KDM5A jmj domain bound to the inhibitor C49 (2-{[(2-{[(E)-2- (DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-oxoethyl) AMINO]METHYL}PYRIDINE-4-carboxylic acid)

5ISL · Lysine-specific demethylase 5A: “Linked KDM5A jmj domain bound to the inhibitor C49 (2-{[(2-{[(E)-2…”. X-ray diffraction, 2 ligands (MMK, MN), 2 pockets (best druggability 0.67). MolNFT v1 #122551 on GenesisL1: 3D structure, binding…

PDB
5ISL
Type
protein
Length
306 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lysine-specific demethylase 5A
EC
1.14.11.-
UniProt
P29375
Ligands
MMK, MN
Pockets
2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALysine-specific demethylase 5A (EC 1.14.11.-)protein30631% helix, 23% strandP29375

Ligands and binding sites

  • MMK · 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid · ligand · chains A
  • MN · Manganese (II) ion · metal · chains A
  • GOL · Glycerol · additive · chains A
  • EDO · 1,2-ethanediol · additive · 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
13970.670.8051MMK, MN
21110.440.7820EDO

Compared structures

  • 5ISL · Linked KDM5A Jmj Domain Bound to the Inhibitor C49… · 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 0.94

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