Research workbench

Linked KDM5A jmj domain bound to the inhibitor 2-((2-CHLOROPHENYL)(2- (1-methyl-1H-imidazol-2-YL)ETHOXY)METHYL)-1H-PYRROLO[3,2-B]PYRIDINE- 7-carboxylic acid (compound N47)

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

PDB: 6BGZ
Type: protein
Length: 293 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: DNV, MN
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 5A, linked KDM5A jmj domain (EC 1.14.11.-)	protein	293	31% helix, 24% strand	P29375

Ligands and binding sites

DNV · 2-{(S)-(2-chlorophenyl)[2-(1-methyl-1H-imidazol-2-yl) ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
MN · Manganese (II) ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.67	0.80	56	DNV, MN, GOL
2	81	0.37	0.76	17	empty
3	53	0.37	0.80	18	empty

Compared structures

6BGZ · 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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P29375
Elsewhere: RCSB PDB 6BGZ · PDBe 6BGZ · UniProt P29375

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