MolNFT v1 · #144027 · protein

Linked KDM5A jmj domain bound to the inhibitor (R)-N-(1-(3-isopropyl- 1H-pyrazole-5-CARBONYL)PYRROLIDIN-3-YL)CYCLOPROPANECARBOXAMIDE (compound N54)

6BH2 · Lysine-specific demethylase 5A, linked KDM5A jmj domain: “Linked KDM5A jmj domain bound to the inhibitor (R)-N-(1-(3-isopropyl…”. X-ray diffraction, 2 ligands (90V, MN), 3 pockets (best druggability 0.69). MolNFT v1 #144027 on…

PDB: 6BH2
Type: protein
Length: 295 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: 90V, MN
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 30% 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	295	30% helix, 24% strand	P29375

Ligands and binding sites

90V · N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide · ligand · chains A
MN · Manganese (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · 5 copies · 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	386	0.69	0.82	54	MN, GOL, 90V
2	89	0.41	0.78	19	empty
3	61	0.34	0.77	22	empty

Compared structures

6BH2 · 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 6BH2 · PDBe 6BH2 · UniProt P29375

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.