MolNFT v1 · #146729 · protein

Linked KDM5A jmj domain bound to the inhibitor N44 I.E. 3-((2- (pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-YL)PYRIMIDIN-4- YL)AMINO)PROPANOIC acid

6DQ6: “Linked KDM5A jmj domain bound to the inhibitor N44 I.E. 3-((2…”. X-ray diffraction, 2 ligands (H6J, MN), 3 pockets (best druggability 0.67). MolNFT v1 #146729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DQ6
Type: protein
Length: 298 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Linked KDM5A jmj domain
EC: 1.14.11.-
UniProt: P29375
Ligands: H6J, MN
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Linked KDM5A jmj domain (EC 1.14.11.-)	protein	298	32% helix, 23% strand	P29375

Ligands and binding sites

H6J · N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine · ligand · chains A
MN · Manganese (II) ion · metal · chains A
GOL · Glycerol · additive · chains A
DMS · Dimethyl sulfoxide · additive · 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	400	0.67	0.80	47	H6J, MN
2	83	0.42	0.79	20	empty
3	63	0.37	0.79	21	empty

Compared structures

6DQ6 · LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e.… · 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

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 6DQ6 · PDBe 6DQ6 · UniProt P29375

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