MolNFT v1 · #122637 · protein

Linked KDM5A jmj domain bound to the inhibitor N3 (4'-[(2- PHENYLETHYL)CARBAMOYL][2,2'-bipyridine]-4-carboxylic acid)

5IVC · Lysine-specific demethylase 5A: “Linked KDM5A jmj domain bound to the inhibitor N3 (4'-[(2…”. X-ray diffraction, 2 ligands (6E7, MN), 3 pockets (best druggability 0.65). MolNFT v1 #122637 on GenesisL1: 3D structure, binding sites…

PDB: 5IVC
Type: protein
Length: 308 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: 6E7, MN
Pockets: 3 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 5A (EC 1.14.11.-)	protein	308	31% helix, 23% strand	P29375

Ligands and binding sites

6E7 · 4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid · ligand · chains A
MN · Manganese (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A
GOL · Glycerol · 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	385	0.65	0.79	50	6E7, MN
2	67	0.45	0.82	22	empty
3	96	0.39	0.76	16	EDO

Compared structures

5IVC · Linked KDM5A Jmj Domain Bound to the Inhibitor N3… · 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 0.93

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 5IVC · PDBe 5IVC · UniProt P29375

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