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Crystal structure of KDM5B in complex with KDOPZ000034A.

Analyse Crystal structure of KDM5B in complex with KDOPZ000034A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EIY
Type: protein
Length: 456 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 5B,LYSINE-specific demethylase 5B
EC: 1.14.11.-
UniProt: Q9UGL1
Ligands: B6W, MN, ZN
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 5B,LYSINE-specific demethylase 5B (EC 1.14.11.-)	protein	456	41% helix, 20% strand	Q9UGL1

Ligands and binding sites

B6W · 2-chloranyl-~{N}-[2-[4-(3-cyano-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidin-5-yl) pyrazol-1-yl]ethyl]ethanamide · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	780	0.82	0.85	69	DMS, MN, B6W
2	186	0.74	0.91	23	EDO
3	207	0.54	0.77	26	empty
4	59	0.35	0.77	12	empty
5	63	0.34	0.76	15	EDO

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6EIY · Crystal structure of KDM5B in complex with KDOPZ000034a. · the same entry in another collection · chain A against A, TM-score 1.00
Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · 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 Q9UGL1
Elsewhere: RCSB PDB 6EIY · PDBe 6EIY · UniProt Q9UGL1

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