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Crystal structure of KDM5B in complex with KDOPZ000049A.

Analyse Crystal structure of KDM5B in complex with KDOPZ000049A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EJ0
Type: protein
Length: 453 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: B7K, MN, ZN
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 37% 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	453	37% helix, 20% strand	Q9UGL1

Ligands and binding sites

B7K · 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
EDO · 1,2-ethanediol · additive · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	816	0.80	0.83	67	DMS, B7K
2	179	0.73	0.90	24	EDO
3	129	0.45	0.77	22	empty
4	53	0.41	0.82	19	DMS
5	53	0.31	0.76	14	EDO

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6EJ0 · Crystal structure of KDM5B in complex with KDOPZ000049a. · 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 0.97

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 6EJ0 · PDBe 6EJ0 · UniProt Q9UGL1

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