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Crystal structure of chromodomain of CBX4 in complex with inhibitor UNC3866

Analyse Crystal structure of chromodomain of CBX4 in complex with inhibitor UNC3866 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EPL
Type: protein
Length: 122 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 sumo-protein ligase CBX4; UNC3866
EC: 6.3.2.-
UniProt: O00257
Ligands: 5R0, UNX
Pockets: 1 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 sumo-protein ligase CBX4 (EC 6.3.2.-)	protein	54	24% helix, 46% strand	O00257
B	E3 sumo-protein ligase CBX4 (EC 6.3.2.-)	protein	58	31% helix, 41% strand	O00257
C, D	UNC3866	protein	5	0% helix, 40% strand	—

Ligands and binding sites

5R0 · 4-~{tert}-butylbenzoic acid · ligand · 2 copies · chains A, C, B, D
UNX · Unknown atom or ion · ion · 8 copies · chains A, C, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.51	0.78	26	5R0, UNX

Interfaces

5 interfaces between chains.

B–D · 580 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 542 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 252 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 81 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 74 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

5EPL · Crystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866 · the same entry in another collection · chain A against A, TM-score 1.00
O00257 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase CBX4 (O00257) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 O00257
Elsewhere: RCSB PDB 5EPL · PDBe 5EPL · UniProt O00257

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