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Crystal structure of murine cereblon in complex with pomalidomide

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

PDB: 4TZU
Type: protein
Length: 361 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein cereblon
UniProt: Q8C7D2
Ligands: Y70, ZN, SO4
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Protein cereblon	protein	90	7% helix, 50% strand	Q8C7D2
B	Protein cereblon	protein	91	7% helix, 49% strand	Q8C7D2

Ligands and binding sites

Y70 · S-Pomalidomide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, D, B, C

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

Pockets

2 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	682	0.71	0.78	41	Y70
2	155	0.54	0.80	30	SO4

Interfaces

4 interfaces between chains.

B–D · 607 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 594 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 588 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 277 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4TZU · Crystal Structure of Murine Cereblon in Complex with Pomalidomide · the same entry in another collection · chain B against B, TM-score 1.00
Q8C7D2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q8C7D2) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q8C7D2
Elsewhere: RCSB PDB 4TZU · PDBe 4TZU · UniProt Q8C7D2

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