Research workbench

Cereblon in complex with DDB1, cc-90009, and GSPT1

Analyse Cereblon in complex with DDB1, cc-90009, and GSPT1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XK9
Type: protein
Length: 3,347 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A; DNA damage-binding…
UniProt: P15170, Q16531, Q96SW2
Ligands: V4M, ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	protein	196	0% helix, 49% strand	P15170
Y	DNA damage-binding protein 1	protein	1106	6% helix, 51% strand	Q16531
Z	Protein cereblon	protein	382	27% helix, 30% strand	Q96SW2
A	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	protein	197	0% helix, 46% strand	P15170
B	DNA damage-binding protein 1	protein	1085	6% helix, 51% strand	Q16531
C	Protein cereblon	protein	381	26% helix, 30% strand	Q96SW2

Ligands and binding sites

V4M · 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide · ligand · 2 copies · chains X, Z, A, C
ZN · Zinc ion · metal · 2 copies · chains Z, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1122	0.86	0.87	99	empty
2	1054	0.86	0.87	83	empty
3	927	0.79	0.81	95	V4M
4	786	0.78	0.82	88	empty
5	912	0.78	0.80	89	V4M

Interfaces

5 interfaces between chains.

Y–Z · 2311 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 2166 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 732 Å² buried · 6 hydrogen bonds · protein-protein
Y–B · 713 Å² buried · 6 hydrogen bonds · protein-protein
X–Z · 699 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6XK9 · Cereblon in complex with DDB1, CC-90009, and GSPT1 · the same entry in another collection · chain C against C, TM-score 1.00
Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain C against A, TM-score 0.99
P15170 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor GTP-binding… · a predicted model of the same protein · chain X against A, TM-score 0.96
Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain Y against A, TM-score 0.85

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 P15170
Every structure of UniProt Q16531
Every structure of UniProt Q96SW2
Elsewhere: RCSB PDB 6XK9 · PDBe 6XK9 · UniProt P15170 · UniProt Q16531 · UniProt Q96SW2

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