MolNFT v1 · #162180 · protein

Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 20A

6R19: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 20A”. X-ray diffraction, 4 ligands (EF2, JON, ZN), 5 pockets (best druggability 0.51). MolNFT v1 #162180 on GenesisL1: 3D structure, binding sites and…

PDB: 6R19
Type: protein
Length: 331 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cereblon isoform 4
UniProt: A4TVL0
Ligands: EF2, JON, ZN, PO4
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cereblon isoform 4	protein	111	8% helix, 47% strand	A4TVL0
B	Cereblon isoform 4	protein	105	9% helix, 52% strand	A4TVL0
C	Cereblon isoform 4	protein	109	6% helix, 52% strand	A4TVL0
F	Cereblon isoform 4	protein	6	0% helix, 0% strand	—

Ligands and binding sites

EF2 · S-Thalidomide · ligand · 2 copies · chains A, C
JON · [(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate · ligand · chains B
ZN · Zinc ion · metal · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.51	0.79	30	empty
2	52	0.50	0.87	17	empty
3	128	0.44	0.77	17	empty
4	144	0.42	0.75	25	empty
5	50	0.37	0.80	13	EF2

Interfaces

4 interfaces between chains.

A–C · 656 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 648 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 78 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6R19 · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a · the same entry in another collection · chain A against A, TM-score 1.00

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 A4TVL0
Elsewhere: RCSB PDB 6R19 · PDBe 6R19 · UniProt A4TVL0

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