MolNFT v1 · #150657 · protein

Structure of DDB1-crbn-pomalidomide complex bound to IKZF1(ZF2)

6H0F · DNA damage-binding protein 1,DNA damage-binding protein 1…: “Structure of DDB1-crbn-pomalidomide complex bound to IKZF1(ZF2)”. X-ray diffraction, 2 ligands (Y70, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #150657 on…

PDB: 6H0F
Type: protein
Length: 4,940 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein…
UniProt: Q96SW2, Q13422
Ligands: Y70, ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1	protein	826	8% helix, 51% strand	—
B, E, H, K	Protein cereblon	protein	374	28% helix, 33% strand	Q96SW2
C, F, I, L	DNA-binding protein ikaros	protein	32	38% helix, 13% strand	Q13422
D	DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1	protein	821	8% helix, 50% strand	—
J	DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1	protein	843	8% helix, 49% strand	—

Ligands and binding sites

Y70 · S-Pomalidomide · ligand · 4 copies · chains B, C, E, F, H, I, K, L
ZN · Zinc ion · metal · 8 copies · chains B, C, E, F, H, I, K, L

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	1124	0.86	0.87	84	empty
2	1150	0.86	0.87	97	empty
3	951	0.84	0.85	96	empty
4	610	0.84	0.89	47	empty
5	1007	0.84	0.85	101	empty

Interfaces

21 interfaces between chains.

G–H · 2662 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 2602 Å² buried · 26 hydrogen bonds · protein-protein
J–K · 2514 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2514 Å² buried · 24 hydrogen bonds · protein-protein
D–G · 583 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6H0F · Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) · the same entry in another collection · chain L against L, 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 Q96SW2
Every structure of UniProt Q13422
Elsewhere: RCSB PDB 6H0F · PDBe 6H0F · UniProt Q96SW2 · UniProt Q13422

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.