MolNFT v1 · #187709 · protein
Crystal structure of the wdr domain of human DCAF1 in complex with cyca-117-70
7SSE · DDB1- and CUL4-associated factor 1: “Crystal structure of the wdr domain of human DCAF1 in complex with cyca-117-70”. X-ray diffraction, 1 ligand (B1I), 5 pockets (best druggability 0.81). MolNFT v1 #187709 on GenesisL1: 3D…
- PDB
- 7SSE
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 1
- EC
- 2.7.11.1
- UniProt
- Q9Y4B6
- Ligands
- B1I
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 298 | 1% helix, 50% strand | Q9Y4B6 |
| B | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 294 | 1% helix, 50% strand | Q9Y4B6 |
Ligands and binding sites
- B1I · N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.81 | 0.82 | 87 | B1I |
| 2 | 1177 | 0.80 | 0.81 | 81 | empty |
| 3 | 181 | 0.53 | 0.79 | 24 | empty |
| 4 | 86 | 0.50 | 0.83 | 20 | empty |
| 5 | 68 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7SSE · Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9Y4B6
- Elsewhere: RCSB PDB 7SSE · PDBe 7SSE · UniProt Q9Y4B6
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