Research workbench
WDR5DELTA23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-YL)METHANOL
Analyse WDR5DELTA23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-YL)METHANOL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PG8
- Type
- protein
- Length
- 1,218 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- OGY, CL, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 310 | 0% helix, 50% strand | P61964 |
| C, D | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- OGY · [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, D
- SO4 · Sulfate ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.83 | 0.84 | 96 | OGY, CL |
| 2 | 863 | 0.81 | 0.83 | 75 | OGY |
| 3 | 880 | 0.80 | 0.83 | 101 | OGY |
| 4 | 1134 | 0.76 | 0.78 | 85 | SO4 |
| 5 | 497 | 0.74 | 0.82 | 44 | CL |
Interfaces
5 interfaces between chains.
- A–D · 495 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 229 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6PG8 · WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol · 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 P61964
- Elsewhere: RCSB PDB 6PG8 · PDBe 6PG8 · UniProt P61964
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