Research workbench
Crystal structure of human WDR5 in complex with compound oicr-9429
Analyse Crystal structure of human WDR5 in complex with compound oicr-9429 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QL1
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 35Q, UNX
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 302 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- 35Q · N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.83 | 0.84 | 93 | 35Q, UNX |
| 2 | 491 | 0.72 | 0.81 | 36 | GOL |
| 3 | 255 | 0.61 | 0.80 | 37 | 35Q |
| 4 | 191 | 0.55 | 0.79 | 31 | empty |
| 5 | 67 | 0.54 | 0.87 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4QL1 · Crystal structure of human WDR5 in complex with compound OICR-9429 · 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 4QL1 · PDBe 4QL1 · UniProt P61964
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