Research workbench
Crystal structure of human WDR5 in complex with compound 9e
Analyse Crystal structure of human WDR5 in complex with compound 9e in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAP
- Type
- protein
- Length
- 310 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.73
- Source
- Homo sapiens
- Molecule
- WD repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 5MO, UNX, CL
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.73 · 1 distinct chain · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WD repeat-containing protein 5 | protein | 310 | 0% helix, 49% strand | P61964 |
Ligands and binding sites
- 5MO · N-[5-(2,3-dihydro-1-benzofuran-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide · ligand · chains A
- UNX · Unknown atom or ion · ion · 14 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.77 | 0.82 | 66 | 5MO, GOL, CL, EDO, UNX |
Compared structures
- 5EAP · Crystal structure of human WDR5 in complex with compound 9E · the same entry in another collection · chain A against A, TM-score 1.00
- P61964 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 5 (P61964) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5EAP · PDBe 5EAP · UniProt P61964
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