Research workbench
Crystal structure of human WDR5 in complex with compound 9H
Analyse Crystal structure of human WDR5 in complex with compound 9H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAL
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 5ML, UNX, CL
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 52% strand | P61964 |
Ligands and binding sites
- 5ML · 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 24 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.80 | 0.81 | 90 | UNX, 5ML, EDO |
| 2 | 444 | 0.71 | 0.82 | 34 | CL, EDO, UNX |
| 3 | 227 | 0.59 | 0.80 | 35 | 5ML, EDO, UNX |
Interfaces
1 interface between chains.
- A–B · 183 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5EAL · Crystal structure of human WDR5 in complex with compound 9h · 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 5EAL · PDBe 5EAL · UniProt P61964
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