Research workbench
Crystal structure of human WDR5 in complex with compound 9D
Analyse Crystal structure of human WDR5 in complex with compound 9D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAR
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 5MQ, UNX, SO4
- Pockets
- 4 · best druggability 0.78
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 | 301 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 301 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- 5MQ · N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.78 | 0.80 | 89 | 5MQ, EDO, UNX |
| 2 | 445 | 0.71 | 0.81 | 33 | UNX |
| 3 | 247 | 0.61 | 0.80 | 37 | 5MQ, EDO |
| 4 | 57 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 160 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EAR · Crystal structure of human WDR5 in complex with compound 9d · 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 5EAR · PDBe 5EAR · UniProt P61964
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