Research workbench
Crystal structure of WDR5, wd repeat domain 5 in complex with compound sgc-ds-mt-0345
Analyse Crystal structure of WDR5, wd repeat domain 5 in complex with compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QQE
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 37F, UNX, CL
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- 37F · N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide · ligand · chains A
- UNX · Unknown atom or ion · ion · 7 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.71 | 0.82 | 33 | EDO, UNX |
| 2 | 245 | 0.60 | 0.80 | 35 | 37F, UNX |
Compared structures
- 4QQE · Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345 · 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 4QQE · PDBe 4QQE · UniProt P61964
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