Research workbench
Displacement of WDR5 from chromatin by a pharmacological win site inhibitor with picomolar affinity
Analyse Displacement of WDR5 from chromatin by a pharmacological win site inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E23
- 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
- HLJ
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 299 | 0% helix, 52% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 53% strand | P61964 |
Ligands and binding sites
- HLJ · N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide · ligand · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.80 | 0.81 | 97 | HLJ |
| 2 | 777 | 0.78 | 0.81 | 74 | HLJ |
| 3 | 55 | 0.40 | 0.81 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6E23 · Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with… · 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 6E23 · PDBe 6E23 · UniProt P61964
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