Research workbench
Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design
Analyse Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E1Y
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.219
- Source
- Homo sapiens
- Molecule
- WD repeat-containing protein 5
- UniProt
- P61964
- Ligands
- HLM
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.219 · 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 | 301 | 0% helix, 52% strand | P61964 |
Ligands and binding sites
- HLM · N-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide · ligand · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.77 | 0.79 | 94 | HLM |
| 2 | 673 | 0.75 | 0.81 | 71 | HLM |
| 3 | 66 | 0.40 | 0.80 | 15 | empty |
| 4 | 53 | 0.35 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 148 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6E1Y · Discovery of potent 2-aryl-6,7-dihydro-5HPYRROLO[ 1,2-A]IMIDAZOLES as WDR5 win-site… · 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 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 6E1Y · PDBe 6E1Y · UniProt P61964
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