MolNFT v1 · #146208 · protein
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
6DAS · Wd repeat-containing protein 5: “Discovery of potent 2-aryl-6,7-dihydro-5HPYRROLO[ 1,2-A]IMIDAZOLES as WDR5 win-site inhibitors using…”. X-ray diffraction, 1 ligand (G2D), 4 pockets (best druggability 0.82). MolNFT v1 #146208 on…
- PDB
- 6DAS
- Type
- protein
- Length
- 609 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- G2D
- Pockets
- 4 · best druggability 0.82
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 | 305 | 0% helix, 53% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- G2D · N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide · 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 | 925 | 0.82 | 0.83 | 76 | G2D |
| 2 | 662 | 0.76 | 0.81 | 71 | G2D |
| 3 | 202 | 0.49 | 0.76 | 24 | empty |
| 4 | 92 | 0.37 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DAS · 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
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 6DAS · PDBe 6DAS · UniProt P61964
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