Research workbench
Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors
Analyse Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DEA
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.214
- Source
- Homo sapiens
- Molecule
- Complement factor D
- EC
- 3.4.21.46
- UniProt
- P00746
- Ligands
- R7X
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.214 · 1 distinct chain · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Complement factor D (EC 3.4.21.46) | protein | 217 | 9% helix, 38% strand | P00746 |
Ligands and binding sites
- R7X · 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.72 | 0.76 | 114 | R7X |
| 2 | 80 | 0.53 | 0.85 | 20 | empty |
| 3 | 191 | 0.52 | 0.77 | 32 | empty |
| 4 | 111 | 0.43 | 0.77 | 27 | R7X |
| 5 | 153 | 0.40 | 0.73 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 446 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 279 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 267 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P00746
- Elsewhere: RCSB PDB 8DEA · PDBe 8DEA · UniProt P00746
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