MolNFT v1 · #149236 · protein
Complement factor D in complex with the inhibitor 3-((3-((3- (AMINOMETHYL)PHENYL)AMINO)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YL)AMINO) phenol
6FUG: “Complement factor D in complex with the inhibitor 3-((3-((3…”. X-ray diffraction, 1 ligand (E85), 20 pockets (best druggability 0.80). MolNFT v1 #149236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FUG
- Type
- protein
- Length
- 1,285 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor D
- EC
- 3.4.21.46
- UniProt
- P00746
- Ligands
- E85
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement factor D (EC 3.4.21.46) | protein | 216 | 9% helix, 38% strand | P00746 |
| B | Complement factor D (EC 3.4.21.46) | protein | 211 | 9% helix, 38% strand | P00746 |
| C | Complement factor D (EC 3.4.21.46) | protein | 218 | 9% helix, 38% strand | P00746 |
| D | Complement factor D (EC 3.4.21.46) | protein | 214 | 9% helix, 38% strand | P00746 |
| E, F | Complement factor D (EC 3.4.21.46) | protein | 213 | 10% helix, 38% strand | P00746 |
Ligands and binding sites
- E85 · 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3, 4-d]pyrimidin-4-yl]amino]phenol · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.80 | 0.84 | 81 | empty |
| 2 | 679 | 0.79 | 0.84 | 62 | empty |
| 3 | 592 | 0.72 | 0.79 | 34 | empty |
| 4 | 387 | 0.66 | 0.80 | 58 | empty |
| 5 | 297 | 0.64 | 0.81 | 41 | empty |
Interfaces
10 interfaces between chains.
- A–C · 663 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 617 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 596 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 446 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 402 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
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 6FUG · PDBe 6FUG · UniProt P00746
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