MolNFT v1 · #148689 · protein
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-1086
6FDX · Phosphodiesterase: “Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-1086”. X-ray diffraction, 4 ligands (GAI, D5Z, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #148689 on GenesisL1: 3D structure…
- PDB
- 6FDX
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- Q8WQX9
- Ligands
- GAI, D5Z, ZN, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase (EC 3.1.4.-) | protein | 333 | 71% helix, 0% strand | Q8WQX9 |
| B | Phosphodiesterase (EC 3.1.4.-) | protein | 332 | 71% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 4 copies · chains A, B
- D5Z · (4aS,8aR)-2-[1-(2-aminoquinazolin-4-yl)piperidin-4-yl]-4-(3,4-dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.73 | 0.83 | 43 | MG, D5Z |
| 2 | 474 | 0.71 | 0.81 | 45 | MG, D5Z |
| 3 | 178 | 0.49 | 0.77 | 33 | FMT |
| 4 | 71 | 0.31 | 0.74 | 15 | empty |
| 5 | 69 | 0.29 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6FDX · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1086 · 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 Q8WQX9
- Elsewhere: RCSB PDB 6FDX · PDBe 6FDX · UniProt Q8WQX9
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