MolNFT v1 · #119758 · protein
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-038
5G5V · Phosphodiesterase B1: “Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-038”. X-ray diffraction, 4 ligands (GAI, 8Z4, ZN), 5 pockets (best druggability 0.75). MolNFT v1 #119758 on GenesisL1: 3D structure…
- PDB
- 5G5V
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase B1
- EC
- 3.1.4.-
- UniProt
- Q8WQX9
- Ligands
- GAI, 8Z4, ZN, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase B1 (EC 3.1.4.-) | protein | 335 | 71% helix, 0% strand | Q8WQX9 |
| B | Phosphodiesterase B1 (EC 3.1.4.-) | protein | 332 | 71% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 11 copies · chains A, B
- 8Z4 · (4as,8ar)-4-(3-{4-[(3R)-3-hydroxypyrrolidine-1- · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- FMT · Formic acid · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.75 | 0.95 | 22 | empty |
| 2 | 502 | 0.74 | 0.83 | 44 | MG, GAI, 8Z4 |
| 3 | 500 | 0.73 | 0.82 | 41 | MG |
| 4 | 291 | 0.59 | 0.78 | 39 | GAI |
| 5 | 248 | 0.54 | 0.76 | 39 | FMT, EDO |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5G5V · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038 · 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 5G5V · PDBe 5G5V · UniProt Q8WQX9
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