MolNFT v1 · #161510 · protein
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-0769
6QGP · Phosphodiesterase: “Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-0769”. X-ray diffraction, 4 ligands (GAI, J2E, ZN), 3 pockets (best druggability 0.73). MolNFT v1 #161510 on GenesisL1: 3D structure…
- PDB
- 6QGP
- 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, J2E, ZN, MG
- Pockets
- 3 · 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 | 72% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 3 copies · chains A, B
- J2E · 1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4, 4-dimethyl-4,5-dihydro-1H-pyrazol-5-one · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.73 | 0.80 | 56 | MG |
| 2 | 454 | 0.72 | 0.82 | 42 | MG, J2E |
| 3 | 252 | 0.52 | 0.76 | 43 | FMT |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6QGP · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-0769 · 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 6QGP · PDBe 6QGP · UniProt Q8WQX9
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