Research workbench
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-340
Analyse Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-340 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9H
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- Q8WQX9
- Ligands
- CVL, ZN, MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% 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 | 334 | 72% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- CVL · 5-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl) phenoxy]butoxy]phenyl]-4,4-dimethyl-2-propan-2-yl-pyrazol-3-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
- GOL · Glycerol · additive · 3 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.73 | 0.81 | 49 | MG, CVL |
| 2 | 493 | 0.71 | 0.80 | 44 | MG, CVL |
| 3 | 152 | 0.46 | 0.76 | 24 | empty |
| 4 | 50 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 740 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5L9H · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-340 · 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 5L9H · PDBe 5L9H · UniProt Q8WQX9
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