Research workbench
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-008
Analyse Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-008 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G2B
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class 1 phosphodiesterase PDEB1
- EC
- 3.1.4.-
- UniProt
- Q8WQX9
- Ligands
- GAI, LQY, ZN, MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class 1 phosphodiesterase PDEB1 (EC 3.1.4.-) | protein | 333 | 71% helix, 0% strand | Q8WQX9 |
| B | Class 1 phosphodiesterase PDEB1 (EC 3.1.4.-) | protein | 332 | 71% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 3 copies · chains A, B
- LQY · N-(2-amino-2-oxoethyl)-5'-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2'-methoxy[1,1'-biphenyl]-4-carboxamide · 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 · 3 copies · chains A
- GOL · Glycerol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.73 | 0.83 | 45 | MG, LQY |
| 2 | 518 | 0.72 | 0.81 | 50 | MG, LQY |
| 3 | 213 | 0.51 | 0.76 | 32 | FMT |
| 4 | 78 | 0.29 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5G2B · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-008 · 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 5G2B · PDBe 5G2B · UniProt Q8WQX9
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