Research workbench
Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-1335
Analyse Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-1335 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXQ
- 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, FFZ, MG, ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase (EC 3.1.4.-) | protein | 333 | 72% helix, 0% strand | Q8WQX9 |
| B | Phosphodiesterase (EC 3.1.4.-) | protein | 332 | 73% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 5 copies · chains A, B
- FFZ · 3-[5-[(4ar,8as)-4-oxidanylidene-3-propan-2-yl-4A,5,8, 8A-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-N-(phenylmethyl)prop-2-ynamide · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.72 | 0.81 | 44 | MG, FFZ |
| 2 | 463 | 0.72 | 0.81 | 46 | MG |
| 3 | 245 | 0.52 | 0.76 | 33 | GOL |
| 4 | 63 | 0.28 | 0.73 | 13 | empty |
| 5 | 57 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GXQ · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1335 · the same entry in another collection · chain B against B, 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 6GXQ · PDBe 6GXQ · UniProt Q8WQX9
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