MolNFT v1 · #120514 · protein
Crystal structure of T brucei phosphodiesterase B2 bound to compound 15B
5H2R: “Crystal structure of T brucei phosphodiesterase B2 bound to compound 15B”. X-ray diffraction, 3 ligands (LLN, ZN, MG), 4 pockets (best druggability 0.74). MolNFT v1 #120514 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5H2R
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- Q38F42
- Ligands
- LLN, ZN, MG
- Pockets
- 4 · best druggability 0.74
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 | 329 | 71% helix, 0% strand | Q38F42 |
| B | Phosphodiesterase (EC 3.1.4.-) | protein | 328 | 72% helix, 0% strand | Q38F42 |
Ligands and binding sites
- LLN · (4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-(2-hydroxyethyloxy)-3-[2-(2-oxidanylideneimidazolidin-1-yl)ethoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-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
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 | 500 | 0.74 | 0.82 | 45 | MG, LLN |
| 2 | 484 | 0.73 | 0.82 | 44 | MG, LLN |
| 3 | 467 | 0.65 | 0.78 | 66 | empty |
| 4 | 63 | 0.31 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 946 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5H2R · Crystal structure of T brucei phosphodiesterase B2 bound to compound 15b · 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 Q38F42
- Elsewhere: RCSB PDB 5H2R · PDBe 5H2R · UniProt Q38F42
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