MolNFT v1 · #103468 · protein
TBRPDEB1-inhibitor complex
4PHL · Class 1 phosphodiesterase PDEB1: “TBRPDEB1-inhibitor complex”. X-ray diffraction, 4 ligands (PIL, GAI, ZN), 6 pockets (best druggability 0.73). MolNFT v1 #103468 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PHL
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class 1 phosphodiesterase PDEB1
- UniProt
- Q8WQX9
- Ligands
- PIL, GAI, ZN, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class 1 phosphodiesterase PDEB1 | protein | 330 | 72% helix, 0% strand | Q8WQX9 |
| B | Class 1 phosphodiesterase PDEB1 | protein | 332 | 71% helix, 0% strand | Q8WQX9 |
Ligands and binding sites
- PIL · 3-(cyclopentyloxy)-N-(3,5-dichloropyridin-4-yl)-4-methoxybenzamide · ligand · 2 copies · chains A, B
- GAI · Guanidine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- EOH · Ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.73 | 0.82 | 48 | MG, PIL, GAI |
| 2 | 493 | 0.72 | 0.81 | 45 | MG, PIL |
| 3 | 285 | 0.57 | 0.77 | 36 | GOL |
| 4 | 175 | 0.46 | 0.75 | 26 | empty |
| 5 | 148 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 413 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4PHL · TbrPDEB1-inhibitor complex · 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 4PHL · PDBe 4PHL · UniProt Q8WQX9
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