MolNFT v1 · #58526 · protein
Crystal structure of human prostacyclin synthase in complex with inhibitor minoxidil
3B6H: “Crystal structure of human prostacyclin synthase in complex with inhibitor minoxidil”. X-ray diffraction, 2 ligands (MXD, HEM), 8 pockets (best druggability 0.85). MolNFT v1 #58526 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3B6H
- Type
- protein
- Length
- 939 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostacyclin synthase
- EC
- 5.3.99.4
- UniProt
- Q16647
- Ligands
- MXD, HEM
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostacyclin synthase (EC 5.3.99.4) | protein | 469 | 51% helix, 14% strand | Q16647 |
| B | Prostacyclin synthase (EC 5.3.99.4) | protein | 470 | 51% helix, 14% strand | Q16647 |
Ligands and binding sites
- MXD · 6-piperidin-1-ylpyrimidine-2,4-diamine 3-oxide · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.85 | 0.86 | 81 | BOG, MXD, HEM |
| 2 | 1171 | 0.85 | 0.86 | 80 | BOG, MXD, HEM |
| 3 | 937 | 0.77 | 0.80 | 75 | empty |
| 4 | 265 | 0.56 | 0.77 | 34 | empty |
| 5 | 242 | 0.51 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3B6H · Crystal structure of human prostacyclin synthase in complex with inhibitor minoxidil · the same entry in another collection · chain A against A, TM-score 1.00
- Q16647 · AlphaFold monomer V2.0 prediction for prostacyclin synthase (Q16647) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q16647
- Elsewhere: RCSB PDB 3B6H · PDBe 3B6H · UniProt Q16647
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