MolNFT v1 · #103456 · protein
The structure of ibuprofen bound to cyclooxygenase-2
4PH9 · Prostaglandin G/H synthase 2: “The structure of ibuprofen bound to cyclooxygenase-2”. X-ray diffraction, 5 ligands (AKR, IBP, HEM), 9 pockets (best druggability 0.81). MolNFT v1 #103456 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PH9
- Type
- protein
- Length
- 1,102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- AKR, IBP, HEM, NAG, MAN
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 551 | 48% helix, 10% strand | Q05769 |
Ligands and binding sites
- AKR · Acrylic acid · ligand · 4 copies · chains A, B
- IBP · Ibuprofen · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.81 | 0.83 | 94 | IBP, BOG, EDO |
| 2 | 755 | 0.81 | 0.84 | 76 | NAG, EDO |
| 3 | 981 | 0.80 | 0.82 | 84 | IBP, BOG, EDO |
| 4 | 434 | 0.77 | 0.86 | 56 | empty |
| 5 | 468 | 0.76 | 0.85 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 2650 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 Q05769
- Elsewhere: RCSB PDB 4PH9 · PDBe 4PH9 · UniProt Q05769
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