MolNFT v1 · #73133 · protein
High resolution structure of NAPROXEN:COX-2 complex.
3NT1 · Prostaglandin-endoperoxide synthase 2: “High resolution structure of NAPROXEN:COX-2 complex.”. X-ray diffraction, 4 ligands (NPS, HEM, NAG), 10 pockets (best druggability 0.81). MolNFT v1 #73133 on GenesisL1: 3D structure, binding…
- PDB
- 3NT1
- Type
- protein
- Length
- 1,104 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin-endoperoxide synthase 2
- EC
- 1.14.99.1
- UniProt
- Q543K3
- Ligands
- NPS, HEM, NAG, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin-endoperoxide synthase 2 (EC 1.14.99.1) | protein | 552 | 47% helix, 9% strand | Q543K3 |
Ligands and binding sites
- NPS · (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid · 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 · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.81 | 0.84 | 82 | NPS, BOG |
| 2 | 1056 | 0.80 | 0.81 | 92 | NPS, BOG |
| 3 | 702 | 0.79 | 0.84 | 63 | empty |
| 4 | 435 | 0.78 | 0.86 | 55 | empty |
| 5 | 478 | 0.77 | 0.85 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 2642 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3NT1 · High resolution structure of naproxen:COX-2 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 Q543K3
- Elsewhere: RCSB PDB 3NT1 · PDBe 3NT1 · UniProt Q543K3
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