MolNFT v1 · #73143 · protein
Structure of 6-methylthio naproxen analog bound to mcox-2.
3NTB · Prostaglandin-endoperoxide synthase 2: “Structure of 6-methylthio naproxen analog bound to mcox-2.”. X-ray diffraction, 3 ligands (HEM, T1N, NAG), 20 pockets (best druggability 0.84). MolNFT v1 #73143 on GenesisL1: 3D structure…
- PDB
- 3NTB
- Type
- protein
- Length
- 2,207 residues
- Chains
- 4
- 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
- HEM, T1N, NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Prostaglandin-endoperoxide synthase 2 (EC 1.14.99.1) | protein | 552 | 47% helix, 9% strand | Q543K3 |
| B | Prostaglandin-endoperoxide synthase 2 (EC 1.14.99.1) | protein | 551 | 46% helix, 9% strand | Q543K3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- T1N · (2S)-2-[6-(methylsulfanyl)naphthalen-2-yl]propanoic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.84 | 0.85 | 111 | T1N, BOG |
| 2 | 654 | 0.81 | 0.86 | 79 | empty |
| 3 | 796 | 0.81 | 0.83 | 78 | T1N, BOG |
| 4 | 686 | 0.79 | 0.84 | 59 | empty |
| 5 | 439 | 0.79 | 0.87 | 49 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2665 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2665 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 3NTB · Structure of 6-methylthio naproxen analog bound to mCOX-2. · 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 3NTB · PDBe 3NTB · UniProt Q543K3
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