MolNFT v1 · #102710 · protein
Crystal structure of lumiracoxib bound to the apo-mouse- cyclooxygenase-2
4OTY · Prostaglandin G/H synthase 2: “Crystal structure of lumiracoxib bound to the apo-mouse- cyclooxygenase-2”. X-ray diffraction, 2 ligands (LUR, NAG), 10 pockets (best druggability 0.84). MolNFT v1 #102710 on GenesisL1: 3D structure…
- PDB
- 4OTY
- Type
- protein
- Length
- 1,103 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
- LUR, NAG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 552 | 45% helix, 9% strand | Q05769 |
| B | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 551 | 46% helix, 9% strand | Q05769 |
Ligands and binding sites
- LUR · {2-[(2-chloro-6-fluorophenyl)amino]-5-methylphenyl}acetic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains 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 | 902 | 0.84 | 0.85 | 115 | LUR |
| 2 | 753 | 0.81 | 0.84 | 74 | empty |
| 3 | 336 | 0.80 | 0.89 | 45 | LUR |
| 4 | 408 | 0.79 | 0.88 | 52 | empty |
| 5 | 456 | 0.78 | 0.86 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 2616 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4OTY · Crystal structure of lumiracoxib bound to the apo-mouse-cyclooxygenase-2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · a predicted model of the same protein · chain B 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 Q05769
- Elsewhere: RCSB PDB 4OTY · PDBe 4OTY · UniProt Q05769
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