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Structure of celecoxib bound at the COX-2 active site
Analyse Structure of celecoxib bound at the COX-2 active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LN1
- Type
- protein
- Length
- 2,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Mus musculus
- Molecule
- Prostaglandin G/H synthase 2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- HEM, CEL, NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 552 | 47% helix, 9% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CEL · 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonamide · 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 · 2 copies · chains A, 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 | 1080 | 0.83 | 0.84 | 105 | HEM |
| 2 | 170 | 0.81 | 0.96 | 26 | CEL |
| 3 | 181 | 0.80 | 0.94 | 27 | CEL |
| 4 | 816 | 0.79 | 0.83 | 79 | empty |
| 5 | 335 | 0.79 | 0.89 | 45 | CEL |
Interfaces
3 interfaces between chains.
- A–B · 2619 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2608 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 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 3LN1 · PDBe 3LN1 · UniProt Q05769
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