Research workbench
The structure of tolfenamic acid bound to human cyclooxygenase-2
Analyse The structure of tolfenamic acid bound to human cyclooxygenase-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IKT
- 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
- P35354
- Ligands
- TLF, COH, NAG, MAN, PO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 9% 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, 9% strand | P35354 |
Ligands and binding sites
- TLF · 2-[(3-chloro-2-methylphenyl)amino]benzoic acid · ligand · 2 copies · chains A, B
- COH · Protoporphyrin IX containing co · 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 · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 6 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 | 1126 | 0.86 | 0.87 | 127 | PO4 |
| 2 | 136 | 0.79 | 0.96 | 28 | TLF |
| 3 | 676 | 0.79 | 0.84 | 62 | empty |
| 4 | 301 | 0.78 | 0.89 | 43 | TLF |
| 5 | 429 | 0.70 | 0.81 | 47 | COH |
Interfaces
1 interface between chains.
- A–B · 2501 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand, glycosylation).
Compared structures
- 5IKT · The Structure of Tolfenamic Acid Bound to Human Cyclooxygenase-2 · the same entry in another collection · chain A against A, TM-score 1.00
- P35354 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (P35354) · a predicted model of the same protein · 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 P35354
- Elsewhere: RCSB PDB 5IKT · PDBe 5IKT · UniProt P35354
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