MolNFT v1 · #122293 · protein
The structure of mefenamic acid bound to human cyclooxygenase-2
5IKR · Prostaglandin G/H synthase 2: “The structure of mefenamic acid bound to human cyclooxygenase-2”. X-ray diffraction, 5 ligands (ID8, COH, NAG), 7 pockets (best druggability 0.82). MolNFT v1 #122293 on GenesisL1: 3D structure, binding…
- PDB
- 5IKR
- 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
- ID8, COH, NAG, MAN, NH4
- Pockets
- 7 · best druggability 0.82
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
- ID8 · 2-[(2,3-dimethylphenyl)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 · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, A
- NH4 · Ammonium ion · ion · 5 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
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.82 | 0.83 | 96 | empty |
| 2 | 1108 | 0.82 | 0.83 | 101 | empty |
| 3 | 192 | 0.81 | 0.95 | 48 | ID8 |
| 4 | 682 | 0.80 | 0.85 | 61 | NAG |
| 5 | 187 | 0.77 | 0.92 | 32 | ID8 |
Interfaces
1 interface between chains.
- A–B · 2504 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand, glycosylation).
Compared structures
- 5IKR · The Structure of Mefenamic 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 5IKR · PDBe 5IKR · UniProt P35354
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