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Cyclooxygenase-2 (prostaglandin synthase-2) complexed with a selective inhibitor, sc-558 in I222 space group
Analyse Cyclooxygenase-2 (prostaglandin synthase-2) complexed with a selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6COX
- Type
- protein
- Length
- 1,104 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclooxygenase-2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- HEM, S58, NAG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclooxygenase-2 (EC 1.14.99.1) | protein | 552 | 44% helix, 6% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- S58 · 1-phenylsulfonamide-3-trifluoromethyl-5-parabromophenylpyrazole · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.80 | 0.96 | 26 | S58 |
| 2 | 838 | 0.80 | 0.83 | 85 | empty |
| 3 | 798 | 0.80 | 0.83 | 74 | empty |
| 4 | 827 | 0.79 | 0.82 | 85 | empty |
| 5 | 321 | 0.79 | 0.89 | 50 | S58 |
Interfaces
1 interface between chains.
- A–B · 2411 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6COX · Cyclooxygenase-2 (prostaglandin synthase-2) complexed with a selective inhibitor, sc-558… · 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 Q05769
- Elsewhere: RCSB PDB 6COX · PDBe 6COX · UniProt Q05769
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