Research workbench
Crystal structure of celecoxib bound to S121P murine COX-2 mutant
Analyse Crystal structure of celecoxib bound to S121P murine COX-2 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JW1
- 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
- COH, CEL, NAG
- Pockets
- 8 · best druggability 0.86
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 | 46% helix, 9% strand | Q05769 |
| B | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 551 | 46% helix, 8% strand | Q05769 |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
- CEL · 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonamide · 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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.86 | 0.86 | 109 | CEL |
| 2 | 668 | 0.79 | 0.84 | 64 | empty |
| 3 | 414 | 0.78 | 0.86 | 60 | CEL |
| 4 | 429 | 0.77 | 0.86 | 55 | empty |
| 5 | 476 | 0.77 | 0.85 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 2615 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5JW1 · Crystal structure of Celecoxib bound to S121P murine COX-2 mutant · 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 5JW1 · PDBe 5JW1 · UniProt Q05769
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