Research workbench
Structure of sc-75416 bound at the COX-2 active site
Analyse Structure of sc-75416 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
- 3MQE
- Type
- protein
- Length
- 2,208 residues
- Chains
- 4
- 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
- HEM, 416, NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 8% 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, 8% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 416 · (2S)-7-tert-butyl-6-chloro-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid · 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, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.84 | 0.90 | 77 | 416 |
| 2 | 373 | 0.83 | 0.92 | 48 | 416 |
| 3 | 427 | 0.83 | 0.91 | 61 | 416 |
| 4 | 474 | 0.83 | 0.90 | 60 | 416 |
| 5 | 766 | 0.83 | 0.86 | 83 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2656 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2594 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 5 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 3MQE · PDBe 3MQE · UniProt Q05769
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