MolNFT v1 · #70522 · protein
Structure of compound 5C-S bound at the active site of COX-2
3LN0 · Prostaglandin G/H synthase 2: “Structure of compound 5C-S bound at the active site of COX-2”. X-ray diffraction, 3 ligands (HEM, 52B, NAG), 19 pockets (best druggability 0.83). MolNFT v1 #70522 on GenesisL1: 3D structure, binding…
- PDB
- 3LN0
- 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, 52B, NAG
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% 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, 9% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 52B · (2S)-6,8-dichloro-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, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.83 | 0.96 | 49 | 52B |
| 2 | 825 | 0.82 | 0.85 | 111 | 52B |
| 3 | 988 | 0.82 | 0.83 | 110 | empty |
| 4 | 653 | 0.80 | 0.85 | 60 | empty |
| 5 | 324 | 0.80 | 0.90 | 44 | 52B |
Interfaces
3 interfaces between chains.
- A–B · 2599 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2591 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 403 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 3LN0 · Structure of compound 5c-S bound at the active site of COX-2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · 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 Q05769
- Elsewhere: RCSB PDB 3LN0 · PDBe 3LN0 · UniProt Q05769
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