Research workbench
Indole-2 carboxamides as selective secreted phospholipase A2 type X (SPLA2-X) inhibitors
Analyse Indole-2 carboxamides as selective secreted phospholipase A2 type X (SPLA2-X)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OW8
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group 10 secretory phospholipase A2
- EC
- 3.1.1.4
- UniProt
- O15496
- Ligands
- AYN, CA, CL
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Group 10 secretory phospholipase A2 (EC 3.1.1.4) | protein | 123 | 46% helix, 7% strand | O15496 |
Ligands and binding sites
- AYN · 1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.58 | 0.80 | 23 | DMS, AYN |
| 2 | 199 | 0.54 | 0.78 | 23 | DMS, AYN |
| 3 | 65 | 0.33 | 0.77 | 18 | DMS |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5OW8 · Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- O15496 · AlphaFold monomer V2.0 prediction for group 10 secretory phospholipase A2 (O15496) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O15496
- Elsewhere: RCSB PDB 5OW8 · PDBe 5OW8 · UniProt O15496
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