Research workbench
S. pneumoniae fabh with small molecule inhibitor 4
Analyse S. pneumoniae fabh with small molecule inhibitor 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BQS
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.180
- UniProt
- C1CIR8
- Ligands
- 4VN, NA
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 323 | 39% helix, 26% strand | C1CIR8 |
Ligands and binding sites
- 4VN · 1-{5-[2-chloro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.68 | 0.85 | 34 | 4VN |
| 2 | 226 | 0.68 | 0.84 | 33 | 4VN |
| 3 | 288 | 0.55 | 0.76 | 33 | empty |
| 4 | 109 | 0.37 | 0.74 | 22 | empty |
| 5 | 68 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2889 Ų buried · 42 hydrogen bonds · protein-protein
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 C1CIR8
- Elsewhere: RCSB PDB 5BQS · PDBe 5BQS · UniProt C1CIR8
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