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Structure of the beta-ketoacyl reductase domain of human fatty acid synthase bound to a spiro-imidazolone inhibitor
Analyse Structure of the beta-ketoacyl reductase domain of human fatty acid synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C37
- Type
- protein
- Length
- 1,256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid synthase
- EC
- 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14
- UniProt
- P49327
- Ligands
- NDP, 4XN, CL
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid synthase (EC 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14) | protein | 632 | 41% helix, 22% strand | P49327 |
| C | Fatty acid synthase (EC 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14) | protein | 624 | 40% helix, 22% strand | P49327 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
- 4XN · 6-{[(3R)-1-(cyclopropylcarbonyl)pyrrolidin-3-yl]methyl}-5-[4-(1-methyl-1H-indazol-5-yl)phenyl]-4,6-diazaspiro[2.4]hept-4-en-7-one · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.85 | 0.86 | 104 | NDP, 4XN |
| 2 | 860 | 0.81 | 0.84 | 92 | NDP, 4XN |
| 3 | 218 | 0.58 | 0.79 | 35 | empty |
| 4 | 151 | 0.55 | 0.82 | 26 | CL |
| 5 | 163 | 0.53 | 0.80 | 30 | CL |
Interfaces
1 interface between chains.
- A–C · 312 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C37 · Structure of the beta-ketoacyl reductase domain of human fatty acid synthase bound to a… · the same entry in another collection · chain A against A, TM-score 1.00
- P49327 · AlphaFold monomer V2.0 prediction for fatty acid synthase (P49327) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P49327
- Elsewhere: RCSB PDB 5C37 · PDBe 5C37 · UniProt P49327
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