MolNFT v1 · #150278 · protein
Development of alkyl glycerone phosphate synthase inhibitors: complex with inhibitor 2I
6GOU · Alkyldihydroxyacetonephosphate synthase, peroxisomal: “Development of alkyl glycerone phosphate synthase inhibitors: complex with inhibitor 2I”. X-ray diffraction, 2 ligands (FAD, F6T), 20 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 6GOU
- Type
- protein
- Length
- 2,169 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyldihydroxyacetonephosphate synthase, peroxisomal
- EC
- 2.5.1.26
- UniProt
- P97275
- Ligands
- FAD, F6T
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 540 | 36% helix, 22% strand | P97275 |
| A | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 554 | 35% helix, 22% strand | P97275 |
| C | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 535 | 37% helix, 22% strand | P97275 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains D, A, B, C
- F6T · (3~{S})-3-[2,6-bis(fluoranyl)phenyl]-~{N}-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl) methyl]butanamide · ligand · 3 copies · chains D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.90 | 0.93 | 113 | FAD, F6T |
| 2 | 922 | 0.90 | 0.92 | 111 | FAD |
| 3 | 949 | 0.90 | 0.92 | 109 | FAD, F6T |
| 4 | 909 | 0.90 | 0.92 | 103 | FAD, F6T |
| 5 | 591 | 0.82 | 0.87 | 71 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3474 Ų buried · 52 hydrogen bonds · protein-protein
- D–B · 506 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 353 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 274 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6GOU · Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I · the same entry in another collection · chain C against C, TM-score 1.00
- P97275 · AlphaFold monomer V2.0 prediction for alkyldihydroxyacetonephosphate synthase… · a predicted model of the same protein · chain B 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 P97275
- Elsewhere: RCSB PDB 6GOU · PDBe 6GOU · UniProt P97275
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