Research workbench
Crystal structure of human fpps in complex with an allosteric inhibitor yf-02037
Analyse Crystal structure of human fpps in complex with an allosteric inhibitor yf-02037 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N82
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10, 2.5.1.1
- UniProt
- P14324
- Ligands
- YF7, CL, PO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Farnesyl pyrophosphate synthase (EC 2.5.1.10, 2.5.1.1) | protein | 341 | 76% helix, 1% strand | P14324 |
Ligands and binding sites
- YF7 · [(1S)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl) ethyl]phosphonic acid · ligand · 2 copies · chains F
- CL · Chloride ion · ion · 2 copies · chains F
- PO4 · Phosphate ion · ion · chains F
- GOL · Glycerol · additive · chains F
- PGE · Triethylene glycol · additive · chains F
- EDO · 1,2-ethanediol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.75 | 0.79 | 64 | YF7, PGE, PO4 |
| 2 | 51 | 0.58 | 0.92 | 16 | empty |
Compared structures
- 6N82 · Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02037 · the same entry in another collection · chain F against F, TM-score 1.00
- P14324 · AlphaFold monomer V2.0 prediction for farnesyl pyrophosphate synthase (P14324) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P14324
- Elsewhere: RCSB PDB 6N82 · PDBe 6N82 · UniProt P14324
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