MolNFT v1 · #116531 · protein
Crystal structure of human fpps in complex with monophosphonate compound 7
5DGM · Farnesyl pyrophosphate synthase: “Crystal structure of human fpps in complex with monophosphonate compound 7”. X-ray diffraction, 2 ligands (59Z, PO4), 1 pocket (best druggability 0.77). MolNFT v1 #116531 on GenesisL1: 3D structure…
- PDB
- 5DGM
- Type
- protein
- Length
- 343 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
- 59Z, PO4
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 75% 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 | 343 | 75% helix, 1% strand | P14324 |
Ligands and binding sites
- 59Z · {2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid · ligand · chains F
- PO4 · Phosphate ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.77 | 0.80 | 65 | 59Z, PO4 |
Compared structures
- 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 5DGM · PDBe 5DGM · UniProt P14324
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