MolNFT v1 · #116532 · protein
Crystal structure of human fpps in complex with compound 13
5DGN · Farnesyl pyrophosphate synthase: “Crystal structure of human fpps in complex with compound 13”. X-ray diffraction, 1 ligand (59Y), 2 pockets (best druggability 0.76). MolNFT v1 #116532 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DGN
- 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
- 59Y
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 77% 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 | 77% helix, 1% strand | P14324 |
Ligands and binding sites
- 59Y · 8-(naphthalen-1-yl)quinoline-2-carboxylic acid · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.76 | 0.79 | 65 | 59Y |
| 2 | 57 | 0.33 | 0.77 | 15 | empty |
Compared structures
- 5DGN · Crystal structure of human FPPS in complex with compound 13 · 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 5DGN · PDBe 5DGN · UniProt P14324
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