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MolNFT v1 · #116601 · protein

Crystal structure of human fpps in complex with salicylic acid derivative 3A

5DIQ · Farnesyl pyrophosphate synthase: “Crystal structure of human fpps in complex with salicylic acid derivative 3A”. X-ray diffraction, 3 ligands (5B9, MG, PO4), 3 pockets (best druggability 0.77). MolNFT v1 #116601 on GenesisL1: 3D…

PDB
5DIQ
Type
protein
Length
345 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
5B9, MG, PO4
Pockets
3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
FFarnesyl pyrophosphate synthase (EC 2.5.1.10, 2.5.1.1)protein34575% helix, 1% strandP14324

Ligands and binding sites

  • 5B9 · 2-(naphthalen-1-ylmethoxy)benzoic acid · ligand · chains F
  • MG · Magnesium ion · metal · chains F
  • PO4 · Phosphate ion · ion · chains F
  • GOL · Glycerol · additive · 2 copies · chains F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110650.770.7982GOL, 5B9, MG, PO4
2600.330.7616empty
3590.300.7514empty

Compared structures

  • 5DIQ · Crystal structure of human FPPS in complex with salicylic acid derivative 3a · 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

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