9CY2 | pdb_00009cy2

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120

• PDB DOI: https://doi.org/10.2210/pdb9CY2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-01 Released: 2025-10-29 
• Deposition Author(s): Pandya, V.R., Park, J.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.212 (DCC) 

Literature

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120

Pandya, V.R., Park, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.64 kDa 
• Atom Count: 2,801 
• Modeled Residue Count: 338 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A [auth F]	375	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324  Go to UniProtKB:  P14324
PHAROS:  P14324 GTEx:  ENSG00000160752

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JD5 (Subject of Investigation/LOI)	C [auth F]	[({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid) C15 H18 N2 O7 P2 QCLQOQRSHDMFKS-UHFFFAOYSA-N
PO4	B [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.212 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.95	α = 90
b = 110.95	β = 90
c = 73.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Pandya, V.R., Park, J.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-04281

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release