6N82

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02037

• PDB DOI: https://doi.org/10.2210/pdb6N82/pdb

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


• Deposited: 2018-11-28 Released: 2019-11-06 
• Deposition Author(s): Park, J., Schilling, M.A., Berghuis, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Chirality-Driven Mode of Binding of alpha-Aminophosphonic Acid-Based Allosteric Inhibitors of the Human Farnesyl Pyrophosphate Synthase (hFPPS).

Feng, Y., Park, J., Li, S.G., Boutin, R., Viereck, P., Schilling, M.A., Berghuis, A.M., Tsantrizos, Y.S.

(2019) J Med Chem 62: 9691-9702

• PubMed: 31577901 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b01104
• Primary Citation of Related Structures:  
  6N7Y, 6N7Z, 6N82, 6N83, 6OAG, 6OAH


• PubMed Abstract: 
  

  Thienopyrimidine-based allosteric inhibitors of the human farnesyl pyrophosphate synthase (hFPPS), characterized by a chiral α-aminophosphonic acid moiety, were synthesized as enantiomerically enriched pairs, and their binding mode was investigated by X-ray crystallography. A general consensus in the binding orientation of all ( R )- and ( S )-enantiomers was revealed. This finding is a prerequisite for establishing a reliable structure-activity relationship (SAR) model.

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Organizational Affiliation: 

Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada.

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: 44.57 kDa 
• Atom Count: 2,924 
• Modelled Residue Count: 341 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YF7	C [auth F], D [auth F]	[(1S)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid C21 H18 Cl F N3 O3 P S ZSPBSSJYWQDARC-IBGZPJMESA-N
PGE	E [auth F]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	I [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth F], H [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
YF7	BindingDB:  6N82	IC50: 860 (nM) from 1 assay(s)
	Binding MOAD:  6N82	IC50: 1100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.92	α = 90
b = 110.92	β = 90
c = 77.53	γ = 90

Software Package:

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

Structure Validation

Currently 6N82 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Park, J., Schilling, M.A., Berghuis, A.M.

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description