2RAH | pdb_00002rah

Human FDPS synthase in complex with novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2RAH/pdb

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


• Deposited: 2007-09-15 Released: 2007-09-25 
• Deposition Author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.258 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Human FDPS synthase in complex with novel inhibitor

Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

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)

Macromolecule Content 

• Total Structure Weight: 43.9 kDa 
• Atom Count: 2,918 
• Modeled Residue Count: 340 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthetase	A	378	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.1 (PDB Primary Data), 2.5.1.10 (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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11P	D [auth A]	[(7R)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-yl(hydroxy)methylene]bis(phosphonic acid) C9 H13 N O7 P2 WBALRBOBYFLYPZ-MRVPVSSYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
11P	BindingDB:  2RAH	IC50: 629.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.258 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.171	α = 90
b = 111.171	β = 90
c = 70.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description