3K8T | pdb_00003k8t

Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound

• PDB DOI: https://doi.org/10.2210/pdb3K8T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-14 Released: 2010-03-02 
• Deposition Author(s): Sun, D., Xu, H., Dealwis, C., Lee, R.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.290 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Design, Synthesis, and Evaluation of 2'-(2-Hydroxyethyl)-2'-deoxyadenosine and the 5'-Diphosphate Derivative as Ribonucleotide Reductase Inhibitors

Sun, D., Xu, H., Wijerathna, S.R., Dealwis, C., Lee, R.E.

(2009) ChemMedChem 4: 1649-1656

• PubMed: 19681093 
• DOI: https://doi.org/10.1002/cmdc.200900236
• Primary Citation Related Structures: 
  3K8T


• PubMed Abstract: 
  

  Analysis of the recently solved X-ray crystal structures of Saccharomyces cerevisiae ribonucleotide reductase I (ScRnr1) in complex with effectors and substrates led to the discovery of a conserved water molecule located at the active site that interacted with the 2'-hydroxy group of the nucleoside ribose. In this study 2'-(2-hydroxyethyl)-2'-deoxyadenosine 1 and the 5'-diphosphate derivative 2 were designed and synthesized to see if the conserved water molecule could be displaced by a hydroxymethylene group, to generate novel RNR inhibitors as potential antitumor agents. Herein we report the synthesis of analogues 1 and 2, and the co-crystal structure of adenosine diphosphate analogue 2 bound to ScRnr1, which shows the conserved water molecule is displaced as hypothesized.

---

Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163 (USA).

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: 100.75 kDa 
• Atom Count: 5,322 
• Modeled Residue Count: 640 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase large chain 1	A	888	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CRT7, RIR1, RNR1, SDS12, YER070W EC: 1.17.4.1
UniProt
Find proteins for P21524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21524  Go to UniProtKB:  P21524

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	C [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
2A5	D [auth A]	2'-deoxy-2'-(2-hydroxyethyl)adenosine 5'-(trihydrogen diphosphate) C12 H19 N5 O10 P2 RHTGRZKDKXTTPI-PNFUHCLESA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.290 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.528	α = 90
b = 116.915	β = 90
c = 64.065	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Sun, D., Xu, H., Dealwis, C., Lee, R.E.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description