4X3V

Crystal structure of human ribonucleotide reductase 1 bound to inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identification of Non-nucleoside Human Ribonucleotide Reductase Modulators.

Ahmad, M.F.Huff, S.E.Pink, J.Alam, I.Zhang, A.Perry, K.Harris, M.E.Misko, T.Porwal, S.K.Oleinick, N.L.Miyagi, M.Viswanathan, R.Dealwis, C.G.

(2015) J.Med.Chem. 58: 9498-9509

  • DOI: 10.1021/acs.jmedchem.5b00929

  • PubMed Abstract: 
  • Ribonucleotide reductase (RR) catalyzes the rate-limiting step of dNTP synthesis and is an established cancer target. Drugs targeting RR are mainly nucleoside in nature. In this study, we sought to identify non-nucleoside small-molecule inhibitors of ...

    Ribonucleotide reductase (RR) catalyzes the rate-limiting step of dNTP synthesis and is an established cancer target. Drugs targeting RR are mainly nucleoside in nature. In this study, we sought to identify non-nucleoside small-molecule inhibitors of RR. Using virtual screening, binding affinity, inhibition, and cell toxicity, we have discovered a class of small molecules that alter the equilibrium of inactive hexamers of RR, leading to its inhibition. Several unique chemical categories, including a phthalimide derivative, show micromolar IC50s and KDs while demonstrating cytotoxicity. A crystal structure of an active phthalimide binding at the targeted interface supports the noncompetitive mode of inhibition determined by kinetic studies. Furthermore, the phthalimide shifts the equilibrium from dimer to hexamer. Together, these data identify several novel non-nucleoside inhibitors of human RR which act by stabilizing the inactive form of the enzyme.


    Organizational Affiliation

    Department of Chemistry, Dehradun Institute of Technology, University of Deharadun , Dehradun 248197, India.,Center for Proteomics and the Department of Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Case Comprehensive Cancer Center, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Department of Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Northeastern-CAT at the Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States.,Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Department of Biochemistry, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Department of Radiation Oncology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Center for Proteomics and Bioinformatics, Case Western Reserve University , Cleveland, Ohio 44106, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase large subunit
A, B
792Homo sapiensMutation(s): 0 
Gene Names: RRM1 (RR1)
EC: 1.17.4.1
Find proteins for P23921 (Homo sapiens)
Go to Gene View: RRM1
Go to UniProtKB:  P23921
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3X4
Query on 3X4

Download SDF File 
Download CCD File 
A
N~6~-{N-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetyl]-2-methyl-D-alanyl}-D-lysine
C20 H26 N4 O6
HSKHXKLBWCBTSW-CQSZACIVSA-N
 Ligand Interaction
TTP
Query on TTP

Download SDF File 
Download CCD File 
A, B
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.880α = 90.00
b = 110.498β = 90.00
c = 216.721γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM100887-01
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA100827-04A1

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2016-01-06
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence