6R4T

Crystal structure of the Pri1 subunit of human primase bound to vidarabine triphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for inhibition of human primase by arabinofuranosyl nucleoside analogues fludarabine and vidarabine.

Holzer, S.Rzechorzek, N.J.Short, I.R.Jenkyn-Bedford, M.Pellegrini, L.Kilkenny, M.L.

(2019) Acs Chem.Biol. --: --

  • DOI: 10.1021/acschembio.9b00367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin lymphomas. Although nucl ...

    Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin lymphomas. Although nucleoside analogues are generally known to function by inhibiting DNA synthesis in rapidly proliferating cells, the identity of their in vivo targets and mechanism of action are often not known in molecular detail. Here we provide a structural basis for arabinose nucleotide-mediated inhibition of human primase, the DNA-dependent RNA polymerase responsible for initiation of DNA synthesis in DNA replication. Our data suggest ways in which the chemical structure of fludarabine could be modified to improve its specificity and affinity towards primase, possibly leading to less toxic and more effective therapeutic agents.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase small subunit
A, D
410Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7.-
Find proteins for P49642 (Homo sapiens)
Go to Gene View: PRIM1
Go to UniProtKB:  P49642
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEJ
Query on HEJ

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Download CCD File 
A, D
9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine
Vidarabine-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-UHTZMRCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 111.090α = 90.00
b = 118.970β = 90.00
c = 150.720γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release