1UOU

Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Human Thymidine Phosphorylase in Complex with a Small Molecule Inhibitor

Norman, R.A.Barry, S.T.Bate, M.Breed, J.Colls, J.G.Ernill, R.J.Luke, R.W.A.Minshull, C.A.Mcalister, M.S.B.Mccall, E.J.Mcmicken, H.H.J.Paterson, D.S.Timms, D.Tucker, J.A.Pauptit, R.A.

(2004) Structure 12: 75


  • PubMed Abstract: 
  • Human thymidine phosphorylase (HTP), also known as platelet-derived endothelial cell growth factor (PD-ECGF), is overexpressed in certain solid tumors where it is linked to poor prognosis. HTP expression is utilized for certain chemotherapeutic strat ...

    Human thymidine phosphorylase (HTP), also known as platelet-derived endothelial cell growth factor (PD-ECGF), is overexpressed in certain solid tumors where it is linked to poor prognosis. HTP expression is utilized for certain chemotherapeutic strategies and is also thought to play a role in tumor angiogenesis. We determined the structure of HTP bound to the small molecule inhibitor 5-chloro-6-[1-(2-iminopyrrolidinyl) methyl] uracil hydrochloride (TPI). The inhibitor appears to mimic the substrate transition state, which may help explain the potency of this inhibitor and the catalytic mechanism of pyrimidine nucleotide phosphorylases (PYNPs). Further, we have confirmed the validity of the HTP structure as a template for structure-based drug design by predicting binding affinities for TPI and other known HTP inhibitors using in silico docking techniques. This work provides the first structural insight into the binding mode of any inhibitor to this important drug target and forms the basis for designing novel inhibitors for use in anticancer therapy.


    Organizational Affiliation

    AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE PHOSPHORYLASE
A
474Homo sapiensGene Names: TYMP (ECGF1)
EC: 2.4.2.4
Find proteins for P19971 (Homo sapiens)
Go to Gene View: TYMP
Go to UniProtKB:  P19971
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMU
Query on CMU

Download SDF File 
Download CCD File 
A
5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL) URACIL
5-CHLORO-6-[(2-IMINOPYRROLIDIN-1-YL)METHYL]PYRIMIDINE-2,4(1H,3H)-DIONE
C9 H11 Cl N4 O2
QQHMKNYGKVVGCZ-WDZFZDKYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CMUKi: 1.3 - 20 nM (99) BINDINGDB
CMUIC50: 20 - 35 nM (99) BINDINGDB
CMUKi: 20 nM BINDINGMOAD
CMUKi: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.990α = 90.00
b = 66.090β = 106.54
c = 96.870γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance