3GN1

Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00067116)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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This is version 1.2 of the entry. See complete history. 


Literature

One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening.

Mpamhanga, C.P., Spinks, D., Tulloch, L.B., Shanks, E.J., Robinson, D.A., Collie, I.T., Fairlamb, A.H., Wyatt, P.G., Frearson, J.A., Hunter, W.N., Gilbert, I.H., Brenk, R.

(2009) J Med Chem 52: 4454-4465

  • DOI: 10.1021/jm900414x
  • Primary Citation of Related Structures:  
    2WD7, 2WD8, 3GN1, 3GN2

  • PubMed Abstract: 

    • The enzyme pteridine reductase 1 (PTR1) is a potential target for new compounds to treat human African trypanosomiasis. A virtual screening campaign for fragments inhibiting PTR1 was carried out. Two novel chemical series were identified containing aminobenzothiazole and aminobenzimidazole scaffolds, respectively ...

    The enzyme pteridine reductase 1 (PTR1) is a potential target for new compounds to treat human African trypanosomiasis. A virtual screening campaign for fragments inhibiting PTR1 was carried out. Two novel chemical series were identified containing aminobenzothiazole and aminobenzimidazole scaffolds, respectively. One of the hits (2-amino-6-chloro-benzimidazole) was subjected to crystal structure analysis and a high resolution crystal structure in complex with PTR1 was obtained, confirming the predicted binding mode. However, the crystal structures of two analogues (2-amino-benzimidazole and 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole) in complex with PTR1 revealed two alternative binding modes. In these complexes, previously unobserved protein movements and water-mediated protein-ligand contacts occurred, which prohibited a correct prediction of the binding modes. On the basis of the alternative binding mode of 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole, derivatives were designed and selective PTR1 inhibitors with low nanomolar potency and favorable physicochemical properties were obtained.

    Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pteridine reductaseA, B, C, D288Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei)
Explore O76290 
Go to UniProtKB:  O76290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76290
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX		A, B, C, D L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
AX7 Binding MOAD:  3GN1 Ki: 2.88e+5 (nM) from 1 assay(s)
BindingDB:  3GN1 Ki: 2.88e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.641α = 90
b = 90.408β = 115.73
c = 82.638γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-09-07
    Changes: Database references