2F64

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.

Bosch, J.Robien, M.A.Mehlin, C.Boni, E.Riechers, A.Buckner, F.S.Van Voorhis, W.C.Myler, P.J.Worthey, E.A.DeTitta, G.Luft, J.R.Lauricella, A.Gulde, S.Anderson, L.A.Kalyuzhniy, O.Neely, H.M.Ross, J.Earnest, T.N.Soltis, M.Schoenfeld, L.Zucker, F.Merritt, E.A.Fan, E.Verlinde, C.L.Hol, W.G.J.

(2006) J Med Chem 49: 5939-5946

  • DOI: 10.1021/jm060429m
  • Primary Citation of Related Structures:  
    2A0K, 2F2T, 2F62, 2F64, 2F67

  • PubMed Abstract: 
  • The 1.8 A resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SADa phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling ...

    The 1.8 A resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SADa phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited "fragment cocktail soaks". Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of approximately 10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.


    Organizational Affiliation

    Department of Biochemistry, Division of Infectious Disease, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside 2-deoxyribosyltransferaseA, B161Trypanosoma bruceiMutation(s): 7 
Gene Names: Tb05.30H13.400
EC: 2.4.2.6
UniProt
Find proteins for Q57VC7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57VC7 
Go to UniProtKB:  Q57VC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57VC7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
12Q
Query on 12Q

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
1-METHYLQUINOLIN-2(1H)-ONE
C10 H9 N O
QYEMNJMSULGQRD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.827α = 90
b = 75.351β = 90.01
c = 87.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance