ISDA

Deposition Date 2005-11-28

Release Date 2005-12-06

Last Version Date 2024-10-09

Entry Detail

PDB ID:

2F62

Keywords:

TRANSFERASE

Title:

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound

Biological Source:

Source Organism:

Trypanosoma brucei (Taxon ID: 5691)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.50 Å

R-Value Free:

0.18

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleoside 2-deoxyribosyltransferase
Gene (Uniprot):Tb05.30H13.400
Chain IDs:A, B
Chain Length:161
Number of Molecules:2
Biological Source:Trypanosoma brucei

UniProt ID:Q57VC7 Pfam ID:PF05014 EC:2.4.2.6

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	A	MET	SELENOMETHIONINE

Ligand Molecules

12M

GOL

SO4

Primary Citation

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.Show

J.Med.Chem. 49 5939 5946 (2006)

PMID: 17004709 DOI: 10.1021/jm060429m

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures