Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.23 kDa 
• Atom Count: 8634 
• Residue Count: 995 
• Unique protein chains: 1

3GN1

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

• DOI: 10.2210/pdb3GN1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-16 Released: 2009-12-29 
• Deposition Author(s): Tulloch, L.B., Brenk, R., Hunter, W.N.

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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 

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

• PubMed: 19527033 
• DOI: 10.1021/jm900414x
• Primary Citation of Related Structures:  
  2WD7, 2WD8, 3GN2, 3GN1


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase	A, B, C, D	288	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PTR1
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290  Go to UniProtKB:  O76290

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	A, B, C, D	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
AX7	A, C, D	1H-benzimidazol-2-amine C7 H7 N3 JWYUFVNJZUSCSM-UHFFFAOYSA-N
ACT	A, C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A,B,C,D	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AX7	Ki:  288000   nM  Binding MOAD

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 = 74.641	α = 90
b = 90.408	β = 115.73
c = 82.638	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-16 
• Released Date: 2009-12-29 
Deposition Author(s): Tulloch, L.B., Brenk, R., Hunter, W.N.

Revision History 

• 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