6BM7

Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Species-Selective Pyrimidineamine Inhibitors of Trypanosoma brucei S-Adenosylmethionine Decarboxylase.

Volkov, O.A.Brockway, A.J.Wring, S.A.Peel, M.Chen, Z.Phillips, M.A.De Brabander, J.K.

(2018) J Med Chem 61: 1182-1203

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01654
  • Primary Citation of Related Structures:  
    6BM7

  • PubMed Abstract: 

    New therapeutic options are needed for treatment of human African trypanosomiasis (HAT) caused by protozoan parasite Trypanosoma brucei. S-Adenosylmethionine decarboxylase (AdoMetDC) is an essential enzyme in the polyamine pathway of T. brucei. Previous attempts to target this enzyme were thwarted by the lack of brain penetration of the most advanced series. Herein, we describe a T. brucei AdoMetDC inhibitor series based on a pyrimidineamine pharmacophore that we identified by target-based high-throughput screening. The pyrimidineamines showed selectivity for T. brucei AdoMetDC over the human enzyme, inhibited parasite growth in whole-cell assay, and had good predicted blood-brain barrier penetration. The medicinal chemistry program elucidated structure-activity relationships within the series. Features of the series that were required for binding were revealed by determining the X-ray crystal structure of TbAdoMetDC bound to one analog. The pyrimidineamine series provides a novel starting point for an anti-HAT lead optimization.


  • Organizational Affiliation

    Scynexis, Inc. (now Avista Pharma Solutions) , 3501 Tricenter Boulevard, Suite C, Durham, North Carolina 27713, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine decarboxylase beta chain
A, C
85Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.6.4410Tb927.6.4460
EC: 4.1.1.50
UniProt
Find proteins for Q587A7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q587A7 
Go to UniProtKB:  Q587A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ587A7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine decarboxylase alpha chain
B, D
285Trypanosoma brucei brucei TREU927Mutation(s): 1 
Gene Names: Tb927.6.4410Tb927.6.4460
EC: 4.1.1.50
UniProt
Find proteins for Q587A7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q587A7 
Go to UniProtKB:  Q587A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ587A7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Inactive S-adenosylmethionine decarboxylase prozyme
E, F
325Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for A5HNV6 (Trypanosoma brucei brucei)
Explore A5HNV6 
Go to UniProtKB:  A5HNV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5HNV6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DY7 (Subject of Investigation/LOI)
Query on DY7

Download Ideal Coordinates CCD File 
H [auth B],
J [auth D]
2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium
C11 H11 Br2 N4
KGGBAZUXVZBIGO-UHFFFAOYSA-O
B3P
Query on B3P

Download Ideal Coordinates CCD File 
G [auth B],
I [auth D]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
O [auth F]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
L [auth E],
M [auth E]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PUT
Query on PUT

Download Ideal Coordinates CCD File 
K [auth E],
N [auth F]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.09α = 90
b = 96.25β = 102.426
c = 98.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2R37AI034432
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI090599

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-10-09
    Changes: Structure summary