3SRR | pdb_00003srr

S. aureus Dihydrofolate Reductase complexed with novel 7-aryl-2,4-diaminoquinazolines

• PDB DOI: https://doi.org/10.2210/pdb3SRR/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-07 Released: 2011-08-31 
• Deposition Author(s): Hilgers, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structure-based design of new DHFR-based antibacterial agents: 7-aryl-2,4-diaminoquinazolines.

Li, X., Hilgers, M., Cunningham, M., Chen, Z., Trzoss, M., Zhang, J., Kohnen, L., Lam, T., Creighton, C., G C, K., Nelson, K., Kwan, B., Stidham, M., Brown-Driver, V., Shaw, K.J., Finn, J.

(2011) Bioorg Med Chem Lett 21: 5171-5176

• PubMed: 21831637 
• DOI: https://doi.org/10.1016/j.bmcl.2011.07.059
• Primary Citation of Related Structures:  
  3SQY, 3SR5, 3SRQ, 3SRR, 3SRS, 3SRU, 3SRW


• PubMed Abstract: 
  

  Dihydrofolate reductase (DHFR) inhibitors such as trimethoprim (TMP) have long played a significant role in the treatment of bacterial infections. Not surprisingly, after decades of use there is now bacterial resistance to TMP and therefore a need to develop novel antibacterial agents with expanded spectrum including these resistant strains. In this study, we investigated the optimization of 2,4-diamnoquinazolines for antibacterial potency and selectivity. Using structure-based drug design, several 7-aryl-2,4-diaminoquinazolines were discovered that have excellent sub-100 picomolar potency against bacterial DHFR. These compounds have good antibacterial activity especially on gram-positive pathogens including TMP-resistant strains.

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Organizational Affiliation: 

Trius Therapeutics, San Diego, CA 92121, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 20.41 kDa 
• Atom Count: 1,469 
• Modelled Residue Count: 157 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	167	Staphylococcus aureus	Mutation(s): 0  Gene Names: folA EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus) Explore P0A017  Go to UniProtKB:  P0A017

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth X]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
Q20	B [auth X]	3-(2,4-diamino-6-methylquinazolin-7-yl)-4-ethoxybenzaldehyde C18 H18 N4 O2 BDVALXKNVWZHIQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q20	BindingDB:  3SRR	Ki: 0.24 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.317	α = 90
b = 79.317	β = 90
c = 107.394	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Hilgers, M.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations