1RSI

DHNA complex with 2-Amino-5-bromo-3-hydroxy-6-phenylpyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.276 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization.

Sanders, W.J.Nienaber, V.L.Lerner, C.G.McCall, J.O.Merrick, S.M.Swanson, S.J.Harlan, J.E.Stoll, V.S.Stamper, G.F.Betz, S.F.Condroski, K.R.Meadows, R.P.Severin, J.M.Walter, K.A.Magdalinos, P.Jakob, C.G.Wagner, R.Beutel, B.A.

(2004) J Med Chem 47: 1709-1718

  • DOI: 10.1021/jm030497y
  • Primary Citation of Related Structures:  
    1RRI, 1RSI, 1RSD, 1RRW, 1RS4, 1RS2, 1RRY, 1U68

  • PubMed Abstract: 
  • Potent inhibitors of 7,8-dihydroneopterin aldolase (DHNA; EC 4.1.2.25) have been discovered using CrystaLEAD X-ray crystallographic high-throughput screening followed by structure-directed optimization. Screening of a 10 000 compound random library provided several low affinity leads and their corresponding X-ray crystal structures bound to the enzyme ...

    Potent inhibitors of 7,8-dihydroneopterin aldolase (DHNA; EC 4.1.2.25) have been discovered using CrystaLEAD X-ray crystallographic high-throughput screening followed by structure-directed optimization. Screening of a 10 000 compound random library provided several low affinity leads and their corresponding X-ray crystal structures bound to the enzyme. The presence of a common structural feature in each of the leads suggested a strategy for the construction of a directed library of approximately 1000 compounds that were screened for inhibitory activity in a traditional enzyme assay. Several lead compounds with IC(50) values of about 1 microM against DHNA were identified, and crystal structures of their enzyme-bound complexes were obtained by cocrystallization. Structure-directed optimization of one of the leads thus identified afforded potent inhibitors with submicromolar IC(50) values.


    Organizational Affiliation

    Infectious Disease Research, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, Illinois 60064-6217, USA. will.sanders@abbott.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroneopterin aldolaseA121Staphylococcus aureusMutation(s): 0 
Gene Names: folB
EC: 4.1.2.25 (PDB Primary Data), 5.1.99.8 (UniProt)
UniProt
Find proteins for P56740 (Staphylococcus aureus)
Explore P56740 
Go to UniProtKB:  P56740
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
977
Query on 977

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-5-BROMO-6-PHENYLPYRIMIDIN-4-OL
C10 H8 Br N3 O
CIUUIPMOFZIWIZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
977IC50:  38000   nM  Binding MOAD
977IC50 :  38000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.276 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.947α = 90
b = 60.947β = 90
c = 123.689γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance