1U68

DHNA 7,8 DIHYDRONEOPTERIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.279 

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:  

  • 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 p ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroneopterin aldolase
A
121Staphylococcus aureusMutation(s): 0 
Gene Names: folB
EC: 4.1.2.25
Find proteins for P56740 (Staphylococcus aureus)
Go to UniProtKB:  P56740
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPR
Query on NPR

Download SDF File 
Download CCD File 
A
2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE
7,8-DIHYDRONEOPTERIN
C9 H13 N5 O4
YQIFAMYNGGOTFB-NJGYIYPDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.279 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.947α = 90.00
b = 60.947β = 90.00
c = 123.689γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance