1V1J

Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

(1R,4S,5R)-3-Fluoro-1,4,5-Trihydroxy-2-Cyclohexene-1-Carboxylic Acid: The Fluoro Analogue of the Enolate Intermediate in the Reaction Catalyzed by Type II Dehydroquinases

Frederickson, M., Roszak, A.W., Coggins, J.R., Lapthorn, A.J., Abell, C.

(2004) Org Biomol Chem 2: 1592

  • DOI: https://doi.org/10.1039/b404535a
  • Primary Citation of Related Structures:  
    1V1J

  • PubMed Abstract: 

    The fluoro analogue of the enolate intermediate in the reaction catalyzed by type II dehydroquinases has been prepared from naturally occurring (-)-quinic acid over seven steps and has been shown to be the most potent inhibitor reported to date of the type II enzyme from Mycobacterium tuberculosis.

    • Organizational Affiliation: 

    University Chemical Laboratory, Lensfield Road, Cambridge, UK CB2 1EW.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
157Streptomyces coelicolorMutation(s): 0 
EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore P15474 
Go to UniProtKB:  P15474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15474
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FA3
Query on FA3
Download Ideal Coordinates CCD File 
BA [auth L]
M [auth A]
O [auth B]
P [auth C]
Q [auth D]
BA [auth L],
M [auth A],
O [auth B],
P [auth C],
Q [auth D],
R [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
Y [auth J],
Z [auth K]
2-ANHYDRO-3-FLUORO-QUINIC ACID
C7 H9 F O5
DGZQZSSRYAJDAX-XAHCXIQSSA-N
TRS
Query on TRS
Download Ideal Coordinates CCD File 
AA [auth K],
N [auth A],
S [auth E],
X [auth I]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
FA3 PDBBind:  1V1J Ki: 1.50e+4 (nM) from 1 assay(s)
Binding MOAD:  1V1J Ki: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.475α = 90
b = 138.941β = 90
c = 141.925γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description