6OJS

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, MTX and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-D-glutamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase.

Czyzyk, D.J.Valhondo, M.Jorgensen, W.L.Anderson, K.S.

(2019) FEBS Lett 593: 2069-2078

  • DOI: https://doi.org/10.1002/1873-3468.13474
  • Primary Citation of Related Structures:  
    6OJS, 6OJU, 6OJV

  • PubMed Abstract: 

    Thymidylate synthase (TS), found in all organisms, is an essential enzyme responsible for the de novo synthesis of deoxythymidine monophosphate. The TS active sites of the protozoal parasite Cryptosporidium hominis and human are relatively conserved. Evaluation of antifolate compound 1 and its R-enantiomer 2 against both enzymes reveals divergent inhibitor selectivity and enzyme stereospecificity. To establish how C. hominis and human TS (ChTS and hTS) selectively discriminate 1 and 2, respectively, we determined crystal structures of ChTS complexed with 2 and hTS complexed with 1 or 2. Coupled with the previously determined structure of ChTS complexed with 1, we discuss a possible mechanism for enzyme stereospecificity and inhibitor selectivity.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B, C, D, E
521Cryptosporidium hominisMutation(s): 0 
Gene Names: CHUDEA4_4460
UniProt
Find proteins for A0A0S4TER9 (Cryptosporidium hominis)
Explore A0A0S4TER9 
Go to UniProtKB:  A0A0S4TER9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TER9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D],
V [auth E]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
MTX
Query on MTX

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
D96
Query on D96

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid
C19 H19 N5 O6
VDHBMZRBPMTLGE-GFCCVEGCSA-N
UFP
Query on UFP

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.622α = 90
b = 116.188β = 95.48
c = 220.884γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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 StatesAI083146
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5T32AI007404

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description