4KY8

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, methotrexate, FdUMP and 4-((2-amino-6-methyl-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)thio)-2-chlorophenyl)-L-glutamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Substituted pyrrolo[2,3-d]pyrimidines as Cryptosporidium hominis thymidylate synthase inhibitors.

Kumar, V.P.Frey, K.M.Wang, Y.Jain, H.K.Gangjee, A.Anderson, K.S.

(2013) Bioorg Med Chem Lett 23: 5426-5428

  • DOI: https://doi.org/10.1016/j.bmcl.2013.07.037
  • Primary Citation of Related Structures:  
    4KY8

  • PubMed Abstract: 

    Cryptosporidiosis, a gastrointestinal disease caused by a protozoan Cryptosporidium hominis is often fatal in immunocompromised individuals. There is little clinical data to show that the existing treatment by nitazoxanide and paromomycin is effective in immunocompromised individuals. Thymidylate synthase (TS) and dihydrofolate reductase (DHFR) are essential enzymes in the folate biosynthesis pathway and are well established as drug targets in cancer and malaria. A novel series of classical antifolates, 2-amino-4-oxo-5-substituted pyrrolo[2,3-d]pyrimidines have been evaluated as Cryptosporidium hominis thymidylate synthase (ChTS) inhibitors. Crystal structure in complex with the most potent compound, a 2'-chlorophenyl with a sulfur bridge with a Ki of 8.83±0.67 nM is discussed in terms of several Van der Waals, hydrophobic and hydrogen bond interactions with the protein residues and the substrate analog 5-fluorodeoxyuridine monophosphate. Of these interactions, two interactions with the non-conserved residues (A287 and S290) offer an opportunity to develop ChTS specific inhibitors. Compound 6 serves as a lead compound for analog design and its crystal structure provides clues for the design of ChTS specific inhibitors.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional thymidylate synthase-dihydrofolate reductase
A, B, C, D, E
521Cryptosporidium hominisMutation(s): 0 
Gene Names: Chro.40506TS-DHFR
EC: 2.1.1.45 (PDB Primary Data), 1.5.1.3 (PDB Primary Data)
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
1UF
Query on 1UF

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
N-{4-[(2-amino-6-methyl-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)sulfanyl]-2-chlorobenzoyl}-L-glutamic acid
C19 H18 Cl N5 O6 S
DTVBRZFMWHDIOO-NSHDSACASA-N
MTX
Query on MTX

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-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: 3.08 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.162α = 90
b = 115.665β = 94.36
c = 218.767γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description