6PFG

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)-4-carbamoylbenzoic acid.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.

Czyzyk, D.J.Valhondo, M.Deiana, L.Tirado-Rives, J.Jorgensen, W.L.Anderson, K.S.

(2019) Eur J Med Chem 183: 111673-111673

  • DOI: https://doi.org/10.1016/j.ejmech.2019.111673
  • Primary Citation of Related Structures:  
    6PF3, 6PF4, 6PF5, 6PF6, 6PF7, 6PF8, 6PF9, 6PFA, 6PFB, 6PFC, 6PFD, 6PFE, 6PFF, 6PFG, 6PFH, 6PFI

  • PubMed Abstract: 

    Cryptosporidiosis is a human gastrointestinal disease caused by protozoans of the genus Cryptosporidium, which can be fatal in immunocompromised individuals. The essential enzyme, thymidylate synthase (TS), is responsible for de novo synthesis of deoxythymidine monophosphate. The TS active site is relatively conserved between Cryptosporidium and human enzymes. In previous work, we identified compound 1, (2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidin-methyl-phenyl-l-glutamic acid), as a promising selective Cryptosporidium hominis TS (ChTS) inhibitor. In the present study, we explore the structure-activity relationship around 1 glutamate moiety by synthesizing and biochemically evaluating the inhibitory activity of analogues against ChTS and human TS (hTS). X-Ray crystal structures were obtained for compounds bound to both ChTS and hTS. We establish the importance of the 2-phenylacetic acid moiety methylene linker in optimally positioning compounds 23, 24, and 25 within the active site. Moreover, through the comparison of structural data for 5, 14, 15, and 23 bound in both ChTS and hTS identified that active site rigidity is a driving force in determining inhibitor selectivity.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D],
Z [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 
CA [auth E],
I [auth A],
N [auth B],
S [auth C],
X [auth D]
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
OFJ (Subject of Investigation/LOI)
Query on OFJ

Download Ideal Coordinates CCD File 
BA [auth E],
H [auth A],
M [auth B],
R [auth C],
W [auth D]
2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-carbamoylbenzoic acid
C22 H18 N6 O5
ZFQOKUXSWWJOFS-UHFFFAOYSA-N
UFP
Query on UFP

Download Ideal Coordinates CCD File 
AA [auth E],
G [auth A],
L [auth B],
Q [auth C],
V [auth D]
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
J [auth A]
O [auth B]
T [auth C]
DA [auth E],
EA [auth E],
J [auth A],
O [auth B],
T [auth C],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.635α = 90
b = 116.595β = 95.21
c = 221.411γ = 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: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description