PDBsum entry 6pfe

Transferase/transferase inhibitor

PDB id: 6pfe

Contents

Protein chains

506 a.a.

Ligands

NDP ×5

UFP ×5

OEA ×5

MTX ×5

Waters ×40

PDB id:

6pfe

Name:

Transferase/transferase inhibitor

Title:

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-methoxybenzoic acid.

Structure:

Bifunctional dihydrofolate reductase-thymidylate synthase. Chain: a, b, c, d, e. Engineered: yes

Source:

Cryptosporidium hominis. Organism_taxid: 237895. Gene: chudea4_4460. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: pa-414

Resolution:

2.81Å R-factor: 0.227 R-free: 0.257

Authors:

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

Key ref:

D.J.Czyzyk et al. (2019). Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Eur J Med Chem, 183, 111673. PubMed id: 31536894 DOI: 10.1016/j.ejmech.2019.111673

Date:

21-Jun-19 Release date: 02-Oct-19

Protein chains

A0A0S4TER9  (A0A0S4TER9_CRYHO) -  Bifunctional dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis

Seq: 521 a.a.

Struc: 506 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate (Bound ligand (Het Group name = MTX) matches with 91.18% similarity) + NADPH + H(+)

• Enzyme class 3: E.C.2.1.1.45 - thymidylate synthase.

Pathway:

• Reaction: dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP

dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate (Bound ligand (Het Group name = UFP) matches with 95.24% similarity) = 7,8-dihydrofolate (Bound ligand (Het Group name = MTX) matches with 91.18% similarity) + dTMP (Bound ligand (Het Group name = NDP) matches with 40.82% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.ejmech.2019.111673

Eur J Med Chem 183:111673 (2019)

PubMed id: 31536894

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

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

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.