ISDA: 4MWO

Deposition Date 2013-09-25

Release Date 2014-09-10

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4MWO

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor CPB-T

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.67 Å

R-Value Free:

0.19

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 43 21 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:5'(3')-deoxyribonucleotidase, mitochondrial
Gene (Uniprot):NT5M
Chain IDs:A
Chain Length:201
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NPB1 Pfam ID:PF06941

Ligand Molecules

2E2

GOL

PO4

Primary Citation

Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.

Simak, O, Pachl, P, Fabry, M, Budesinsky, M, Jandusik, T, Hnizda, A, Sklenickova, R, Petrova, M, Veverka, V, Rezacova, P, Brynda, J, Rosenberg, I.Show

Org.Biomol.Chem. 12 7971 7982 (2014)

PMID: 25178098 DOI: 10.1039/c4ob01332h

Abstact

This work describes novel in vitro inhibitors of human mitochondrial (mdN) and cytosolic (cdN) 5'(3')-deoxynucleotidases. We designed a series of derivatives of the lead compound (S)-1-[2-deoxy-3,5-O-(phosphonobenzylidene)-β-d-threo-pentofuranosyl]thymine bearing various substituents in the para position of the benzylidene moiety. Detailed kinetic study revealed that certain para substituents increase the inhibitory potency (iodo derivative; K = 2.71 μM) and some induce a shift in selectivity toward cdN (carboxy derivative, K = 11.60 μM; iodoxy derivative, K = 6.60 μM). Crystal structures of mdN in complex with three of these compounds revealed that various para substituents lead to two alternative inhibitor binding modes within the enzyme active site. Two binding modes were also identified for cdN complexes by heteronuclear NMR spectroscopy.

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Primary Citation of related structures

Abstact

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