6DYW

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.

Harijan, R.K., Hoff, O., Ducati, R.G., Firestone, R.S., Hirsch, B.M., Evans, G.B., Schramm, V.L., Tyler, P.C.

(2019) J Med Chem 62: 3286-3296

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01642
  • Primary Citation of Related Structures:  
    6DYU, 6DYV, 6DYW, 6DYY, 6DYZ, 6DZ0, 6DZ2, 6DZ3

  • PubMed Abstract: 

    • Bacterial 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase (MTAN) hydrolyzes adenine from its substrates to form S-methyl-5-thioribose and S-ribosyl-l-homocysteine. MTANs are involved in quorum sensing, menaquinone synthesis, and 5'-methylthioadenosine recycling to S-adenosylmethionine ...

    Bacterial 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase (MTAN) hydrolyzes adenine from its substrates to form S-methyl-5-thioribose and S-ribosyl-l-homocysteine. MTANs are involved in quorum sensing, menaquinone synthesis, and 5'-methylthioadenosine recycling to S-adenosylmethionine. Helicobacter pylori uses MTAN in its unusual menaquinone pathway, making H. pylori MTAN a target for antibiotic development. Human 5'-methylthioadenosine phosphorylase (MTAP), a reported anticancer target, catalyzes phosphorolysis of 5'-methylthioadenosine to salvage S-adenosylmethionine. Transition-state analogues designed for HpMTAN and MTAP show significant overlap in specificity. Fifteen unique transition-state analogues are described here and are used to explore inhibitor specificity. Several analogues of HpMTAN bind in the picomolar range while inhibiting human MTAP with orders of magnitude weaker affinity. Structural analysis of HpMTAN shows inhibitors extending through a hydrophobic channel to the protein surface. The more enclosed catalytic sites of human MTAP require the inhibitors to adopt a folded structure, displacing the phosphate nucleophile from the catalytic site.

    Organizational Affiliation: 

    Ferrier Research Institute , Victoria University of Wellington , Wellington 5040 , New Zealand.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidaseA, B245Helicobacter pyloriMutation(s): 0 
Gene Names: BW246_00770, BZL55_04980, CEP79_03920
EC: 3.2.2.9 (PDB Primary Data), 3.2.2.30 (UniProt)
UniProt
Find proteins for Q9ZMY2 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZMY2 
Go to UniProtKB:  Q9ZMY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZMY2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS5
Query on OS5
Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B]		(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol
C24 H30 N8 O S
BROXRHKDLDDNBO-CTNGQTDRSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
NH4
Query on NH4
Download Ideal Coordinates CCD File 
P [auth B]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OS5 Binding MOAD:  6DYW Kd: 0.04 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.346α = 90
b = 73.346β = 90
c = 176.378γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-24
    Changes: Data collection, Database references