Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex 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

  • Resolution: 1.99 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.4 of the entry. See complete history


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. 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

    Department of Biochemistry , Albert Einstein College of Medicine , New York 10461 , New York , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-methyl-5'-thioadenosine phosphorylase
A, B, C
297Homo sapiensMutation(s): 0 
Gene Names: MTAPMSAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q13126 (Homo sapiens)
Explore Q13126 
Go to UniProtKB:  Q13126
PHAROS:  Q13126
GTEx:  ENSG00000099810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13126
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OS5

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
U [auth C]
C24 H30 N8 O S
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth B]
N [auth C]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C]
C2 H6 O2
Query on ACY

Download Ideal Coordinates CCD File 
C2 H4 O2
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B],
T [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
OS5 Binding MOAD:  6DZ2 Kd: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.39α = 90
b = 135.316β = 90
c = 159.268γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

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
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description