5TC4

Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.

Gustafsson, R.Jemth, A.S.Gustafsson, N.M.Farnegardh, K.Loseva, O.Wiita, E.Bonagas, N.Dahllund, L.Llona-Minguez, S.Haggblad, M.Henriksson, M.Andersson, Y.Homan, E.Helleday, T.Stenmark, P.

(2017) Cancer Res. 77: 937-948

  • DOI: 10.1158/0008-5472.CAN-16-1476

  • PubMed Abstract: 
  • To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methyle ...

    To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD+ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. ©2017 AACR.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
A
316Homo sapiensMutation(s): 0 
Gene Names: MTHFD2 (NMDMC)
Find proteins for P13995 (Homo sapiens)
Go to Gene View: MTHFD2
Go to UniProtKB:  P13995
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L34
Query on L34

Download SDF File 
Download CCD File 
A
4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMIC ACID
LY345899
C20 H21 N7 O7
JSNFRYBHBVDHSG-NEPJUHHUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 74.323α = 90.00
b = 74.323β = 90.00
c = 98.620γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
Wenner-Gren FoundationSweden--
Goran Gustafsson's Foundation for Science and Medical ResearchSweden--
Svenska SmartafondenSweden--
Ragnar Soderberg FoundationSweden--
Swedish Childhood Cancer FoundationSweden--
Svenska Sallskapet for Medicinsk Forskning (SSMF)Sweden--
Karolinska Institutet (KI)Sweden--
Helleday FoundationSweden--
Swedish Cancer SocietySweden--
Torsten Soderberg FoundationSweden--
Ake Wiberg FoundationSweden--

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Data collection
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence