7QEI

Structure of human MTHFD2L in complex with TH7299


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The First Structure of Human MTHFD2L and Its Implications for the Development of Isoform-Selective Inhibitors.

Scaletti, E.R.Gustafsson Westergren, R.Andersson, Y.Wiita, E.Henriksson, M.Homan, E.J.Jemth, A.S.Helleday, T.Stenmark, P.

(2022) ChemMedChem 17: e202200274-e202200274

  • DOI: https://doi.org/10.1002/cmdc.202200274
  • Primary Citation of Related Structures:  
    7QEI

  • PubMed Abstract: 

    Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is a mitochondrial 1-carbon metabolism enzyme, which is an attractive anticancer drug target as it is highly upregulated in cancer but is not expressed in healthy adult cells. Selective MTHFD2 inhibitors could therefore offer reduced side-effects during treatment, which are common with antifolate drugs that target other 1C-metabolism enzymes. This task is challenging however, as MTHFD2 shares high sequence identity with the constitutively expressed isozymes cytosolic MTHFD1 and mitochondrial MTHFD2L. In fact, one of the most potent MTHFD2 inhibitors reported to date, TH7299, is actually more active against MTHFD1 and MTHFD2L. While structures of MTHFD2 and MTHFD1 exist, no MTHFD2L structures are available. We determined the first structure of MTHFD2L and its complex with TH7299, which reveals the structural basis for its highly potent MTHFD2L inhibition. Detailed analysis of the MTHFD2L structure presented here clearly highlights the challenges associated with developing truly isoform-selective MTHFD2 inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm, 106 91, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2299Homo sapiensMutation(s): 0 
Gene Names: MTHFD2L
EC: 1.5.1.15 (PDB Primary Data), 3.5.4.9 (PDB Primary Data), 1.5.1.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H903 (Homo sapiens)
Explore Q9H903 
Go to UniProtKB:  Q9H903
PHAROS:  Q9H903
GTEx:  ENSG00000163738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H903
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATR
Query on ATR

Download Ideal Coordinates CCD File 
C [auth A]2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
9L9 (Subject of Investigation/LOI)
Query on 9L9

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid
C17 H19 N7 O7
WBQDVZMETQWVQD-VIFPVBQESA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.11α = 90
b = 109.264β = 90
c = 73.025γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CancerfondenSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary