9IS9

human MTHFD2 in complex with LY374571


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Development of Potent and Selective Inhibitors of Methylenetetrahydrofolate Dehydrogenase 2 for Targeting Acute Myeloid Leukemia: SAR, Structural Insights, and Biological Characterization.

Chang, H.H.Lee, L.C.Hsu, T.Peng, Y.H.Huang, C.H.Yeh, T.K.Lu, C.T.Huang, Z.T.Hsueh, C.C.Kung, F.C.Lin, L.M.Huang, Y.C.Wang, Y.H.Li, L.H.Tang, Y.C.Chang, L.Hsieh, C.C.Jiaang, W.T.Kuo, C.C.Wu, S.Y.

(2024) J Med Chem 67: 21106-21125

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01775
  • Primary Citation of Related Structures:  
    9IS9, 9ISC, 9ISE, 9ISL, 9ISR, 9IT3, 9IT6, 9ITA, 9ITD, 9IUO

  • PubMed Abstract: 

    Methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 (MTHFD2), a pivotal mitochondrial enzyme in one-carbon metabolism, is significantly upregulated in various cancers but minimally expressed in normal proliferating cells. In contrast, MTHFD1, which performs similar functions, is predominantly expressed in normal cells. Therefore, targeting MTHFD2 with selective inhibitors holds promise for a broader therapeutic window with reduced toxicity and fewer side effects. This study identified selective 2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl ureido-based derivatives through systematic chemical modifications and SAR studies. Structural biology investigations revealed substitutions in the phenyl ring and tail region modulate potency and selectivity toward MTHFD2. Additionally, a comprehensive cell screening platform revealed acute myeloid leukemia cells with FLT3 internal tandem duplication mutations are particularly sensitive to these inhibitors. Furthermore, synergistic effects were observed when combining potential compounds with Alimta. Compound 16e emerged as a leading candidate, demonstrating superior inhibition and selectivity for MTHFD2, favorable pharmacokinetics, and potent antitumor efficacy in MOLM-14 xenograft models.


  • Organizational Affiliation

    Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road Zhunan Town, Miaoli County 350, Taiwan, Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
A, B
319Homo sapiensMutation(s): 0 
Gene Names: MTHFD2NMDMC
EC: 1.5.1.15 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P13995 (Homo sapiens)
Explore P13995 
Go to UniProtKB:  P13995
PHAROS:  P13995
GTEx:  ENSG00000065911 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13995
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
9L9 (Subject of Investigation/LOI)
Query on 9L9

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.605α = 90
b = 115.605β = 90
c = 113.326γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release