6KG2

Human MTHFD2 in complex with Compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Potent, Selective, and Orally Available MTHFD2 Inhibitor (DS18561882) with in Vivo Antitumor Activity.

Kawai, J.Toki, T.Ota, M.Inoue, H.Takata, Y.Asahi, T.Suzuki, M.Shimada, T.Ono, K.Suzuki, K.Takaishi, S.Ohki, H.Matsui, S.Tsutsumi, S.Hirota, Y.Nakayama, K.

(2019) J Med Chem 62: 10204-10220

  • DOI: 10.1021/acs.jmedchem.9b01113
  • Primary Citation of Related Structures:  
    6KG2

  • PubMed Abstract: 
  • We report the discovery of a potent and isozyme-selective MTHFD2 inhibitor, DS18561882 ( 2 ). Through investigation of the substituents on our tricyclic coumarin scaffold (1,2,3,4-tetrahydrochromeno[3,4- c ]pyridin-5-one), MTHFD2 inhibitory activity was shown to be elevated by incorporating an amine moiety at the 8-position and a methyl group at the 7-position of the initial lead 1 ...

    We report the discovery of a potent and isozyme-selective MTHFD2 inhibitor, DS18561882 ( 2 ). Through investigation of the substituents on our tricyclic coumarin scaffold (1,2,3,4-tetrahydrochromeno[3,4- c ]pyridin-5-one), MTHFD2 inhibitory activity was shown to be elevated by incorporating an amine moiety at the 8-position and a methyl group at the 7-position of the initial lead 1 . X-ray structure analysis revealed that a key interaction for enhanced potency was salt bridge formation between the amine moiety and the diphosphate linker of an NAD + cofactor. Furthermore, ortho-substituted sulfonamide in place of benzoic acid of 1 significantly improved cell permeability and cell-based growth inhibition against a human breast cancer cell line. The thus-optimized DS18561882 showed the strongest cell-based activity (GI 50 = 140 nM) in the class, a good oral pharmacokinetic profile, and thereby tumor growth inhibition in a mouse xenograft model upon oral administration.


    Organizational Affiliation

    Daiichi Sankyo Co., Ltd. , 3-5-1 Nihonbashi-honcho , Chuo-ku, Tokyo 103-8426 , Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrialA, B323Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
D8C
Query on D8C

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]N-[2-chloranyl-4-[[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxidanylidene-2,4-dihydro-1H-chromeno[3,4-c]pyridin-3-yl]carbonyl]phenyl]methanesulfonamide
C26 H29 Cl N4 O5 S
DHJUEJALVPLBJH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D8CIC50:  48   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.992α = 90
b = 116.992β = 90
c = 112.869γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references