6JIB

Human MTHFD2 in complex with DS44960156

• PDB DOI:  https://doi.org/10.2210/pdb6JIB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-20 Released: 2019-06-05 
• Deposition Author(s): Suzuki, M., Matsui, Y., Kawai, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold.

Kawai, J., Ota, M., Ohki, H., Toki, T., Suzuki, M., Shimada, T., Matsui, S., Inoue, H., Sugihara, C., Matsuhashi, N., Matsui, Y., Takaishi, S., Nakayama, K.

(2019) ACS Med Chem Lett 10: 893-898

• PubMed: 31223444 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00069
• Primary Citation of Related Structures:  
  6JIB, 6JID


• PubMed Abstract: 
  

  Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) plays a key role in one-carbon (1C) metabolism in human mitochondria, and its high expression correlates with poor survival of patients with various types of cancer. An isozyme-selective MTHFD2 inhibitor is highly attractive for potential use in cancer treatment. Herein, we disclose a novel isozyme-selective MTHFD2 inhibitor DS44960156, with a tricyclic coumarin scaffold, which was initially discovered via high-throughput screening (HTS) and improved using structure-based drug design (SBDD). DS44960156 would offer a good starting point for further optimization based on the following features: (1) unprecedented selectivity (>18-fold) for MTHFD2 over MTHFD1, (2) a molecular weight of less than 400, and (3) good ligand efficiency (LE).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.48 kDa 
• Atom Count: 4,680 
• Modelled Residue Count: 587 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial	A, B	323	Homo sapiens	Mutation(s): 0  Gene Names: MTHFD2, NMDMC 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BQF (Subject of Investigation/LOI)	C [auth A], E [auth A], I [auth B], J [auth B]	4-(5-oxo-1,5-dihydro-2H-[1]benzopyrano[3,4-c]pyridine-3(4H)-carbonyl)benzoic acid C20 H15 N O5 OXUKTNZACAKVRG-UHFFFAOYSA-N
PO4	D [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A], G [auth A], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BQF	Binding MOAD:  6JIB	IC50: 1600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.424	α = 90
b = 116.424	β = 90
c = 113.178	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Suzuki, M., Matsui, Y., Kawai, J.

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description