We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 6jid

X-ray diffraction
2.5Å resolution

Human MTHFD2 in complex with Compound 1

Released:
DOI: 10.2210/pdb6jid/pdb
Model geometry
Fit model/data
PDB entry 6jid coloured by chain, front view.
PDB entry 6jid coloured by chain, side view.
PDB entry 6jid coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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
ACS Med Chem Lett 10 893-898 (2019)
PMID: 31223444

Function and Biology Details

Reactions catalysed: 
(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NAD(+) = (6R)-5,10-methenyltetrahydrofolate + NADH.
(6R)-5,10-methenyltetrahydrofolate + H2O = (6R)-10-formyltetrahydrofolate+ H(+).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146835 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 323 amino acids
Theoretical weight: 35.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13995 (Residues: 36-338; Coverage: 87%)
  • Best match: P13995-2 (Residues: 1-236)
Gene names: MTHFD2, NMDMC
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand BQC 2 x BQC
Ligand PO4 2 x PO4
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P65
Unit cell:
a: 116.48Å b: 116.48Å c: 113.21Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.2 0.26
Expression system: Escherichia coli

Quick links

Citations

5 review citations

More Than a Metabolic Enzyme: MTHFD2 as a Novel Target for Anticancer Therapy?
Zhu et al. (2020)
4 more

5 mentions without citation

A Review of Small-Molecule Inhibitors of One-Carbon Enzymes: SHMT2 and MTHFD2 in the Spotlight.
Cuthbertson et al. (2021)
4 more