Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.54 kDa 
• Atom Count: 2,546 
• Modelled Residue Count: 292 
• Deposited Residue Count: 316 
• Unique protein chains: 1

 5TC4

Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors

• PDB DOI: 10.2210/pdb5TC4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2016-12-14 
• Deposition Author(s): Gustafsson, R., Jemth, A.-S., Gustafsson Sheppard, N., Farnegardh, K., Loseva, O., Wiita, E., Bonagas, N., Dahllund, L., Llona-Minguez, S., Haggblad, M., Henriksson, M., Andersson, Y., Homan, E., Helleday, T., Stenmark, P.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, Wenner-Gren Foundation, Goran Gustafsson's Foundation for Science and Medical Research, Svenska Smartafonden, Ragnar Soderberg Foundation, Swedish Childhood Cancer Foundation, Svenska Sallskapet for Medicinsk Forskning (SSMF), Karolinska Institutet (KI), Helleday Foundation, Swedish Cancer Society, Torsten Soderberg Foundation, Ake Wiberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.212 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.

Gustafsson, R., Jemth, A.S., Gustafsson, N.M., Farnegardh, K., Loseva, O., Wiita, E., Bonagas, N., Dahllund, L., Llona-Minguez, S., Haggblad, M., Henriksson, M., Andersson, Y., Homan, E., Helleday, T., Stenmark, P.

(2017) Cancer Res 77: 937-948

• PubMed: 27899380 
• DOI: 10.1158/0008-5472.CAN-16-1476
• Primary Citation of Related Structures:  
  5TC4


• PubMed Abstract: 
  

To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD ⁺ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. ©2017 AACR .

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial	A	316	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
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
L34	C [auth A]	4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID C20 H21 N7 O7 JSNFRYBHBVDHSG-NEPJUHHUSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
L34	Binding MOAD:  5TC4	IC50: 663 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.212 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.323	α = 90
b = 74.323	β = 90
c = 98.62	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Gustafsson, R., Jemth, A.-S., Gustafsson Sheppard, N., Farnegardh, K., Loseva, O., Wiita, E., Bonagas, N., Dahllund, L., Llona-Minguez, S., Haggblad, M., Henriksson, M., Andersson, Y., Homan, E., Helleday, T., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--
Wenner-Gren Foundation	Sweden	--
Goran Gustafsson's Foundation for Science and Medical Research	Sweden	--
Svenska Smartafonden	Sweden	--
Ragnar Soderberg Foundation	Sweden	--
Swedish Childhood Cancer Foundation	Sweden	--
Svenska Sallskapet for Medicinsk Forskning (SSMF)	Sweden	--
Karolinska Institutet (KI)	Sweden	--
Helleday Foundation	Sweden	--
Swedish Cancer Society	Sweden	--
Torsten Soderberg Foundation	Sweden	--
Ake Wiberg Foundation	Sweden	--

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Data collection
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence