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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.79 kDa 
• Atom Count: 2,464 
• Modelled Residue Count: 292 
• Deposited Residue Count: 316 
• Unique protein chains: 1

 6S4E

Structure of human MTHFD2 in complex with TH7299

• PDB DOI: 10.2210/pdb6S4E/pdb

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


• Deposited: 2019-06-27 Released: 2021-07-07 
• Deposition Author(s): Gustafsson, R., Scaletti, E.R., Bonagas, N., Gustafsson, N.M., Henriksson, M., Abdurakhmanov, E., Andersson, Y., Bengtsson, C., Borhade, S., Desroses, M., Farnegardh, K., Garg, N., Gokturk, C., Haraldsson, M., Iliev, P., Jarvius, M., Jemth, A.S., Kalderen, C., Karsten, S., Klingegard, F., Koolmeister, T., Martens, U., Llona-Minguez, S., Loseva, O., Marttila, P., Michel, M., Moulson, R., Nordstrom, H., Paulin, C., Pham, T., Pudelko, L., Rasti, A., Roos, A.K., Sarno, A., Sandberg, L., Scobie, M., Sjoberg, B., Svensson, R., Unterlass, J.E., Vallin, K., Vo, D., Wiita, E., Warpman-Berglund, U., Homan, E.J., Helleday, T., Stenmark, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress.

Bonagas, N., Gustafsson, N.M.S., Henriksson, M., Marttila, P., Gustafsson, R., Wiita, E., Borhade, S., Green, A.C., Vallin, K.S.A., Sarno, A., Svensson, R., Gokturk, C., Pham, T., Jemth, A.S., Loseva, O., Cookson, V., Kiweler, N., Sandberg, L., Rasti, A., Unterlass, J.E., Haraldsson, M., Andersson, Y., Scaletti, E.R., Bengtsson, C., Paulin, C.B.J., Sanjiv, K., Abdurakhmanov, E., Pudelko, L., Kunz, B., Desroses, M., Iliev, P., Farnegardh, K., Kramer, A., Garg, N., Michel, M., Haggblad, S., Jarvius, M., Kalderen, C., Jensen, A.B., Almlof, I., Karsten, S., Zhang, S.M., Haggblad, M., Eriksson, A., Liu, J., Glinghammar, B., Nekhotiaeva, N., Klingegard, F., Koolmeister, T., Martens, U., Llona-Minguez, S., Moulson, R., Nordstrom, H., Parrow, V., Dahllund, L., Sjoberg, B., Vargas, I.L., Vo, D.D., Wannberg, J., Knapp, S., Krokan, H.E., Arvidsson, P.I., Scobie, M., Meiser, J., Stenmark, P., Berglund, U.W., Homan, E.J., Helleday, T.

(2022) Nat Cancer 3: 156-172

• PubMed: 35228749 
• DOI: 10.1038/s43018-022-00331-y
• Primary Citation of Related Structures:  
  6S4A, 6S4E, 6S4F


• PubMed Abstract: 
  

The folate metabolism enzyme MTHFD2 (methylenetetrahydrofolate dehydrogenase/cyclohydrolase) is consistently overexpressed in cancer but its roles are not fully characterized, and current candidate inhibitors have limited potency for clinical development. In the present study, we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and perform a drug screen to identify potent and selective nanomolar MTHFD2 inhibitors; protein cocrystal structures demonstrated binding to the active site of MTHFD2 and target engagement. MTHFD2 inhibitors reduced replication fork speed and induced replication stress followed by S-phase arrest and apoptosis of acute myeloid leukemia cells in vitro and in vivo, with a therapeutic window spanning four orders of magnitude compared with nontumorigenic cells. Mechanistically, MTHFD2 inhibitors prevented thymidine production leading to misincorporation of uracil into DNA and replication stress. Overall, these results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors.

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Organizational Affiliation: 

Weston Park Cancer Centre, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK. [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	G [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
9L9 (Subject of Investigation/LOI)	B [auth A]	(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	C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.559	α = 90
b = 74.559	β = 90
c = 99.248	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Gustafsson, R., Scaletti, E.R., Bonagas, N., Gustafsson, N.M., Henriksson, M., Abdurakhmanov, E., Andersson, Y., Bengtsson, C., Borhade, S., Desroses, M., Farnegardh, K., Garg, N., Gokturk, C., Haraldsson, M., Iliev, P., Jarvius, M., Jemth, A.S., Kalderen, C., Karsten, S., Klingegard, F., Koolmeister, T., Martens, U., Llona-Minguez, S., Loseva, O., Marttila, P., Michel, M., Moulson, R., Nordstrom, H., Paulin, C., Pham, T., Pudelko, L., Rasti, A., Roos, A.K., Sarno, A., Sandberg, L., Scobie, M., Sjoberg, B., Svensson, R., Unterlass, J.E., Vallin, K., Vo, D., Wiita, E., Warpman-Berglund, U., Homan, E.J., Helleday, T., Stenmark, P.

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references