6S4A

Structure of human MTHFD2 in complex with TH9028

PDB DOI: https://doi.org/10.2210/pdb6S4A/pdb

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.211
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

Organizational Affiliation

Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.

Macromolecule Content

Total Structure Weight: 72.27 kDa
Atom Count: 4,991
Modelled Residue Count: 591
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial	A, B	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 GTEx: ENSG00000065911
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13995
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B]	G [auth A], O [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
KUK (Subject of Investigation/LOI) Query on KUK Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	(2~{S})-2-[[5-[[2,4-bis(azanyl)-6-oxidanylidene-5~{H}-pyrimidin-5-yl]carbamoylamino]pyridin-2-yl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid C₁₆ H₁₈ N₁₂ O₅ AFYCZELCTVXAOG-WPRPVWTQSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	H [auth A] I [auth A] J [auth A] P [auth B] Q [auth B] H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]