SMTL ID : 6s4f.1

Structure of human MTHFD2 in complex with TH9619

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x KUN: (E,4S)-4-[[5-[2-[2,6-bis(azanyl)-4-oxidanylidene-1H-pyrimidin-5-yl]ethanoylamino]-3-fluoranyl-pyridin-2-yl]carbonylamino]pent-2-enedioic acid(Non-covalent)

KUN.1: 19 residues within 4Å: Chain A: S.49, Y.50, N.53, K.54, L.96, V.97, Q.98, L.99, D.121, F.123, I.242, R.244, L.255, P.275, G.276, G.279, P.280, T.282, V.283 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.50, A:L.255 Hydrogen bonds: A:S.49, A:N.53, A:K.54, A:V.97, A:Q.98, A:L.99, A:L.99, A:L.99, A:R.244, A:G.276, A:G.279 Water bridges: A:V.97, A:A.141, A:T.142, A:T.142, A:G.277, A:T.282 Salt bridges: A:D.121 pi-Stacking: A:Y.50 pi-Cation interactions: A:K.54 KUN.9: 18 residues within 4Å: Chain B: S.49, Y.50, N.53, K.54, L.96, V.97, Q.98, L.99, D.121, F.123, I.242, L.255, P.275, G.276, G.279, P.280, T.282, V.283 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.50, B:Y.50 Hydrogen bonds: B:S.49, B:N.53, B:K.54, B:V.97, B:Q.98, B:L.99, B:L.99, B:L.99, B:G.276, B:G.279 Water bridges: B:A.141, B:T.142, B:G.277 Salt bridges: B:D.121 pi-Stacking: B:Y.50 pi-Cation interactions: B:K.54 Halogen bonds: B:Y.50

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: R.167, R.199 Chain B: D.182, H.185 Ligands: ADP.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.167, B:D.182 Salt bridges: A:R.167, A:R.199, B:H.185 PO4.3: 5 residues within 4Å: Chain A: D.182, H.185 Chain B: R.167, R.199 Ligands: PO4.11 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:R.167 Salt bridges: B:R.167, B:R.199, A:H.185 Hydrogen bonds: A:D.182, A:D.182, A:D.182 PO4.4: 5 residues within 4Å: Chain A: L.133, D.134, Q.135, H.185, E.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.186 Salt bridges: A:H.185 PO4.5: 5 residues within 4Å: Chain A: D.106, R.108 Chain B: Q.135, E.186 Ligands: PO4.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.135, A:D.106, A:D.106 PO4.6: 6 residues within 4Å: Chain A: R.130, Q.135 Chain B: D.106, R.108, R.109, N.112 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.130, A:Q.135, B:N.112 Water bridges: A:R.130, B:D.106, B:D.106 PO4.10: 6 residues within 4Å: Chain B: L.133, D.134, Q.135, H.185, E.186 Ligands: PO4.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.133, B:E.186 Salt bridges: B:H.185 PO4.11: 7 residues within 4Å: Chain B: G.166, R.167, S.168, H.198, R.199, A.220 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.167, B:S.168, B:R.199, B:A.220 Salt bridges: B:R.199 PO4.12: 7 residues within 4Å: Chain B: N.87, N.112, A.113, V.114, S.115, P.116, H.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.112, B:A.113, B:H.124 Water bridges: B:N.87

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 15 residues within 4Å: Chain A: A.165, G.166, R.167, S.168, V.171, S.197, H.198, R.199, L.206, A.219, A.220, G.221, I.222, L.225 Ligands: PO4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.167, A:S.168, A:R.199, A:R.199 Water bridges: A:S.168, A:G.172, A:R.199, A:T.201

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: L.139, W.144, W.147, L.178, R.187, P.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.188 GOL.13: 5 residues within 4Å: Chain B: L.139, W.144, W.147, R.187, P.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.147, B:P.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonagas, N. et al., Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress. Nat Cancer (2022)

Release Date

2021-07-07

Peptides

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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