SMTL ID : 6s4e.1

Structure of human MTHFD2 in complex with TH7299

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 9L9: (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

9L9.1: 18 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 Ligands: NAD.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.50, A:I.242 Hydrogen bonds: A:S.49, A:N.53, A:K.54, A:V.97, A:Q.98, A:L.99, A:L.99, A:G.276, A:G.279 Water bridges: A:K.54, A:D.121, A:A.141, A:T.142, A:T.142, A:G.277 Salt bridges: A:D.121, A:R.244 pi-Stacking: A:Y.50 pi-Cation interactions: A:K.54 9L9.7: 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, R.244, L.255, P.275, G.276, G.279, P.280 Ligands: NAD.12 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.50, B:I.242 Hydrogen bonds: B:S.49, B:N.53, B:K.54, B:V.97, B:Q.98, B:L.99, B:L.99, B:G.276, B:G.279 Water bridges: B:K.54, B:D.121, B:A.141, B:T.142, B:T.142, B:G.277 Salt bridges: B:D.121, B:R.244 pi-Stacking: B:Y.50 pi-Cation interactions: B:K.54

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: NAD.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.182 Water bridges: B:D.182, A:R.167, A:R.167 Salt bridges: B:H.185, A:R.167, A:R.199 PO4.3: 5 residues within 4Å: Chain A: L.133, D.134, Q.135, H.185, E.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.134, A:E.186 Salt bridges: A:H.185 PO4.4: 5 residues within 4Å: Chain A: L.139, W.144, W.147, R.187, P.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.147, A:P.188 PO4.5: 3 residues within 4Å: Chain A: I.126, R.130 Chain B: V.125 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.130 Hydrogen bonds: B:N.112 PO4.8: 5 residues within 4Å: Chain A: D.182, H.185 Chain B: R.167, R.199 Ligands: NAD.12 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.182 Water bridges: A:D.182, A:H.185, B:R.167 Salt bridges: A:H.185, B:R.167, B:R.199 PO4.9: 5 residues within 4Å: Chain B: L.133, D.134, Q.135, H.185, E.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.134, B:E.186 Salt bridges: B:H.185 PO4.10: 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 PO4.11: 3 residues within 4Å: Chain A: V.125 Chain B: I.126, R.130 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.130 Hydrogen bonds: A:N.112

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 21 residues within 4Å: Chain A: T.142, G.166, R.167, S.168, N.170, V.171, H.198, R.199, A.219, A.220, G.221, I.222, V.240, G.241, I.242, N.243, V.278, G.279, T.282 Ligands: 9L9.1, PO4.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.142, A:R.167, A:S.168, A:S.168, A:N.170, A:R.199, A:R.199, A:I.242, A:N.243 Water bridges: A:S.168, A:S.168, A:R.199 NAD.12: 21 residues within 4Å: Chain B: T.142, G.166, R.167, S.168, N.170, V.171, H.198, R.199, A.219, A.220, G.221, I.222, V.240, G.241, I.242, N.243, V.278, G.279, T.282 Ligands: 9L9.7, PO4.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.142, B:R.167, B:S.168, B:S.168, B:N.170, B:R.199, B:R.199, B:I.242, B:N.243 Water bridges: B:S.168, B:S.168, B:R.199

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
A

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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