SMTL ID : 7ehv.1

Human MTHFD2 in complex with compound 21 and 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

2 x J4L: 1-(3,4-dichlorobenzyl)-8-(((1R,4R)-4-hydroxycyclohexyl)amino)-3,7-dimethyl-3,7-dihydro-1H-purine-2,6-dione(Non-covalent)

J4L.1: 16 residues within 4Å: Chain A: L.98, F.122, V.127, M.130, P.139, P.142, K.168, N.169, V.170, M.172, P.173, M.176 Chain B: C.131, L.132, M.176 Ligands: J49.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.98, A:V.127, A:V.170, A:P.173, B:L.132 pi-Stacking: A:F.122, A:F.122 J4L.3: 13 residues within 4Å: Chain A: C.131 Chain B: G.121, F.122, V.127, M.130, P.139, K.168, N.169, V.170, M.172, P.173, M.176 Ligands: J49.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.127, B:V.170, B:P.173 Water bridges: B:S.167 pi-Stacking: B:F.122, B:F.122 Halogen bonds: B:K.168

2 x J49: (2S)-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl)carbamoylamino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

J49.2: 15 residues within 4Å: Chain A: S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, P.274, G.275, G.278, P.279, V.282 Ligands: J4L.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.49, A:Y.49, A:V.282 Hydrogen bonds: A:S.48, A:N.52, A:K.53, A:Q.97, A:L.98, A:L.98, A:G.275 pi-Stacking: A:Y.49 pi-Cation interactions: A:K.53 J49.4: 18 residues within 4Å: Chain B: S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, I.241, L.254, P.274, G.275, G.278, P.279, T.281, V.282 Ligands: J4L.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.254, B:T.281, B:V.282 Hydrogen bonds: B:S.48, B:N.52, B:K.53, B:Q.97, B:L.98, B:L.98, B:R.243, B:G.275, B:G.278 Water bridges: B:G.276, B:G.276 pi-Stacking: B:Y.49 pi-Cation interactions: B:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, L.C. et al., Xanthine Derivatives Reveal an Allosteric Binding Site in Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2). J.Med.Chem. (2021)

Release Date

2021-08-11

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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