SMTL ID : 8fjt.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF362 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

1 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 21 residues within 4Å: Chain A: S.65, S.131, G.132, S.133, H.160, H.163, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 Chain B: Y.85, E.87, Y.130, G.314, G.315 Ligands: Y72.3 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.242 Hydrogen bonds: A:S.65, A:G.132, A:S.133, A:T.214, A:K.269, B:Y.85, B:Y.85, B:E.87, B:Y.130, B:G.314, B:G.315 Water bridges: A:S.131, A:N.136, A:R.275 Salt bridges: A:H.243, A:H.268, A:K.269, A:R.414 pi-Stacking: A:H.160

2 x Y72: N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-3-fluorothiophene-2-carbonyl}-L-glutamic acid(Non-covalent)

Y72.2: 18 residues within 4Å: Chain A: E.87, Y.94, Y.95, F.306, F.309, P.310 Chain B: L.155, G.158, G.159, H.160, L.161, Y.165, I.172, S.215, A.216, N.399, R.414 Ligands: GLY.4 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.94, A:Y.94, A:Y.95, A:F.306, A:F.309, B:L.161 Hydrogen bonds: B:G.158, B:G.159, B:G.159, B:L.161, B:N.399 Y72.3: 16 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, I.172, S.215, A.216, R.414 Chain B: E.87, K.92, Y.94, F.306, F.309, P.310 Ligands: PLG.1 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.161, B:Y.94, B:Y.94, B:F.306, B:F.309 Hydrogen bonds: A:L.155, A:G.159, A:L.161 Water bridges: B:K.92, B:K.92, B:K.92 Salt bridges: B:K.92

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 11 residues within 4Å: Chain A: Y.85, E.87, Y.95 Chain B: S.65, H.160, S.215, H.243, K.269, R.414 Ligands: Y72.2, PLP.5 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.87, A:Y.95, B:S.65 Salt bridges: B:H.243, B:K.269, B:R.414

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.5: 16 residues within 4Å: Chain A: Y.85, G.314, G.315 Chain B: S.131, G.132, S.133, H.160, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269 Ligands: GLY.4 15 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.242, B:K.269 Hydrogen bonds: B:G.132, B:S.133, B:H.243, B:K.269, A:Y.85, A:G.314, A:G.315, G.4 Water bridges: B:S.131, B:R.275 Salt bridges: B:H.268, B:K.269 pi-Stacking: B:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayeen, M.J. et al., Structure-Based Design of Transport-Specific Multitargeted One-Carbon Metabolism Inhibitors in Cytosol and Mitochondria. J.Med.Chem. (2023)

Release Date

2023-09-06

Peptides

Serine hydroxymethyltransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase, mitochondrial

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