SMTL ID : 8fju.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

2 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, 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.95, Y.130, G.314, G.315 Ligands: Y79.2 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.242 Hydrogen bonds: A:S.65, A:S.131, A:G.132, A:S.133, A:S.215, A:H.243, A:K.269, A:K.269, B:Y.85, B:Y.85, B:Y.95, B:Y.130, B:G.314, B:G.315 Water bridges: A:S.131, A:R.275 Salt bridges: A:H.243, A:H.268, A:K.269, A:K.269, A:R.414 pi-Stacking: A:H.160 PLG.3: 23 residues within 4Å: Chain A: Y.85, E.87, Y.95, Y.130, G.314, G.315 Chain B: S.65, S.131, G.132, S.133, N.136, H.160, H.163, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 Ligands: Y79.4 21 PLIP interactions: 7 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:Y.85, A:Y.85, A:Y.95, A:Y.95, A:Y.130, A:G.314, A:G.315, B:S.65, B:G.132, B:S.133, B:N.136, B:T.214 Hydrophobic interactions: B:A.242 Water bridges: B:S.131, B:R.275 Salt bridges: B:H.243, B:H.268, B:K.269, B:K.269, B:R.414 pi-Stacking: B:H.160

2 x Y79: N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoyl}-L-glutamic acid(Non-covalent)

Y79.2: 19 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, Y.165, V.169, K.170, I.172, S.215, A.216, R.414 Chain B: E.87, Y.94, Y.95, F.306, F.309, P.310 Ligands: PLG.1 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.155, A:L.161, A:I.172, A:I.172, B:Y.94, B:F.306, B:P.310, B:P.310 Hydrogen bonds: A:G.158, A:G.159, A:G.159, A:L.161, A:S.215, B:Y.94 Y79.4: 17 residues within 4Å: Chain A: E.87, Y.94, Y.95, F.309, P.310 Chain B: L.155, G.158, G.159, H.160, L.161, Y.165, I.172, S.215, A.216, A.407, R.414 Ligands: PLG.3 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.94, A:Y.94, A:P.310, B:L.161, B:L.161 Hydrogen bonds: B:L.155, B:G.158, B:G.159, B:L.161, B:S.215

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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