SMTL ID : 5yg3.1 (1 other biounit)

Plasmodium vivax SHMT bound with PLP-glycine and S-GS834

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 19 residues within 4Å: Chain A: S.34, S.100, G.101, S.102, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 Chain B: Y.54, Y.64, G.271, G.272 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.34, A:G.101, A:S.102, A:N.105, A:T.183, A:S.210, B:Y.54, B:Y.64, B:G.271, B:G.272 Water bridges: A:S.100, A:S.100, A:S.100, A:R.243, B:Y.54 Salt bridges: A:H.211, A:H.236, A:K.237, A:R.371 pi-Stacking: A:H.129 PLG.4: 19 residues within 4Å: Chain A: Y.54, E.56, Y.64, G.271, G.272 Chain B: S.34, S.100, G.101, S.102, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.183 Hydrogen bonds: B:S.34, B:G.101, B:S.102, B:S.102, B:T.183, B:S.210, A:Y.54, A:G.271, A:G.272 Water bridges: B:S.100, B:S.100, B:R.243 Salt bridges: B:H.211, B:H.236, B:K.237, B:R.371 pi-Stacking: B:H.129

2 x 8UC: (3~{S})-6'-azanyl-7-fluoranyl-2,2,3'-trimethyl-5-pyridin-4-yl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5'-carbonitrile(Non-covalent)

8UC.2: 13 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, T.183, N.354, K.355, T.357, C.364 Chain B: E.56, Y.63, Y.64 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.124, B:Y.63, B:Y.64 Hydrogen bonds: A:G.128, A:L.130, A:T.183, A:T.357, B:E.56 8UC.5: 15 residues within 4Å: Chain A: E.56, Y.63, Y.64 Chain B: L.124, G.127, G.128, H.129, L.130, T.183, S.184, N.354, K.355, N.356, T.357, C.364 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.63, A:Y.64, B:L.124, B:L.124 Hydrogen bonds: A:E.56, A:Y.63, B:G.127, B:L.130, B:T.357

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: N.276, K.277 Chain B: N.276, K.277 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwertz, G. et al., Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold. ChemMedChem (2018)

Release Date

2018-06-06

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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