SMTL ID : 5yg2.2 (1 other biounit)

Plasmodium vivax SHMT bound with PLP-glycine and GS705

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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: 20 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, E.56, Y.64, G.271, G.272 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.34, A:G.101, A:S.102, A:S.102, A:N.105, A:S.210, A:K.237, A:K.237, B:Y.54, B:Y.64, B:G.271, B:G.272 Water bridges: A:S.100, A:S.100, A:S.100, A:T.232, A:R.243 Salt bridges: A:H.211, A:H.236, A:K.237, A:R.371 pi-Stacking: A:H.129 PLG.4: 20 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, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.34, B:G.101, B:S.102, B:S.102, B:N.105, B:S.210, B:K.237, B:K.237, A:Y.54, A:Y.54, A:Y.64, A:Y.64, A:G.271, A:G.272 Water bridges: B:S.100, 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 N05: 3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic acid(Non-covalent)

N05.2: 18 residues within 4Å: Chain A: L.124, G.128, H.129, L.130, V.141, T.183, S.184, N.354, K.355, N.356, T.357, C.364, P.367, R.371 Chain B: E.56, Y.63, Y.64, P.267 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.124, A:L.124, A:V.141, B:Y.64, B:P.267 Hydrogen bonds: A:G.128, A:T.357, B:E.56 N05.5: 18 residues within 4Å: Chain A: E.56, Y.63, Y.64, P.267 Chain B: L.124, G.128, H.129, L.130, V.141, T.183, S.184, N.354, K.355, N.356, T.357, C.364, P.367, R.371 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.124, B:L.124, B:V.141, A:Y.64, A:P.267 Hydrogen bonds: B:G.128, B:T.183, B:T.357, A:E.56

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

CL.3: 5 residues within 4Å: Chain A: N.276, K.277 Chain B: N.276, K.277 Ligands: CL.6 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: N.276, K.277 Chain B: N.276, K.277 Ligands: CL.3 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
C

B
C

Serine hydroxymethyltransferase

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