SMTL ID : 4tn4.1 (1 other biounit)

Crystal structure of ternary complex of Plasmodium vivax SHMT with glycine and a novel pyrazolopyran 33G: (4S)-6-amino-4-(5-cyano-3'-fluorobiphenyl-3-yl)-4-cyclobutyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile

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, H.132, 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: 17 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.129 Hydrogen bonds: A:S.34, A:G.101, A:S.102, A:S.102, A:N.105, A:T.183, A:S.210, A:K.237, B:Y.54, B:G.271, B:G.272 Water bridges: A:S.100, A:S.100, A:R.243 Salt bridges: A:H.211, A:H.236, A:K.237, A:R.371 pi-Cation interactions: A:H.129 PLG.5: 19 residues within 4Å: Chain A: Y.54, 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 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.34, B:G.101, B:S.102, B:N.105, B:H.129, B:S.210, B:K.237, A:Y.54, A:Y.64, A:G.271, A:G.272 Water bridges: B:S.100, B:S.100, B:A.103, B:R.243 Salt bridges: B:H.211, B:H.236, B:K.237, B:K.237, B:R.371 pi-Stacking: B:H.129

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 7 residues within 4Å: Chain A: A.84, N.86, A.217, C.218, V.288, H.289, K.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.86, A:H.289 Water bridges: A:N.219 BME.6: 7 residues within 4Å: Chain B: A.84, N.86, A.217, C.218, V.288, H.289, K.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86, B:H.289

2 x 33G: (4S)-6-amino-4-(5-cyano-3'-fluorobiphenyl-3-yl)-4-cyclobutyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile(Non-covalent)

33G.3: 14 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, F.134, T.183, N.354, K.355, N.356, P.367 Chain B: E.56, Y.63, Y.64 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.124, B:Y.63, B:Y.63, B:Y.64 Hydrogen bonds: A:G.127, B:E.56 33G.7: 15 residues within 4Å: Chain A: E.56, Y.63, Y.64, P.267 Chain B: L.124, G.127, G.128, H.129, F.134, T.183, N.354, K.355, N.356, P.367, R.371 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.63, A:Y.63, A:P.267, B:L.124, B:T.183 Hydrogen bonds: A:E.56, B:H.129, B:T.183, B:T.183

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

CL.4: 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

Witschel, M.C. et al., Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT): Cocrystal Structures of Pyrazolopyrans with Potent Blood- and Liver-Stage Activities. J.Med.Chem. (2015)

Release Date

2015-03-25

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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