SMTL ID : 4ufv.2 (2 other biounits)

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 18)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NHW: 2-oxopentadecyl-CoA(Non-covalent)

NHW.1: 34 residues within 4Å: Chain A: Y.3, K.4, F.5, W.6, N.69, Y.70, V.71, V.135, N.136, F.137, L.138, C.139, V.140, R.145, S.146, K.147, R.148, L.149, A.150, P.151, I.154, T.158, I.161, N.162, W.167, Q.168, A.169, Y.171, T.172, A.173, V.175, L.177, Y.368 Ligands: MG.4 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:W.6, A:W.6, A:Y.70, A:V.71, A:L.138, A:L.138, A:L.138, A:V.140, A:A.150, A:I.154, A:I.161, A:I.161, A:A.169, A:Y.171, A:Y.171, A:Y.368 Hydrogen bonds: A:Y.3, A:K.4, A:F.5, A:W.6, A:Y.70, A:F.137, A:L.138, A:L.138, A:V.140, A:R.145, A:R.145, A:S.146, A:R.148, A:L.149, A:A.150 Water bridges: A:R.145, A:R.148, A:R.148 Salt bridges: A:R.148, A:R.148

1 x 31A: N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide(Non-covalent)

31A.2: 18 residues within 4Å: Chain A: V.71, E.72, D.73, F.78, F.80, Y.82, T.172, Y.186, F.201, Y.290, L.292, S.294, Y.309, N.340, L.342, L.363, L.384, L.385 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.71, A:D.73, A:F.80, A:Y.186, A:Y.186, A:Y.186, A:L.292, A:N.340, A:L.342, A:L.363 Hydrogen bonds: A:Y.82, A:S.294, A:L.385 Water bridges: A:N.136, A:T.172, A:L.385 pi-Stacking: A:F.80, A:Y.309

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.185, Y.187, K.348 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.185, A:R.185, A:E.358 Salt bridges: A:R.185, A:K.348

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: L.144, R.145, S.146, K.147, R.148, L.149 Ligands: NHW.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.144

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

CL.5: 3 residues within 4Å: Chain A: T.222, L.223, R.333 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 4 residues within 4Å: Chain A: E.134, F.256, W.264, V.383 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:E.134 pi-Cation interactions: A:W.264, A:W.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Z. et al., Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase. Medchemcomm (2015)

Release Date

2016-02-03

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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