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

Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor (compound 20b)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.184, Y.186, K.347 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.184, A:K.347 Salt bridges: A:R.184, A:K.347

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: V.139, L.143, R.144, S.145, K.146, R.147, L.148 Ligands: NHW.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.143

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

CL.3: 2 residues within 4Å: Chain A: Y.39, K.154 Ligand excluded by PLIP

1 x 3F3: 4-[(2-{5-[(3-METHOXYPHENYL)METHYL]-1,3,4-OXADIAZOL-2-YL}-1-BENZOTHIOPHEN-3-YL)OXY]PIPERIDINE(Non-covalent)

3F3.4: 21 residues within 4Å: Chain A: V.70, E.71, D.72, F.77, F.79, Y.81, T.171, Y.185, F.200, Y.289, L.291, S.293, Y.308, S.309, N.339, A.340, L.341, L.362, V.382, L.383, L.384 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.70, A:F.79, A:L.291, A:N.339, A:L.341, A:L.341, A:V.382 Hydrogen bonds: A:Y.81, A:S.293 Water bridges: A:N.135, A:N.135, A:N.135, A:T.171, A:T.171 pi-Stacking: A:F.79, A:F.79, A:Y.185, A:Y.308, A:Y.308

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

DMS.5: 3 residues within 4Å: Chain A: E.133, W.263, I.381 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.133 pi-Cation interactions: A:W.263

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

NHW.6: 35 residues within 4Å: Chain A: Y.2, K.3, F.4, W.5, N.68, Y.69, V.70, V.134, N.135, F.136, L.137, C.138, V.139, R.144, S.145, K.146, R.147, L.148, A.149, P.150, I.153, T.157, I.160, N.161, I.165, W.166, Q.167, A.168, Y.170, T.171, A.172, V.174, L.176, Y.367 Ligands: MG.2 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:W.5, A:W.5, A:Y.69, A:V.134, A:L.137, A:L.137, A:L.137, A:V.139, A:A.149, A:I.153, A:I.160, A:I.160, A:A.168, A:Y.170, A:Y.170, A:Y.367 Hydrogen bonds: A:K.3, A:F.4, A:W.5, A:Y.69, A:F.136, A:L.137, A:L.137, A:V.139, A:R.144, A:R.144, A:S.145, A:R.147, A:A.149 Water bridges: A:Y.2, A:Y.2, A:Y.2, A:R.144, A:R.144, A:S.145, A:R.147, A:R.147, A:R.147, A:R.147 Salt bridges: A:R.147, A:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rackham, M.D. et al., Design and Synthesis of High Affinity Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N-Myristoyltransferases Directed by Ligand Efficiency Dependent Lipophilicity (Lelp). J.Med.Chem. (2014)

Release Date

2014-04-02

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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