SMTL ID : 4caf.1 (2 other biounits)

Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor (compound 34a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 370: 4-[(2-{5-[(3,5-dimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine(Non-covalent)

370.1: 22 residues within 4Å: Chain A: V.70, E.71, D.72, F.77, F.79, Y.81, T.171, Y.185, H.187, Y.289, L.291, S.293, Y.308, S.309, N.339, A.340, L.341, L.362, V.382, L.383, L.384 Ligands: NH4.6 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: 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, A:Y.308, A:L.384 Water bridges: A:N.135, A:T.171, A:S.293, A:Y.308, A:Y.308 pi-Stacking: A:F.79, A:Y.185, A:Y.308, A:Y.308

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

DMS.2: 7 residues within 4Å: Chain A: N.269, Y.272, S.290, N.305, N.333, N.334, F.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.269 pi-Cation interactions: A:F.335 DMS.3: 5 residues within 4Å: Chain A: E.133, F.255, W.263, I.381, L.383 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.133 pi-Cation interactions: A:W.263

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

SO4.4: 2 residues within 4Å: Chain A: R.184, K.347 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.347, A:K.347 Salt bridges: A:R.184, A:K.347

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: L.143, R.144, S.145, K.146, R.147, L.148 Ligands: NHW.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.143

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.6: 5 residues within 4Å: Chain A: N.135, T.171, L.384 Ligands: 370.1, NHW.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.135, A:L.384 Water bridges: A:T.171

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

CL.7: 2 residues within 4Å: Chain A: Y.39, K.154 Ligand excluded by PLIP

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

NHW.8: 36 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.5, NH4.6 39 PLIP interactions: 39 interactions with chain A Hydrophobic interactions: A:W.5, A:W.5, A:Y.69, A:V.70, A:V.134, A:V.134, A:L.137, A:L.137, A:V.139, A:A.149, A:I.153, 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:L.137, A:L.137, A:V.139, A:R.144, A:S.145, A:R.147, A:L.148, A:A.149 Water bridges: A:Y.2, A:Y.2, A:R.144, A:R.144, A:S.145, 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
A

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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