SMTL ID : 4b12.1 (2 other biounits)

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x C23: 1-[3-METHYL-4-(PIPERIDIN-4-YLOXY)-1-BENZOFURAN-2-YL]-3-PHENYLPROPAN-1-ONE(Non-covalent)

C23.1: 20 residues within 4Å: Chain A: V.71, E.72, D.73, F.78, F.80, Y.82, T.172, Y.186, H.188, Y.290, L.292, S.294, Y.309, N.340, A.341, L.342, L.363, L.384, L.385 Ligands: DMS.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.71, A:D.73, A:F.78, A:F.80, A:Y.186, A:Y.186, A:L.292, A:Y.309, A:N.340, A:L.342, A:L.363 Hydrogen bonds: A:Y.82 Water bridges: A:Y.82, A:N.136, A:T.172, A:T.172, A:Y.290 pi-Stacking: A:Y.186, A:Y.309

1 x NHW: 2-OXOPENTADECYL-COA(Non-covalent)

NHW.2: 35 residues within 4Å: Chain A: M.1, 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.7 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.6, A:W.6, A:Y.70, A:V.71, A:V.135, A:L.138, A:L.138, A:L.138, A:V.140, A:I.161, A:I.161, A:A.169, A:Y.171, A:Y.368 Hydrogen bonds: A:K.4, A:F.5, A:W.6, A:L.138, A:L.138, A:V.140, A:R.145, A:S.146, A:R.148, A:L.149, A:A.150 Water bridges: A:R.145, A:S.146, A:R.148, A:R.148 Salt bridges: A:R.148, A:R.148

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

DMS.3: 4 residues within 4Å: Chain A: E.134, F.256, W.264, I.382 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:E.134 pi-Cation interactions: A:W.264, A:W.264 DMS.4: 8 residues within 4Å: Chain A: H.188, F.201, L.305, A.307, Y.309, V.338, N.340 Ligands: C23.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.340 DMS.5: 7 residues within 4Å: Chain A: E.269, N.270, Y.273, S.291, N.306, N.334, F.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.270 pi-Cation interactions: A:F.336

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

CL.6: 2 residues within 4Å: Chain A: Y.40, K.155 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 7 residues within 4Å: Chain A: L.144, R.145, S.146, K.147, R.148, L.149 Ligands: NHW.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.144

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Z. et al., Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Anti-Malarial Drug Discovery. J.Med.Chem. (2012)

Release Date

2012-10-17

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

Related Entries With Identical Sequence