SMTL ID : 6fz2.1 (1 other biounit)

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

31A.1: 16 residues within 4Å: Chain A: V.88, E.89, D.90, F.95, F.97, Y.99, Y.203, F.218, Y.308, S.312, L.323, Y.327, N.358, A.359, L.360, Q.403 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.90, A:F.95, A:Y.203, A:N.358, A:L.360 Hydrogen bonds: A:Y.203, A:S.312 Water bridges: A:Y.87, A:Y.99, A:N.153, A:N.153, A:T.189, A:Y.327 pi-Stacking: A:F.97, A:Y.327

1 x MYA: TETRADECANOYL-COA(Non-covalent)

MYA.2: 34 residues within 4Å: Chain A: Y.24, Q.25, F.26, W.27, N.86, Y.87, V.88, I.152, N.153, F.154, L.155, C.156, V.157, R.162, S.163, K.164, R.165, V.166, A.167, P.168, I.171, T.175, V.178, H.179, I.183, F.184, Q.185, A.186, Y.188, T.189, A.190, L.194, Y.386 Ligands: MG.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.27, A:W.27, A:Y.87, A:I.152, A:L.155, A:L.155, A:V.157, A:I.171, A:V.178, A:A.186, A:Y.188, A:Y.188, A:Y.386 Hydrogen bonds: A:Q.25, A:F.26, A:W.27, A:Y.87, A:F.154, A:L.155, A:L.155, A:V.157, A:R.162, A:R.162, A:S.163, A:R.165, A:V.166, A:A.167 Water bridges: A:G.191

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: V.157, L.161, S.163, K.164, R.165, V.166 Ligands: MYA.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.161

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: P.33, K.196, V.198, Y.384, L.385, W.388, K.389, C.390, P.391, S.392 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.197, A:L.385, A:L.385, A:W.388, A:C.390 Water bridges: A:K.196, A:W.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kersten, C. et al., How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System. J.Med.Chem. (2020)

Release Date

2019-03-27

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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