SMTL ID : 6fz5.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x BXN: 4-[3-[(8~{a}~{R})-3,4,6,7,8,8~{a}-hexahydro-1~{H}-pyrrolo[1,2-a]pyrazin-2-yl]propyl]-2,6-bis(chloranyl)-~{N}-methyl-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide(Non-covalent)

BXN.1: 17 residues within 4Å: Chain A: V.67, D.69, F.74, R.75, F.76, N.132, T.168, Y.182, H.184, F.197, S.291, L.302, Y.306, G.358, L.381, Q.382 Ligands: MYA.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.74, A:Y.182, A:F.197, A:L.302 Hydrogen bonds: A:S.291, A:N.337 Water bridges: A:N.132, A:D.357 Halogen bonds: A:Y.306

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

MYA.2: 34 residues within 4Å: Chain A: Y.3, Q.4, F.5, W.6, N.65, Y.66, V.67, I.131, N.132, F.133, L.134, C.135, V.136, R.141, S.142, K.143, R.144, V.145, A.146, P.147, I.150, T.154, V.157, I.162, F.163, Q.164, A.165, Y.167, T.168, A.169, L.173, Y.365 Ligands: BXN.1, MG.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.6, A:W.6, A:Y.66, A:V.67, A:I.131, A:L.134, A:L.134, A:V.136, A:I.150, A:V.157, A:A.165, A:Y.167, A:Y.365 Hydrogen bonds: A:Q.4, A:F.5, A:W.6, A:Y.66, A:F.133, A:L.134, A:L.134, A:V.136, A:R.141, A:R.141, A:S.142, A:R.144, A:V.145, A:A.146 Water bridges: A:R.141

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain A: V.136, L.140, R.141, S.142, K.143, R.144, V.145 Ligands: MYA.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.140

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: P.12, K.175, P.176, V.177, Y.363, L.364, W.367, K.368, C.369, P.370, S.371 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.176, A:V.177, A:L.364, A:L.364, A:W.367, A:C.369 Water bridges: A:K.175 GOL.5: 8 residues within 4Å: Chain A: E.130, P.250, W.260, F.308, Y.309, L.379, V.380, Q.382 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.130, A:Y.309, A:Y.309, A:V.380, A:Q.382 Water bridges: A:W.260

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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