SMTL ID : 6wh8.1

The structure of NTMT1 in complex with compound BM-30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x 4HP- PRO- LYS- ARG- NH2: 4HP-PRO-LYS-ARG-NH2, BM-30(Non-covalent)

4HP-PRO-LYS-ARG-NH2.1: 15 residues within 4Å: Chain A: Y.37, W.38, M.48, L.49, G.50, Y.52, I.55, W.154, N.186, D.195, D.198, S.200, E.231, I.232, Y.233 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.38, A:Y.52, A:I.55, A:W.154, A:W.154, A:I.232 Hydrogen bonds: A:Y.37, A:Y.37, A:N.186, A:S.200, A:Y.233 4HP-PRO-LYS-ARG-NH2.2: 15 residues within 4Å: Chain B: Y.37, W.38, M.48, L.49, G.50, Y.52, I.55, W.154, N.186, D.195, D.198, S.200, E.231, I.232, Y.233 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.38, B:Y.52, B:I.55, B:W.154, B:W.154, B:I.232 Hydrogen bonds: B:N.186, B:D.195, B:D.198, B:D.198, B:Y.233 Water bridges: B:Y.37

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 24 residues within 4Å: Chain A: Y.31, W.38, M.48, L.49, C.86, G.87, A.88, G.89, R.92, I.93, V.108, D.109, I.110, T.111, F.114, C.135, G.136, L.137, Q.138, Q.153, W.154, V.155, H.158, L.159 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.89, A:D.109, A:D.109, A:I.110, A:T.111, A:L.137, A:Q.138, A:Q.153 Water bridges: A:Q.153, A:H.158 Salt bridges: A:R.92 SAH.4: 24 residues within 4Å: Chain B: Y.31, W.38, M.48, L.49, C.86, G.87, A.88, G.89, R.92, I.93, V.108, D.109, I.110, T.111, F.114, C.135, G.136, L.137, Q.138, Q.153, W.154, V.155, H.158, L.159 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.89, B:D.109, B:D.109, B:I.110, B:T.111, B:T.111, B:L.137, B:Q.138, B:Q.138, B:Q.153 Water bridges: B:R.92, B:Q.153 Salt bridges: B:R.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackie, B.D. et al., Selective Peptidomimetic Inhibitors of NTMT1/2: Rational Design, Synthesis, Characterization, and Crystallographic Studies. J.Med.Chem. (2020)

Release Date

2020-08-26

Peptides

N-terminal Xaa-Pro-Lys N-methyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

N-terminal Xaa-Pro-Lys N-methyltransferase 1

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