SMTL ID : 6chh.1

Structure of human NNMT in complex with bisubstrate inhibitor MS2756

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x F0P: (2~{S})-5-[2-(3-aminocarbonylphenyl)ethyl-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]amino]-2-azanyl-pentanoic acid(Non-covalent)

F0P.1: 29 residues within 4Å: Chain A: Y.30, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, Q.89, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.187, A.188, D.216, S.220, Y.222, Y.223, S.232, Y.261 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.39, A:Y.39, A:Y.43, A:L.183, A:Y.223, A:Y.261 Hydrogen bonds: A:Y.44, A:T.86, A:Y.88, A:D.104, A:Y.105, A:S.106, A:N.109, A:D.161, A:D.161, A:V.162, A:T.182, A:T.182, A:T.182, A:D.186, A:S.220, A:S.232, A:S.232 Water bridges: A:T.182, A:A.187 pi-Stacking: A:Y.30, A:Y.223 F0P.2: 27 residues within 4Å: Chain B: Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, Q.89, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.187, A.188, A.217, S.220, Y.223, S.232, Y.261 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.39, B:Y.43, B:Y.223, B:Y.223, B:Y.261 Hydrogen bonds: B:Y.39, B:Y.44, B:G.82, B:Y.88, B:D.104, B:Y.105, B:S.106, B:N.109, B:D.161, B:D.161, B:V.162, B:T.182, B:S.220, B:S.232, B:S.232 Water bridges: B:T.182, B:A.187 pi-Stacking: B:Y.223 F0P.3: 27 residues within 4Å: Chain C: Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, Q.89, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.187, A.188, A.217, S.220, Y.223, S.232, Y.261 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.39, C:Y.43, C:Y.223, C:Y.223, C:Y.261 Hydrogen bonds: C:G.82, C:T.86, C:Y.105, C:S.106, C:N.109, C:D.161, C:V.162, C:T.182, C:T.182, C:D.186, C:S.220, C:S.232, C:S.232 Water bridges: C:T.182, C:A.187 pi-Stacking: C:Y.223 F0P.6: 28 residues within 4Å: Chain D: Y.30, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, Q.89, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.187, A.188, D.216, S.220, Y.223, S.232, Y.261 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.39, D:Y.43, D:Y.223, D:Y.261 Hydrogen bonds: D:Y.39, D:G.82, D:Y.105, D:S.106, D:N.109, D:D.161, D:V.162, D:S.220, D:S.232, D:S.232 Water bridges: D:T.182, D:A.187 pi-Stacking: D:Y.30, D:Y.223

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain D: N.267 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.267 EDO.5: 4 residues within 4Å: Chain D: G.18, S.19, M.20, E.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.18, D:S.19, D:M.20, D:E.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Babault, N. et al., Discovery of Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT). J. Med. Chem. (2018)

Release Date

2018-06-13

Peptides

Nicotinamide N-methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Nicotinamide N-methyltransferase

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