SMTL ID : 6orr.5 (4 other biounits)

Co-crystal structure of human NicotinamideN-Methyltransferase (NNMT) in complex with High-Affinity Alkynyl Bisubstrate Inhibitor NS1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x N37: 9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine(Non-covalent)

N37.1: 29 residues within 4Å: Chain A: K.27, Y.30, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.188, D.216, A.217, S.220, Y.222, Y.223, S.232, Y.261 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.43, A:Y.223, 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:S.220, A:S.232, A:S.232 Water bridges: A:T.182 pi-Stacking: A:Y.30, A:Y.223 N37.6: 29 residues within 4Å: Chain B: K.27, Y.30, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.188, D.216, A.217, S.220, Y.222, Y.223, S.232, Y.261 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.43, B:L.183, B:Y.223, B:Y.223, B:Y.261 Hydrogen bonds: B:Y.39, B:Y.39, B:Y.44, B:Y.44, B:Y.88, B:Y.105, B:S.106, B:N.109, B:D.161, B:D.161, B:V.162, B:S.220, B:S.232, B:S.232 pi-Stacking: B:Y.30, B:Y.223 N37.7: 29 residues within 4Å: Chain C: K.27, Y.30, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.188, D.216, A.217, S.220, Y.222, Y.223, S.232, Y.261 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.39, C:Y.39, C:Y.43, C:Y.223, C:Y.223, C:Y.261 Hydrogen bonds: C:Y.39, 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:S.220, C:S.232, C:S.232 Water bridges: C:T.182 pi-Stacking: C:Y.30, C:Y.223 N37.8: 29 residues within 4Å: Chain D: K.27, Y.30, F.34, Y.39, Y.43, Y.44, G.82, S.83, G.84, T.86, Y.88, D.104, Y.105, S.106, N.109, C.160, D.161, V.162, T.182, L.183, C.184, D.186, A.188, D.216, A.217, S.220, Y.223, S.232, Y.261 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:F.34, D:Y.39, D:Y.43, D:L.183, D:Y.223, D:Y.223, D:Y.261 Hydrogen bonds: D:Y.39, D:D.104, D:Y.105, D:S.106, D:N.109, D:D.161, D:V.162, D:T.182, D:T.182, D:S.220, D:S.232, D:S.232 pi-Stacking: D:Y.30, D:Y.223

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.246 Chain D: C.196, E.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.246 GOL.3: 6 residues within 4Å: Chain A: H.9, S.11, R.17, G.18, S.19, M.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.11, A:S.11, A:G.18, A:M.20 GOL.4: 3 residues within 4Å: Chain A: Q.55, K.58, Y.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.55, A:K.58, A:Y.132 Water bridges: A:R.49 GOL.5: 1 residues within 4Å: Chain A: T.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.250 GOL.9: 1 residues within 4Å: Chain D: K.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.27 Water bridges: D:D.28, D:D.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Policarpo, R.L. et al., High-Affinity Alkynyl Bisubstrate Inhibitors of NicotinamideN-Methyltransferase (NNMT). J.Med.Chem. (2019)

Release Date

2019-10-23

Peptides

NNMT protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

NNMT protein

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