SMTL ID : 5dhu.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: K.127, D.150, Y.163, M.184, A.185 Chain C: D.150, Y.163, L.167, M.184, A.185 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.163, A:D.150, A:Y.163 Water bridges: C:A.185, A:K.127, A:A.185

4 x 5A8: 5'-azido-5'-deoxy-8-[(2-{[2-(1H-indol-3-yl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine(Non-covalent)

5A8.2: 13 residues within 4Å: Chain A: L.49, N.122, E.123, A.162, Y.163, S.166, H.223 Chain C: G.131, P.132, R.148, G.149, D.150, A.185 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.122, A:E.123, A:Y.163, A:S.166, A:H.223, C:D.150, C:A.185 pi-Stacking: A:Y.163 Hydrophobic interactions: C:P.132 5A8.4: 15 residues within 4Å: Chain B: L.49, N.122, E.123, A.162, Y.163, S.166, H.223 Chain D: G.131, P.132, F.133, R.148, G.149, D.150, A.185, I.187 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:P.132, D:R.148 Hydrogen bonds: D:D.150, D:D.150, B:N.122, B:E.123, B:Y.163, B:S.166 pi-Stacking: B:Y.163 5A8.5: 14 residues within 4Å: Chain A: G.131, P.132, R.148, G.149, D.150, A.185 Chain C: L.49, N.122, E.123, A.162, Y.163, S.166, D.222, H.223 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.122, C:E.123, C:Y.163, C:S.166, A:D.150, A:D.150 pi-Stacking: C:Y.163 Hydrophobic interactions: A:P.132 5A8.6: 13 residues within 4Å: Chain B: G.131, P.132, R.148, G.149, D.150, A.185 Chain D: N.122, E.123, A.162, Y.163, S.166, D.222, H.223 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.122, D:E.123, D:Y.163, D:S.166, D:D.222, B:D.150, B:A.185 pi-Stacking: D:Y.163

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 9 residues within 4Å: Chain A: H.205 Chain B: V.98, Y.100, H.173, S.175, F.251, P.252, F.253, R.256 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Water bridges: A:N.140, B:R.256 Salt bridges: A:H.205, B:H.173, B:H.173, B:R.256 Hydrophobic interactions: B:V.98, B:Y.100, B:F.253 Hydrogen bonds: B:F.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paoletti, J. et al., 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode. Eur.J.Med.Chem. (2016)

Release Date

2016-09-14

Peptides

NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD kinase 1

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