SMTL ID : 8b47.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a cyclic di-adenosine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-tetramer

Ligands

4 x OWU: (1~{R},23~{R},24~{S},25~{R})-14-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-7-azanyl-24,25-bis(oxidanyl)-20,20-bis(oxidanylidene)-26-oxa-20$l^{6}-thia-2,4,6,9,14,17,21-heptazatetracyclo[21.2.1.0^{2,10}.0^{3,8}]hexacosa-3,5,7,9-tetraen-11-yn-16-one(Non-covalent)

OWU.1: 19 residues within 4Å: Chain A: D.45, G.46, L.49, L.72, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222 Chain D: R.148, D.150, A.185, I.187 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:D.45, A:L.49 Hydrogen bonds: A:D.45, A:D.45, A:Y.75, A:N.122, A:N.122, A:Y.163, A:S.166, A:D.222, D:R.148, D:A.185 Water bridges: A:D.45, A:N.122, A:N.164, D:N.189 OWU.4: 17 residues within 4Å: Chain B: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 Chain C: D.150, A.185, I.187 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:D.45 Hydrogen bonds: B:D.45, B:N.122, B:S.158, B:T.161, B:Y.163, B:S.166, B:D.222, C:A.185 Water bridges: B:D.45, B:E.123, B:G.159, C:N.189 OWU.6: 19 residues within 4Å: Chain B: R.148, D.150, A.185, I.187 Chain C: D.45, G.46, L.49, L.72, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:D.45, C:L.49 Hydrogen bonds: C:D.45, C:D.45, C:Y.75, C:N.122, C:N.122, C:Y.163, C:S.166, C:D.222, B:R.148, B:A.185 Water bridges: C:D.45, C:N.122, C:N.164, B:N.189 OWU.9: 17 residues within 4Å: Chain A: D.150, A.185, I.187 Chain D: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:D.45 Hydrogen bonds: D:D.45, D:N.122, D:S.158, D:T.161, D:Y.163, D:S.166, D:D.222, A:A.185 Water bridges: D:D.45, D:E.123, D:G.159, A:N.189

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 9 residues within 4Å: Chain A: M.1, E.37, D.60, E.61, I.62, A.63, Y.95, K.97, H.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.97 1PE.7: 9 residues within 4Å: Chain C: M.1, E.37, D.60, E.61, I.62, A.63, Y.95, K.97, H.244 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.97

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: K.8, G.44, D.45, G.46, T.47 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.44, A:G.46, A:T.47, A:T.47 Water bridges: A:D.45, A:D.45 PO4.5: 6 residues within 4Å: Chain B: K.8, G.44, D.45, G.46, T.47, G.70 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.44, B:G.46, B:T.47, B:T.47 Water bridges: B:D.45 Salt bridges: B:K.8 PO4.8: 5 residues within 4Å: Chain C: K.8, G.44, D.45, G.46, T.47 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.44, C:G.46, C:T.47, C:T.47 Water bridges: C:D.45, C:D.45 PO4.10: 6 residues within 4Å: Chain D: K.8, G.44, D.45, G.46, T.47, G.70 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.44, D:G.46, D:T.47, D:T.47 Water bridges: D:D.45 Salt bridges: D:K.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clement, D.A. et al., Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria. Eur.J.Med.Chem. (2023)

Release Date

2023-01-11

Peptides

NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NAD kinase 1

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