SMTL ID : 7zzc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 7 residues within 4Å: Chain A: V.98, Y.100, H.173, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.251, A:F.251, A:F.253 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.4: 7 residues within 4Å: Chain B: V.98, Y.100, H.173, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.251, B:F.251, B:F.253 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256 CIT.7: 7 residues within 4Å: Chain C: V.98, Y.100, H.173, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.251, C:F.251, C:F.253 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.10: 7 residues within 4Å: Chain D: V.98, Y.100, H.173, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.251, D:F.251, D:F.253 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:K.8, A:D.45, A:G.46, A:T.47, A:T.47, A:T.47 GOL.5: 5 residues within 4Å: Chain B: K.8, G.44, D.45, G.46, T.47 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.8, B:D.45, B:G.46, B:T.47, B:T.47, B:T.47 GOL.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:K.8, C:D.45, C:G.46, C:T.47, C:T.47 Water bridges: C:D.45 GOL.11: 5 residues within 4Å: Chain D: K.8, G.44, D.45, G.46, T.47 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.8, D:D.45, D:G.46, D:T.47, D:T.47 Water bridges: D:D.45

4 x KIG: 2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(2-azanylethylsulfonylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid(Non-covalent)

KIG.3: 18 residues within 4Å: Chain A: 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 D: P.132, D.150, A.185, I.187 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain A Hydrogen bonds: D:A.185, A:D.45, A:N.122, A:S.158, A:T.161, A:Y.163, A:S.166, A:D.222 Hydrophobic interactions: A:D.45, A:L.49 pi-Stacking: A:Y.163 KIG.6: 18 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: P.132, D.150, A.185, I.187 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:D.45, B:L.49 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 pi-Stacking: B:Y.163 KIG.9: 18 residues within 4Å: Chain B: P.132, D.150, A.185, I.187 Chain C: 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 12 PLIP interactions: 11 interactions with chain C, 1 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:S.158, C:Y.163, C:S.166, C:D.222, B:A.185 pi-Stacking: C:Y.163 KIG.12: 18 residues within 4Å: Chain A: P.132, 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 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:D.45, D:L.49 Hydrogen bonds: D:D.45, D:D.45, D:Y.75, D:N.122, D:S.158, D:Y.163, D:S.166, D:D.222, A:A.185 pi-Stacking: D:Y.163

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
A

C
A

D
A

NAD kinase 1

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