SMTL ID : 7zzj.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 1.99 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 7 residues within 4Å: Chain A: V.98, Y.100, H.173, R.247, F.251, P.252, F.253 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.251, A:F.251, A:F.251, A:F.253 Salt bridges: A:H.173, A:R.247 CIT.2: 8 residues within 4Å: Chain A: K.8, G.43, G.44, D.45, G.46, T.47, H.71 Ligands: KIT.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.44, A:D.45, A:G.46, A:T.47, A:T.47, A:H.71 Water bridges: A:L.72, A:L.72, A:L.72, D:Y.192, D:Y.192 Salt bridges: A:K.8, A:K.8, A:H.71 CIT.4: 7 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.251, B:F.251, B:F.251, B:F.253 Salt bridges: B:H.173, B:R.247 CIT.5: 8 residues within 4Å: Chain B: K.8, G.43, G.44, D.45, G.46, T.47, H.71 Ligands: KIT.6 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.44, B:D.45, B:G.46, B:T.47, B:T.47, B:H.71 Water bridges: B:L.72, B:L.72, B:L.72, C:Y.192, C:Y.192 Salt bridges: B:K.8, B:K.8, B:H.71 CIT.7: 7 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.251, C:F.251, C:F.251, C:F.253 Salt bridges: C:H.173, C:R.247 CIT.8: 8 residues within 4Å: Chain C: K.8, G.43, G.44, D.45, G.46, T.47, H.71 Ligands: KIT.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.44, C:D.45, C:G.46, C:T.47, C:H.71 Water bridges: C:D.45, C:L.72, C:L.72, C:L.72 Salt bridges: C:K.8, C:K.8, C:H.71 CIT.10: 7 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.251, D:F.251, D:F.251, D:F.253 Salt bridges: D:H.173, D:R.247 CIT.11: 8 residues within 4Å: Chain D: K.8, G.43, G.44, D.45, G.46, T.47, H.71 Ligands: KIT.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.44, D:D.45, D:G.46, D:T.47, D:H.71 Water bridges: D:D.45, D:L.72, D:L.72, D:L.72 Salt bridges: D:K.8, D:K.8, D:H.71

4 x KIT: (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)-26-oxa-2,4,6,9,14,17,21-heptazatetracyclo[21.2.1.0^{2,10}.0^{3,8}]hexacosa-3(8),4,6,9-tetraen-11-yne-16,20-dione(Non-covalent)

KIT.3: 27 residues within 4Å: Chain A: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222, H.223, F.261 Chain D: P.132, G.149, D.150, A.185, S.186, I.187, N.189, Y.192 Ligands: CIT.2 15 PLIP interactions: 3 interactions with chain D, 12 interactions with chain A Hydrogen bonds: D:A.185, D:N.189, A:G.73, A:N.122, A:E.123, A:S.158, A:T.161, A:Y.163, A:S.166 Water bridges: D:Y.192, A:D.45, A:L.72, A:L.72 Hydrophobic interactions: A:D.45, A:L.49 KIT.6: 27 residues within 4Å: Chain B: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222, H.223, F.261 Chain C: P.132, G.149, D.150, A.185, S.186, I.187, N.189, Y.192 Ligands: CIT.5 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:D.45, B:L.49 Hydrogen bonds: B:G.73, B:N.122, B:E.123, B:S.158, B:T.161, B:Y.163, B:S.166, C:A.185, C:N.189 Water bridges: B:D.45, B:L.72, B:L.72, C:Y.192 KIT.9: 27 residues within 4Å: Chain B: P.132, G.149, D.150, A.185, S.186, I.187, N.189, Y.192 Chain C: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222, H.223, F.261 Ligands: CIT.8 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:G.73, C:Y.75, C:N.122, C:E.123, C:S.158, C:Y.163, C:S.166, B:A.185, B:N.189 Water bridges: C:D.45, C:L.72, C:L.72, B:Y.192 KIT.12: 27 residues within 4Å: Chain A: P.132, G.149, D.150, A.185, S.186, I.187, N.189, Y.192 Chain D: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, G.159, T.161, A.162, Y.163, S.166, D.222, H.223, F.261 Ligands: CIT.11 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:D.45, D:L.49 Hydrogen bonds: D:D.45, D:G.73, D:Y.75, D:N.122, D:E.123, D:S.158, D:Y.163, D:S.166, A:A.185, A:N.189 Water bridges: D:D.45, D:L.72, D:L.72, A:Y.192

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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