SMTL ID : 8pyw.1

Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-hexamer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: N.3, H.147, Y.151, E.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.3, A:H.147 Water bridges: A:N.3 GOL.3: 4 residues within 4Å: Chain B: N.3, H.147, Y.151, E.152 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.3, B:H.147, B:E.152 Water bridges: B:D.148, B:E.152 GOL.6: 5 residues within 4Å: Chain A: D.148, W.149 Chain D: Y.67, S.70, R.114 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.114

6 x IF9: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate(Non-covalent)

IF9.2: 12 residues within 4Å: Chain A: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115 Chain C: E.152 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:T.94, A:V.112 Water bridges: A:K.12, A:R.88, A:T.94, A:D.121, C:E.152, C:E.152, C:E.152, C:E.152 Salt bridges: A:R.88 pi-Stacking: A:F.60, A:F.60 pi-Cation interactions: A:F.60 Hydrogen bonds: C:E.152 IF9.4: 13 residues within 4Å: Chain B: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, D.121 Chain F: E.152 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:T.94, B:V.112 Hydrogen bonds: B:R.58, B:R.58, F:E.152 Water bridges: B:K.12, B:R.88, B:R.88, B:R.88, B:R.88, F:E.152, F:E.152 Salt bridges: B:R.88 pi-Stacking: B:F.60, B:F.60 IF9.5: 12 residues within 4Å: Chain C: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115 Chain D: E.152 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.112 Hydrogen bonds: C:R.58, C:R.58, D:E.152 Water bridges: C:R.88, C:R.88, C:T.94, C:T.94, C:T.94, D:E.152, D:E.152, D:E.152 Salt bridges: C:R.88 pi-Stacking: C:F.60 IF9.7: 14 residues within 4Å: Chain A: E.152 Chain D: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, H.118, D.121 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:E.152 Water bridges: A:E.152, D:Y.52, D:R.88, D:R.88 Hydrophobic interactions: D:T.94 Salt bridges: D:R.88 pi-Stacking: D:F.60, D:F.60 IF9.8: 14 residues within 4Å: Chain B: E.152 Chain E: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, H.118, D.121 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:T.94 Water bridges: E:K.12, E:Y.52, E:Y.52, E:R.88, E:R.88, E:R.114, B:E.152 Salt bridges: E:R.88 pi-Stacking: E:F.60, E:F.60 pi-Cation interactions: E:F.60 Hydrogen bonds: B:E.152 IF9.9: 13 residues within 4Å: Chain E: E.152 Chain F: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, D.121 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:E.152, F:R.58, F:R.58 Water bridges: E:E.152, E:E.152, F:Y.52, F:R.88, F:R.88, F:R.114, F:D.121 Hydrophobic interactions: F:T.94 Salt bridges: F:R.88 pi-Stacking: F:F.60, F:F.60 pi-Cation interactions: F:F.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shannon, A. et al., An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res. (2024)

Release Date

2023-12-27

Peptides

Nucleoside diphosphate kinase B: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase B