SMTL ID : 8pie.1

Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x 7QT: [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate(Non-covalent)

7QT.1: 14 residues within 4Å: Chain A: K.31, Y.71, L.74, R.77, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137, D.140 Chain B: E.171 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.77, A:T.113, B:E.171 Water bridges: A:R.107, A:R.107, B:E.171 Salt bridges: A:R.107 pi-Stacking: A:F.79 pi-Cation interactions: A:F.79 7QT.3: 13 residues within 4Å: Chain B: K.31, Y.71, L.74, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137, D.140 Chain C: E.171 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.131 Salt bridges: B:R.107 pi-Stacking: B:F.79 pi-Cation interactions: B:F.79 Hydrogen bonds: C:E.171 7QT.4: 13 residues within 4Å: Chain A: E.171 Chain C: K.31, Y.71, L.74, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137, D.140 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.131 Hydrogen bonds: C:K.31, C:N.134, A:E.171 Salt bridges: C:R.107 pi-Stacking: C:F.79 pi-Cation interactions: C:F.79 Halogen bonds: C:Y.71 7QT.5: 13 residues within 4Å: Chain D: K.31, Y.71, L.74, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137, D.140 Chain F: E.171 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:V.131 Hydrogen bonds: D:K.31, D:T.113, D:D.140, F:E.171 Salt bridges: D:R.107 pi-Stacking: D:F.79, D:F.79 pi-Cation interactions: D:F.79 7QT.6: 14 residues within 4Å: Chain D: E.171 Chain E: K.31, Y.71, L.74, R.77, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137, D.140 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.31, E:T.113, E:N.134, D:E.171 Salt bridges: E:R.107 pi-Stacking: E:F.79, E:F.79 pi-Cation interactions: E:F.79 Halogen bonds: E:Y.71 7QT.7: 12 residues within 4Å: Chain E: E.171 Chain F: K.31, Y.71, L.74, F.79, L.83, R.107, T.113, V.131, G.132, N.134, H.137 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:V.131 Hydrogen bonds: F:K.31, F:T.113, F:N.134, E:E.171 Salt bridges: F:R.107 pi-Stacking: F:F.79, F:F.79 pi-Cation interactions: F:F.79

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: N.22, H.166, Y.170, E.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.22, A:H.166, A:E.171 Water bridges: A:E.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chazot, A. et al., The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution. Plos Biol. (2024)

Release Date

2024-07-31

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