SMTL ID : 9ec2.1

Crystal structure of SAMHD1 dimer bound to an inhibitor obtained from high-throughput chemical tethering to the guanine antiviral acyclovir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-tetramer

Ligands

4 x 01: N-[5-({2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl}amino)-5-oxopentyl]-4,7-dibromo-3-hydroxynaphthalene-2-carboxamide

01.1: 19 residues within 4Å: Chain A: M.5, K.6, V.7, I.8, N.9, V.23, I.26, D.27, Q.32, R.35, F.55 Chain C: Y.45, V.46, F.47, P.48, R.262, H.266, V.268, R.341 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:F.47, A:V.7, A:N.9 Hydrogen bonds: C:H.266, C:R.341, C:R.341, A:V.7, A:Q.32, A:R.35, A:R.35 pi-Cation interactions: C:R.341, C:R.341 Salt bridges: A:D.27 01.3: 19 residues within 4Å: Chain B: D.3, T.4, K.6, I.8, V.23, I.26, D.27, Q.32, R.35, F.55 Chain D: Y.45, V.46, F.47, P.48, H.266, V.268, R.341, L.343, K.345 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:V.268, D:L.343 Hydrogen bonds: D:R.341, D:R.341, B:K.6, B:Q.32, B:R.35, B:R.35 pi-Cation interactions: D:R.341 Salt bridges: B:D.27 01.4: 20 residues within 4Å: Chain B: Y.45, V.46, F.47, P.48, R.261, R.262, H.266, V.268, R.341 Chain D: K.6, V.7, I.8, N.9, H.15, V.23, I.26, D.27, Q.32, R.35, F.55 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:R.261, B:H.266, B:R.341, B:R.341, D:Q.32, D:R.35, D:R.35 Water bridges: B:R.341, D:Q.32 pi-Cation interactions: B:R.262, B:R.262, B:R.341, B:R.341 Salt bridges: D:D.27 01.6: 20 residues within 4Å: Chain A: Y.45, V.46, F.47, P.48, H.266, K.267, V.268, R.341, L.343, K.345, Y.346 Chain C: K.6, V.7, I.8, V.23, I.26, D.27, Q.32, R.35, F.55 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:K.6, A:V.268 Hydrogen bonds: C:K.6, C:Q.32, C:R.35, A:R.341, A:R.341 Salt bridges: C:D.27 pi-Cation interactions: A:R.341, A:R.341

4 x FE: FE (III) ION(Non-covalent)

FE.2: 7 residues within 4Å: Chain A: R.54, H.57, V.61, H.96, D.97, D.201, Y.205 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.57, A:H.96, A:D.97, A:D.201, A:D.201 FE.5: 6 residues within 4Å: Chain B: R.54, H.57, H.96, D.97, D.201, Y.205 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.57, B:H.96, B:D.97, B:D.201, H2O.2 FE.7: 7 residues within 4Å: Chain C: R.54, H.57, V.61, H.96, D.97, D.201, Y.205 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.57, C:H.96, C:D.97, C:D.201, C:D.201 FE.8: 7 residues within 4Å: Chain D: R.54, H.57, V.61, H.96, D.97, D.201, Y.205 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.57, D:H.96, D:D.97, D:D.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egleston, M. et al., Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir. Biochemistry (2025)

Release Date

2025-03-12

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

Related Entries With Identical Sequence