SMTL ID : 7kw1.1

Structure of hSTING in complex with novel carbocyclic pyrimidine CDN-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x X4M: (2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione(Non-covalent)

X4M.1: 20 residues within 4Å: Chain A: S.26, Y.27, G.30, Y.31, R.102, Y.104, E.124, T.127, P.128 Chain B: S.26, Y.27, G.30, Y.31, R.96, R.102, Y.104, T.127, P.128, T.131 Ligands: X4M.2 23 PLIP interactions: 13 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Y.31, A:R.102, A:R.102, A:T.127, B:R.102, B:R.102 Water bridges: A:R.96, A:E.124, A:E.124, A:E.124, A:T.127, B:Y.31, B:R.96, B:T.131 Salt bridges: A:E.124 pi-Stacking: A:Y.31 pi-Cation interactions: A:Y.31, A:R.102, B:R.102 Hydrophobic interactions: B:Y.27, B:Y.31, B:Y.31, B:Y.104 X4M.2: 20 residues within 4Å: Chain A: S.26, Y.27, G.30, Y.31, R.96, R.102, Y.104, T.127, P.128, T.131 Chain B: S.26, Y.27, G.30, Y.31, R.102, Y.104, E.124, T.127, P.128 Ligands: X4M.1 21 PLIP interactions: 8 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:Y.27, A:Y.31, A:Y.31, A:Y.104 Hydrogen bonds: A:R.102, A:R.102, B:Y.31, B:R.102, B:R.102, B:T.127 Water bridges: A:R.96, B:Y.31, B:Y.31, B:R.96, B:E.124, B:T.127 pi-Cation interactions: A:R.102, B:Y.31, B:R.102 Salt bridges: B:E.124 pi-Stacking: B:Y.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyskocil, S. et al., Identification of Novel Carbocyclic Pyrimidine Cyclic Dinucleotide STING Agonists for Antitumor Immunotherapy Using Systemic Intravenous Route. J.Med.Chem. (2021)

Release Date

2021-06-02

Peptides

Stimulator of interferon genes protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Stimulator of interferon genes protein

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