SMTL ID : 9mdd.1

Crystal Structure of human cyclic GMP-AMP synthase (cGAS) in complex with compound 23; (S)-1-(6,7-dichloro-1-methyl-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)-2-methoxyethan-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.234, C.240, C.241, C.248 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.234, A:C.240, A:C.241, A:C.248

1 x 01: 3-{[(2S)-1-{[(5P)-3-chloro-5-(1H-imidazol-2-yl)phenyl]amino}-1-oxopropan-2-yl](methyl)carbamoyl}pyridine-2-carboxylic acid

01.2: 19 residues within 4Å: Chain A: T.55, E.69, D.71, M.73, R.146, G.148, S.149, P.150, D.163, T.165, V.204, K.206, R.220, L.221, S.222, S.224, S.278 Ligands: ANP.3, MN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.150, A:V.204, A:K.206 Hydrogen bonds: A:R.146, A:T.165, A:K.206, A:S.222 Water bridges: A:T.165 Salt bridges: A:R.146 pi-Cation interactions: A:R.146

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 15 residues within 4Å: Chain A: G.56, S.57, K.63, E.69, D.71, R.220, S.224, E.227, K.258, S.279, Y.280, K.283 Ligands: 01.2, MN.4, MN.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.57, A:S.57, A:R.220, A:K.258, A:K.258, A:S.279, A:K.283, A:K.283 Water bridges: A:Y.58, A:K.63, A:E.69, A:K.258, A:S.279, A:Y.280 pi-Stacking: A:Y.280, A:Y.280

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: E.69, D.71, D.163 Ligands: 01.2, ANP.3, MN.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.69, A:D.71, A:D.163 MN.5: 5 residues within 4Å: Chain A: S.57, E.69, D.71 Ligands: ANP.3, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.69, A:D.71, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cyr, P. et al., Discovery of Potent and Orally Bioavailable Pyrimidine Amide cGAS Inhibitors via Structure-Guided Hybridization. Acs Med.Chem.Lett. (2024)

Release Date

2025-01-01

Peptides

Cyclic GMP-AMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclic GMP-AMP synthase