SMTL ID : 9j2w.1

Human cGAS catalytic domain bound with XL-3156

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 01: 2-(1~{H}-benzimidazol-2-yl)-4-[[1-(1~{H}-benzimidazol-2-yl)-3-methyl-5-oxidanyl-pyrazol-4-yl]-pyridin-2-yl-methyl]-5-methyl-pyrazol-3-ol

01.1: 14 residues within 4Å: Chain A: V.62, K.63, D.71, T.165, R.220, L.221, E.262, K.265, S.278, S.279, Y.280, N.326, F.332, L.334 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.63, A:E.262, A:K.265, A:Y.280, A:F.332, A:L.334 Hydrogen bonds: A:R.220, A:S.279, A:S.279, A:Y.280 Water bridges: A:S.278 pi-Stacking: A:Y.280 pi-Cation interactions: A:K.206, A:R.220, A:K.265 01.3: 17 residues within 4Å: Chain B: K.63, D.71, A.91, S.149, P.150, T.165, R.220, L.221, E.262, K.265, S.278, S.279, Y.280, K.283, N.326, F.332, L.334 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.63, B:A.91, B:P.150, B:E.262, B:K.265, B:Y.280, B:F.332, B:L.334 Hydrogen bonds: B:R.220, B:S.279, B:Y.280 Water bridges: B:R.220, B:L.221 pi-Stacking: B:Y.280 pi-Cation interactions: B:R.220, B:K.265

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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 ZN.4: 4 residues within 4Å: Chain B: H.234, C.240, C.241, C.248 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.234, B:C.240, B:C.241, B:C.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, W. et al., De novo design of protein condensation inhibitors by targeting an allosteric site of cGAS. Nat Commun (2025)

Release Date

2025-06-04

Peptides

Cyclic GMP-AMP synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclic GMP-AMP synthase

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