Structure of PDB 6dxg Chain A Binding Site BS02

Receptor Information

>6dxg Chain A (length=177) Species: 9606 (Homo sapiens)

FNVAHGLAWSYYIGYLRLILPELQARIRTYNQHYNNLLRGAVSQRLYILL
PLDCGVPDNLSMADPNIRFLDKLPQQVYSNSIYELLENGQRAGTCVLEYA
TPLQTLFAMSQYSQAGFSREDRLEQAKLFCRTLEDILADAPESQNNCRLI
AYQEPAFSLSQEVLRHLRQEEKEEVTV

Ligand information

• Ligand ID: HGJ
• InChI: InChI=1S/C23H24N6O3/c1-3-29-19(11-14(2)27-29)22(32)26-23-25-17-12-16(21(24)31)9-10-18(17)28(23)13-20(30)15-7-5-4-6-8-15/h4-12,20,30H,3,13H2,1-2H3,(H2,24,31)(H,25,26,32)/t20-/m0/s1
• InChIKey: NMXJYHHOVIHSBO-FQEVSTJZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CCn1c(cc(n1)C)C(=O)Nc2nc3cc(ccc3n2C[C@@H](c4ccccc4)O)C(=O)N
  OpenEye OEToolkits 2.0.6: CCn1c(cc(n1)C)C(=O)Nc2nc3cc(ccc3n2CC(c4ccccc4)O)C(=O)N
  CACTVS 3.385: CCn1nc(C)cc1C(=O)Nc2nc3cc(ccc3n2C[CH](O)c4ccccc4)C(N)=O
  ACDLabs 12.01: c1c3c(cc(c1)C(N)=O)nc(NC(c2cc(nn2CC)C)=O)n3CC(O)c4ccccc4
  CACTVS 3.385: CCn1nc(C)cc1C(=O)Nc2nc3cc(ccc3n2C[C@H](O)c4ccccc4)C(N)=O
• Formula: C23 H24 N6 O3
• Name: 2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-1-[(2R)-2-hydroxy-2-phenylethyl]-1H-benzimidazole-5-carboxamide
• PDB chain: 6dxg Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dxg Design of amidobenzimidazole STING receptor agonists with systemic activity.
• Resolution: 1.905 Å
• Binding residue (original residue number in PDB): L159 S162 Y163 Y167 Y240 S241 T263 P264
• Binding residue (residue number reindexed from 1): L7 S10 Y11 Y15 Y78 S79 T101 P102
• Annotation score: 1
• Binding affinity: MOAD: ic50=14uM
  PDBbind-CN: -logKd/Ki=4.85,IC50=14uM

Gene Ontology

Biological Process

• GO:0002218 activation of innate immune response
• GO:0032481 positive regulation of type I interferon production

External links

• PDB: RCSB:6dxg, PDBe:6dxg, PDBj:6dxg
• PDBsum: 6dxg
• PubMed: 30405246
• UniProt: Q86WV6|STING_HUMAN Stimulator of interferon genes protein (Gene Name=STING1)