Structure of PDB 5vdp Chain A Binding Site BS02

Receptor Information

>5vdp Chain A (length=360) Species: 9606 (Homo sapiens)

MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLL
NTGSYYEHVKAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENP
LSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLL
ISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVP
KHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLK
LMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLG
LCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYE
RNNEFPVFDE

Ligand information

• Ligand ID: 1SY
• InChI: InChI=1S/C20H24N10O13P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(32)12-7(41-18)2-39-45(36,37)43-13-10(31)6(1-38-44(34,35)42-12)40-19(13)30-5-26-9-16(30)27-20(22)28-17(9)33/h3-7,10-13,18-19,31-32H,1-2H2,(H,34,35)(H,36,37)(H2,21,23,24)(H3,22,27,28,33)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
• InChIKey: XRILCFTWUCUKJR-INFSMZHSSA-N
• SMILES:
  ACDLabs 12.01: O=C7N=C(N)Nc1c7ncn1C5OC6COP(=O)(O)OC4C(OC(n2c3ncnc(N)c3nc2)C4O)COP(=O)(OC5C6O)O
  CACTVS 3.370: NC1=NC(=O)c2ncn([CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]3[CH]4O)n6cnc7c(N)ncnc67)c2N1
  CACTVS 3.370: NC1=NC(=O)c2ncn([C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@@H]3[C@@H]4O)n6cnc7c(N)ncnc67)c2N1
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5n6cnc7c6NC(=NC7=O)N)O)O)O)N
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H]([C@@H](COP(=O)(O4)O)O[C@H]5n6cnc7c6NC(=NC7=O)N)O)O)O)N
• Formula: C20 H24 N10 O13 P2
• Name: cGAMP;
  2',3' cGAMP;
  c-GMP-AMP;
  c[G(2',5')pA(3',5')p]
• ChEMBL: CHEMBL4465054
• ZINC: ZINC000096095421
• PDB chain: 5vdp Chain A Residue 605

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vdp The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): G303 G304 S305 P306 D319 K362 R376 S434 Y436
• Binding residue (residue number reindexed from 1): G142 G143 S144 P145 D158 K201 R215 S273 Y275
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=4.05,Kd=89uM

Enzymatic activity

• Enzyme Commision number: 2.7.7.86: cyclic GMP-AMP synthase.

External links

• PDB: RCSB:5vdp, PDBe:5vdp, PDBj:5vdp
• PDBsum: 5vdp
• PubMed: 28940468
• UniProt: Q8N884|CGAS_HUMAN Cyclic GMP-AMP synthase (Gene Name=CGAS)