Structure of PDB 5vdr Chain B Binding Site BS03

Receptor Information
>5vdr Chain B (length=353) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLL
NTGAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEG
EILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISV
DITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGN
GFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLE
QLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCV
TYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPV
FDE
Ligand information
Ligand ID9B7
InChIInChI=1S/C20H22N8O14P2/c29-11-13-7(39-19(11)27-5-25-9-15(27)21-3-23-17(9)31)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)30)28-6-26-10-16(28)22-4-24-18(10)32/h3-8,11-14,19-20,29-30H,1-2H2,(H,33,34)(H,35,36)(H,21,23,31)(H,22,24,32)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyVFTRASQVWRBMKD-XPWFQUROSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH]2O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O[P](O)(=O)OC[CH]2O[CH]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67
CACTVS 3.385O[C@@H]1[C@@H]2O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O[P](O)(=O)OC[C@H]2O[C@H]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67
OpenEye OEToolkits 2.0.6c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O
OpenEye OEToolkits 2.0.6c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O
ACDLabs 12.01C5(C(C1C(COP(=O)(OC2C(COP(O1)(O)=O)OC(C2O)n4c3c(C(N=CN3)=O)nc4)O)O5)O)n7c6NC=NC(=O)c6nc7
FormulaC20 H22 N8 O14 P2
Name3',3'-cdIMP;
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H, 7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione
ChEMBLCHEMBL4803833
DrugBank
ZINC
PDB chain5vdr Chain B Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vdr The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Resolution3.042 Å
Binding residue
(original residue number in PDB)
M229 P306 K362 R376 S378 S380 S434 Y436
Binding residue
(residue number reindexed from 1)
M61 P138 K194 R208 S210 S212 S266 Y268
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.7.86: cyclic GMP-AMP synthase.
External links
PDB RCSB:5vdr, PDBe:5vdr, PDBj:5vdr
PDBsum5vdr
PubMed28940468
UniProtQ8N884|CGAS_HUMAN Cyclic GMP-AMP synthase (Gene Name=CGAS)

[Back to BioLiP]