Structure of PDB 5vdr Chain A Binding Site BS02

Receptor Information
>5vdr Chain A (length=357) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLL
NTGSYYEHVKAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENP
LSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLL
ISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVP
KHAKGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMK
YLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCF
DNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNN
EFPVFDE
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 A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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 T321 R376 S378 S380 S434 Y436
Binding residue
(residue number reindexed from 1)
M68 T160 R212 S214 S216 S270 Y272
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=3.30,Kd>500uM
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)

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