Structure of PDB 5vdq Chain A Binding Site BS02

Receptor Information
>5vdq Chain A (length=359) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLL
NTGSYYEHVAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPL
SQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLI
SEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPK
HAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKL
MKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGL
CFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYER
NNEFPVFDE
Ligand information
Ligand ID9BG
InChIInChI=1S/C20H26N10O14P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(33)12(43-45(35,36)37)7(42-18)2-40-46(38,39)44-13-10(32)6(1-31)41-19(13)30-5-26-9-16(30)27-20(22)28-17(9)34/h3-7,10-13,18-19,31-33H,1-2H2,(H,38,39)(H2,21,23,24)(H2,35,36,37)(H3,22,27,28,34)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
InChIKeyOVXKSNAROFCXFB-INFSMZHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=NC(=O)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)O)N
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)O)N
ACDLabs 12.01c2nc1C(=O)N=C(N)Nc1n2C3C(C(C(O3)CO)O)OP(O)(OCC6OC(n5c4ncnc(N)c4nc5)C(C6OP(O)(=O)O)O)=O
CACTVS 3.385NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1
FormulaC20 H26 N10 O14 P2
Name2',5'-GpAp;
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5vdq 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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PDB5vdq The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Resolution3.246 Å
Binding residue
(original residue number in PDB)
E216 S305 R376 S434 S435 Y436
Binding residue
(residue number reindexed from 1)
E57 S143 R214 S272 S273 Y274
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=3.67,Kd=215uM
Enzymatic activity
Enzyme Commision number 2.7.7.86: cyclic GMP-AMP synthase.
External links
PDB RCSB:5vdq, PDBe:5vdq, PDBj:5vdq
PDBsum5vdq
PubMed28940468
UniProtQ8N884|CGAS_HUMAN Cyclic GMP-AMP synthase (Gene Name=CGAS)

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