Structure of PDB 5vdo Chain A Binding Site BS02

Receptor Information

>5vdo Chain A (length=360) 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
KHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLK
LMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLG
LCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYE
RNNEFPVFDE

Ligand information

Ligand ID

1YC

InChI

InChI=1S/C20H24N10O13P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-12-10(31)6(40-18)1-38-45(36,37)43-13-11(32)7(2-39-44(34,35)42-12)41-19(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

BQZWXNITEWDGCM-INFSMZHSSA-N

SMILES

Software	SMILES
ACDLabs 12.01	O=C7NC(=Nc1c7ncn1C5OC6COP(=O)(O)OC4C(O)C(OC4n2c3ncnc(N)c3nc2)COP(=O)(O)OC5C6O)N
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O[C@@H]5[C@@H]([C@@H](COP(=O)(O4)O)O[C@H]5n6cnc7c6N=C(NC7=O)N)O)O)O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@@H]5[C@H](O)[C@@H](CO[P](O)(=O)O[C@@H]3[C@@H]4O)O[C@H]5n6cnc7c(N)ncnc67
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5n6cnc7c6N=C(NC7=O)N)O)O)O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](CO[P](O)(=O)O[CH]3[CH]4O)O[CH]5n6cnc7c(N)ncnc67

Formula

C20 H24 N10 O13 P2

Name

PDB chain

5vdo Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5vdo The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Resolution	3.218 Å
Binding residue (original residue number in PDB)	S305 A307 D319 K362 R376 S434 Y436
Binding residue (residue number reindexed from 1)	S144 A146 D158 K201 R215 S273 Y275
Annotation score	4
Binding affinity	PDBbind-CN: -logKd/Ki=3.30,Kd>500uM

Enzymatic activity

Enzyme Commision number

2.7.7.86: cyclic GMP-AMP synthase.

External links

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

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