Structure of PDB 5vdu Chain A Binding Site BS02

Receptor Information

>5vdu Chain A (length=361) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLL
NTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKE
NPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVT
LLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYL
VPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDC
LKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKD
LGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIE
YERNNEFPVFD

Ligand information

Ligand ID

9BS

InChI

InChI=1S/C9H7N3/c1-2-5-10-8(4-1)9-11-6-3-7-12-9/h1-7H

InChIKey

YJVKLLJCUMQBHN-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 12.01	n2c(c1ncccc1)nccc2
OpenEye OEToolkits 2.0.6	c1ccnc(c1)c2ncccn2
CACTVS 3.385	c1ccc(nc1)c2ncccn2

Formula

C9 H7 N3

Name

2-(pyridin-2-yl)pyrimidine

PDB chain

5vdu 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	5vdu The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Resolution	2.729 Å
Binding residue (original residue number in PDB)	R376 Y436
Binding residue (residue number reindexed from 1)	R217 Y277
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=3.70,Kd~200uM

Enzymatic activity

Enzyme Commision number

2.7.7.86: cyclic GMP-AMP synthase.

External links

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

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