Structure of PDB 5vdw Chain A Binding Site BS02

Receptor Information

>5vdw 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]

GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLN
TGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKEN
PLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTL
LISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLV
PKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCL
KLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDL
GLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEY
ERNNEFPVFD

Ligand information

Ligand ID

9BY

InChI

InChI=1S/C12H9N3O2S/c16-11(17)5-15-10-4-2-1-3-8(10)14-12(15)9-6-18-7-13-9/h1-4,6-7H,5H2,(H,16,17)

InChIKey

QJFKGTPZZBLCJY-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	c1ccc2c(c1)nc(n2CC(=O)O)c3cscn3
ACDLabs 12.01	n3c(c2n(c1ccccc1n2)CC(O)=O)csc3
CACTVS 3.385	OC(=O)Cn1c2ccccc2nc1c3cscn3

Formula

C12 H9 N3 O2 S

Name

[2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid

PDB chain

5vdw 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	5vdw The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Resolution	2.711 Å
Binding residue (original residue number in PDB)	R376 L377 S434 Y436 N482 F488
Binding residue (residue number reindexed from 1)	R216 L217 S274 Y276 N322 F328
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:5vdw, PDBe:5vdw, PDBj:5vdw
PDBsum	5vdw
PubMed	28940468
UniProt	Q8N884\|CGAS_HUMAN Cyclic GMP-AMP synthase (Gene Name=CGAS)

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