Structure of PDB 5sre Chain A Binding Site BS01

Receptor Information
>5sre Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL
Ligand information
Ligand IDR8R
InChIInChI=1S/C19H19FN4O2/c20-11-2-3-12-14(8-11)23-16-15(12)17(22-10-21-16)24-7-6-19(4-1-5-19)13(9-24)18(25)26/h2-3,8,10,13H,1,4-7,9H2,(H,25,26)(H,21,22,23)/t13-/m1/s1
InChIKeyBNVOKYLFRJDXFX-CYBMUJFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)[C@H]1CN(CCC12CCC2)c3ncnc4[nH]c5cc(F)ccc5c34
OpenEye OEToolkits 2.0.7c1cc2c(cc1F)[nH]c3c2c(ncn3)N4CCC5(CCC5)[C@H](C4)C(=O)O
CACTVS 3.385OC(=O)[CH]1CN(CCC12CCC2)c3ncnc4[nH]c5cc(F)ccc5c34
OpenEye OEToolkits 2.0.7c1cc2c(cc1F)[nH]c3c2c(ncn3)N4CCC5(CCC5)C(C4)C(=O)O
ACDLabs 12.01O=C(O)C1CN(CCC21CCC2)c1ncnc2[NH]c3cc(F)ccc3c21
FormulaC19 H19 F N4 O2
Name(5R)-7-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-7-azaspiro[3.5]nonane-5-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain5sre Chain A Residue 201 [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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PDB5sre Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		I23 G48 V49 A52 A129 G130 V155 F156 D157
Binding residue
(residue number reindexed from 1)		I21 G46 V47 A50 A127 G128 V153 F154 D155
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
2.7.7.50: mRNA guanylyltransferase.
3.1.13.-
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
4.6.1.-
External links
PDB RCSB:5sre, PDBe:5sre, PDBj:5sre
PDBsum5sre
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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