Structure of PDB 5spd Chain A Binding Site BS03

Receptor Information
>5spd 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 IDQRU
InChIInChI=1S/C21H21N3O5/c25-17-3-1-2-14-15(17)10-16(20(27)28)18(14)24-19(26)11-4-6-12(7-5-11)22-21(29)23-13-8-9-13/h1-7,13,16,18,25H,8-10H2,(H,24,26)(H,27,28)(H2,22,23,29)/t16-,18+/m1/s1
InChIKeyHULQKGAWTDMSSA-AEFFLSMTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)O)CC(C2NC(=O)c3ccc(cc3)NC(=O)NC4CC4)C(=O)O
CACTVS 3.385OC(=O)[CH]1Cc2c(O)cccc2[CH]1NC(=O)c3ccc(NC(=O)NC4CC4)cc3
CACTVS 3.385OC(=O)[C@@H]1Cc2c(O)cccc2[C@@H]1NC(=O)c3ccc(NC(=O)NC4CC4)cc3
ACDLabs 12.01O=C(NC1CC1)Nc1ccc(cc1)C(=O)NC1c2cccc(O)c2CC1C(=O)O
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)O)C[C@H]([C@H]2NC(=O)c3ccc(cc3)NC(=O)NC4CC4)C(=O)O
FormulaC21 H21 N3 O5
Name(1R,2R)-1-[4-(cyclopropylcarbamamido)benzamido]-4-hydroxy-2,3-dihydro-1H-indene-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain5spd Chain A Residue 203 [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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PDB5spd 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)		D22 G48 V49 A52 L126 A129 G130 I131 F156
Binding residue
(residue number reindexed from 1)		D20 G46 V47 A50 L124 A127 G128 I129 F154
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:5spd, PDBe:5spd, PDBj:5spd
PDBsum5spd
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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