Structure of PDB 8uvm Chain D Binding Site BS01

Receptor Information
>8uvm Chain D (length=311) 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]
TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGK
TFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTS
IKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILA
YCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVE
AVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYEL
KHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDV
FYKENSYTTTI
Ligand information
Ligand IDY3R
InChIInChI=1S/C28H31N3O5S/c1-3-36-27(34)14-13-26(33)31-30-25(32)12-11-20-7-4-5-10-24(20)28(35)29-19(2)21-8-6-9-22(17-21)23-15-16-37-18-23/h4-10,15-19H,3,11-14H2,1-2H3,(H,29,35)(H,30,32)(H,31,33)
InChIKeyVCEOCCSGIGLDNU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[C@H](C)c2cccc(c2)c3cscc3
OpenEye OEToolkits 2.0.7CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)NC(C)c2cccc(c2)c3ccsc3
CACTVS 3.385CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[CH](C)c2cccc(c2)c3cscc3
ACDLabs 12.01O=C(OCC)CCC(=O)NNC(=O)CCc1ccccc1C(=O)NC(C)c1cccc(c1)c1ccsc1
OpenEye OEToolkits 2.0.7CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[C@H](C)c2cccc(c2)c3ccsc3
FormulaC28 H31 N3 O5 S
Nameethyl 4-oxo-4-(2-{3-[2-({(1S)-1-[(3P)-3-(thiophen-3-yl)phenyl]ethyl}carbamoyl)phenyl]propanoyl}hydrazinyl)butanoate
ChEMBL
DrugBank
ZINC
PDB chain8uvm Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8uvm Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model
Resolution2.85 Å
Binding residue
(original residue number in PDB)
W106 N109 C111 L162 G163 D164 E167 P247 P248 Y264 Y268 Q269 G271 Y273
Binding residue
(residue number reindexed from 1)
W103 N106 C108 L159 G160 D161 E164 P244 P245 Y261 Y265 Q266 G268 Y270
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.-
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function

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Biological Process
External links
PDB RCSB:8uvm, PDBe:8uvm, PDBj:8uvm
PDBsum8uvm
PubMed38547259
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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