Structure of PDB 7cmd Chain B Binding Site BS02

Receptor Information
>7cmd Chain B (length=308) 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]
AEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNS
HEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVN
GLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCA
LILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTL
KGVEAVMYMGTLSYEQFKKGVQITKYLVQQESPFVMMSAPPAQYELKHGT
FTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKE
NSYTTTIK
Ligand information
Ligand IDTTT
InChIInChI=1S/C20H20N2O/c1-13-10-11-16(21)12-19(13)20(23)22-14(2)17-9-5-7-15-6-3-4-8-18(15)17/h3-12,14H,21H2,1-2H3,(H,22,23)/t14-/m1/s1
InChIKeyUVERBUNNCOKGNZ-CQSZACIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1ccc(cc1C(=O)N[C@H](C)c2cccc3c2cccc3)N
CACTVS 3.341C[CH](NC(=O)c1cc(N)ccc1C)c2cccc3ccccc23
OpenEye OEToolkits 1.5.0Cc1ccc(cc1C(=O)NC(C)c2cccc3c2cccc3)N
CACTVS 3.341C[C@@H](NC(=O)c1cc(N)ccc1C)c2cccc3ccccc23
ACDLabs 10.04O=C(c1cc(N)ccc1C)NC(c3c2ccccc2ccc3)C
FormulaC20 H20 N2 O
Name5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide
ChEMBLCHEMBL549695
DrugBankDB08656
ZINCZINC000043012570
PDB chain7cmd Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7cmd Crystal structure of SARS-CoV-2 papain-like protease.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		D164 P248 Y264 Y268 Q269 T301
Binding residue
(residue number reindexed from 1)		D165 P241 Y257 Y261 Q262 T294
Annotation score1
Binding affinityBindingDB: IC50=1610nM,Kd=2700nM,EC50=27600nM
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:7cmd, PDBe:7cmd, PDBj:7cmd
PDBsum7cmd
PubMed32895623
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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