Structure of PDB 7cmd Chain D Binding Site BS01

Receptor Information
>7cmd Chain D (length=307) 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
KGVEAVMYMGTLSYEQFKKGVQTKYLVQQESPFVMMSAPPAQYELKHGTF
TCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKEN
SYTTTIK
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 D Residue 601 [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)		L162 G163 D164 P248 Y264 Y268 Q269
Binding residue
(residue number reindexed from 1)		L163 G164 D165 P240 Y256 Y260 Q261
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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