7SDR | pdb_00007sdr

Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 Inhibitor

PDB DOI: https://doi.org/10.2210/pdb7SDR/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-29 Released: 2021-10-06
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Wang, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.173 (Depositor), 0.176 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 Inhibitor

Osipiuk, J., Tesar, C., Endres, M., Wang, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 109.34 kDa
Atom Count: 7,749
Modeled Residue Count: 939
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B, C	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JW9 (Subject of Investigation/LOI) Query on JW9 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain N [auth C]	D [auth A], G [auth B], N [auth C]	4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol C₂₀ H₂₁ N O QFTKMDZKABQMHI-OAHLLOKOSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth C]	E [auth A], H [auth B], O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain O [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	F [auth A], K [auth B], L [auth B], M [auth B], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]