5C5N | pdb_00005c5n

Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type inhibitor

PDB DOI: https://doi.org/10.2210/pdb5C5N/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Severe acute respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-06-21 Released: 2016-06-22
Deposition Author(s): Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.321 (Depositor), 0.322 (DCC)
R-Value Work:
0.290 (Depositor), 0.291 (DCC)
R-Value Observed:
0.292 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors

Shimamoto, Y., Hattori, H., Kobayashi, K., Teruya, K., Sanjho, A., Nakagawa, A., Yamashita, E., Akaji, K.

To be published.

Macromolecule Content

Total Structure Weight: 34.27 kDa
Atom Count: 2,496
Modeled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 1 EC: 3.4.22.69
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLH Query on SLH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal C₂₅ H₃₅ N₅ O₂ HCMRRQNNHUOUJM-NVXDSCFRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.321 (Depositor), 0.322 (DCC)
R-Value Work: 0.290 (Depositor), 0.291 (DCC)
R-Value Observed: 0.292 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.801	α = 90
b = 82.091	β = 104.35
c = 53.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data reduction
PDB_EXTRACT	data extraction
MOLREP	model building
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Derived calculations
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.