6BQK | pdb_00006bqk

CRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TRIPEPTIDIC ACYL SULFONAMIDE INHIBITOR (COMPOUND 18)

PDB DOI: https://doi.org/10.2210/pdb6BQK/pdb

Classification: HYDROLASE
Organism(s): Orthohepacivirus hominis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-28 Released: 2018-03-21
Deposition Author(s): Klei, H.E., Sack, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.267 (Depositor), 0.269 (DCC)
R-Value Work:
0.254 (Depositor), 0.256 (DCC)
R-Value Observed:
0.254 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor.

Zheng, B., D'Andrea, S.V., Sun, L.Q., Wang, A.X., Chen, Y., Hrnciar, P., Friborg, J., Falk, P., Hernandez, D., Yu, F., Sheaffer, A.K., Knipe, J.O., Mosure, K., Rajamani, R., Good, A.C., Kish, K., Tredup, J., Klei, H.E., Paruchuri, M., Ng, A., Gao, Q., Rampulla, R.A., Mathur, A., Meanwell, N.A., McPhee, F., Scola, P.M.

(2018) ACS Med Chem Lett 9: 143-148

PubMed: 29456803 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.7b00503
Primary Citation Related Structures:
6BQJ, 6BQK

PubMed Abstract:
The design and synthesis of potent, tripeptidic acylsulfonamide inhibitors of HCV NS3 protease that contain a difluoromethyl cyclopropyl amino acid at P1 are described. A cocrystal structure of 18 with a NS3/4A protease complex suggests the presence of a H-bond between the polarized C-H of the CHF ₂ moiety and the backbone carbonyl of Leu135 of the enzyme. Structure-activity relationship studies indicate that this H-bond enhances enzyme inhibitory potency by 13- and 17-fold compared to the CH ₃ and CF ₃ analogues, respectively, providing insight into the deployment of this unique amino acid.

Organizational Affiliation

Research and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States.

Macromolecule Content

Total Structure Weight: 48.2 kDa
Atom Count: 3,034
Modeled Residue Count: 386
Deposited Residue Count: 438
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease	A, B	219	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958 Go to UniProtKB: P27958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27958
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Z1E Query on Z1E Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-[(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-(difluoromethyl)cyclopropyl]-L-prolinamide C₃₄ H₄₄ Cl F₂ N₅ O₉ S PSVSXONHXYMVQH-GGFAASIMSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
Z1E	BindingDB: 6BQK	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.267 (Depositor), 0.269 (DCC)
R-Value Work: 0.254 (Depositor), 0.256 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.65	α = 90
b = 68.06	β = 109.58
c = 61.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.