3OYP | pdb_00003oyp

HCV NS3/4A in complex with ligand 3

PDB DOI: https://doi.org/10.2210/pdb3OYP/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Hepatitis C virus (isolate Japanese)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-23 Released: 2010-12-01
Deposition Author(s): Hagel, M., Niu, D., St.Martin, T., Sheets, M.P., Qiao, L., Bernard, H., Karp, R.M., Zhu, Z., Labenski, M.T., Chaturvedi, P.C., Nacht, M., Westlin, W.F., Petter, R.C., Singh, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.274 (Depositor), 0.235 (DCC)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine.

Hagel, M., Niu, D., St.Martin, T., Sheets, M.P., Qiao, L., Bernard, H., Karp, R.M., Zhu, Z., Labenski, M.T., Chaturvedi, P., Nacht, M., Westlin, W.F., Petter, R.C., Singh, J.

(2011) Nat Chem Biol 7: 22-24

PubMed: 21113170 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.492
Primary Citation Related Structures:
3OYP

PubMed Abstract:
Designing selective inhibitors of proteases has proven problematic, in part because pharmacophores that confer potency exploit the conserved catalytic apparatus. We developed a fundamentally different approach by designing irreversible inhibitors that target noncatalytic cysteines that are structurally unique to a target in a protein family. We have successfully applied this approach to the important therapeutic target HCV protease, which has broad implications for the design of other selective protease inhibitors.

Organizational Affiliation

Avila Therapeutics, Inc., Waltham, Massachusetts, USA.

Macromolecule Content

Total Structure Weight: 44.36 kDa
Atom Count: 2,827
Modeled Residue Count: 383
Deposited Residue Count: 416
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	A, B	187	Hepatitis C virus (isolate Japanese)	Mutation(s): 2 EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662 Go to UniProtKB: P26662
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26662
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 4A	C, D	16	Hepatitis C virus (isolate Japanese)	Mutation(s): 0
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662 Go to UniProtKB: P26662
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26662
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidomimetic inhibitor	E, F	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0Y8 Query on 0Y8	E, F	L-PEPTIDE LINKING	C₁₄ H₁₃ Br N₂ O₃		PRO
0Y9 Query on 0Y9	E, F	PEPTIDE LINKING	C₆ H₉ N O₂		--
DAL Query on DAL	E, F	D-PEPTIDE LINKING	C₃ H₇ N O₂		--

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000823 Query on PRD_000823	E, F	N-propanoyl-D-alanyl-(4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide	Peptide-like / Antiviral		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.274 (Depositor), 0.235 (DCC)
R-Value Work: 0.215 (Depositor)
R-Value Observed: 0.219 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.401	α = 90
b = 94.401	β = 90
c = 83.129	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2012-12-19
Changes: Non-polymer description, Structure summary
Version 1.4: 2018-01-24
Changes: Database references
Version 1.5: 2018-01-31
Changes: Database references, Structure summary
Version 1.6: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations