6DIS | pdb_00006dis

Crystal structure of HCV NS3/4A protease in complex with P4-1 (AJ-71)

PDB DOI: https://doi.org/10.2210/pdb6DIS/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Orthohepacivirus hominis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-23 Released: 2019-07-31
Deposition Author(s): Matthew, A.N., Schiffer, C.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.227 (Depositor), 0.225 (DCC)
R-Value Work:
0.187 (Depositor), 0.189 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design of Hepatitis C NS3/4A Protease Inhibitors Leveraging Untapped Regions of the Substrate Envelope

Matthew, A.N., Schiffer, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 22.53 kDa
Atom Count: 1,800
Modeled Residue Count: 199
Deposited Residue Count: 199
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease	A	199	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for A0A0B4WYC6 (Hepacivirus hominis) Explore A0A0B4WYC6 Go to UniProtKB: A0A0B4WYC6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0B4WYC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GKG (Subject of Investigation/LOI) Query on GKG 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]	1,1,1-trifluoro-2-methylpropan-2-yl [(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5, 16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6- yl]carbamate C₃₇ H₄₇ F₃ N₆ O₉ S ZOQBCVXDXFPSSL-DDAYHPHASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.227 (Depositor), 0.225 (DCC)
R-Value Work: 0.187 (Depositor), 0.189 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.607	α = 90
b = 58.628	β = 90
c = 59.966	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Matthew, A.N.

Schiffer, C.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI085051
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F31 GM119345

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary