1N1L | pdb_00001n1l

CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X)

• PDB DOI: https://doi.org/10.2210/pdb1N1L/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orthohepacivirus hominis, Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-10-18 Released: 2003-10-21 
• Deposition Author(s): Andrews, D.M., Chaignot, H., Coomber, B.A., Good, A.C., Hind, S.L., Jones, P.S., Mill, G., Robinson, J.E., Skarzynski, T., Slater, M.J., Somers, D.O.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.220 (Depositor) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Pyrrolidine-5,5-trans-lactams. 2. The use of X-ray Crystal Structure Data in the Optimisation of P3 and P4 Substituents

Andrews, D.M., Chaignot, H., Coomber, B.A., Good, A.C., Hind, S.L., Johnson, M.R., Jones, P.S., Mill, G., Robinson, J.E., Skarzynski, T., Slater, M.J., Somers, D.O.N.

(2002) Org Lett 4: 4479-4482

• PubMed: 12465917 
• DOI: https://doi.org/10.1021/ol027014p
• Primary Citation Related Structures: 
  1N1L


• PubMed Abstract: 
  

  [reaction: see text] In this, the second of two letters, we describe the elaboration of the pyrrolidine-5,5-trans-lactam template to delineate the requirements for optimal substitution of the pyrrolidine and lactam nitrogen atoms. Central to the strategy is the use of rapid iterative synthesis in conjunction with X-ray crystal structure determination of ligand-protein complexes.

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Organizational Affiliation: 
• GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.44 kDa 
• Atom Count: 2,870 
• Modeled Residue Count: 370 
• Deposited Residue Count: 442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS3 SERINE PROTEASE	A, B	198	Orthohepacivirus hominis	Mutation(s): 1  Gene Names: H STRAIN
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4A COFACTOR	C, D	23	N/A	Mutation(s): 0
UniProt
Find proteins for O39914 (Hepacivirus hominis) Explore O39914  Go to UniProtKB:  O39914

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRL	F [auth A]	{1-[2-(1-FORMYL-PROPYL)-3-METHANESULFONYLAMINO-PYRROLIDINE-1-CARBONYL]-2-METHYL-PROPYL}-CARBAMIC ACID TERT-BUTYL ESTER C19 H35 N3 O6 S NOWIRVOXJOWTSQ-FXUDXRNXSA-N
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.220 (Depositor) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.45	α = 90
b = 225.45	β = 90
c = 75.89	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-21 
Deposition Author(s): Andrews, D.M., Chaignot, H., Coomber, B.A., Good, A.C., Hind, S.L., Jones, P.S., Mill, G., Robinson, J.E., Skarzynski, T., Slater, M.J., Somers, D.O.N.

Revision History  

• Version 1.0: 2003-10-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary