4JEC | pdb_00004jec

Joint neutron and X-ray structure of per-deuterated HIV-1 protease in complex with clinical inhibitor amprenavir

• PDB DOI: https://doi.org/10.2210/pdb4JEC/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-26 Released: 2013-07-24 
• Deposition Author(s): Kovalevsky, A.Y., Weber, I.T., Langan, P.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.261 (Depositor) 
• R-Value Work: 
  0.244 (Depositor) 
• R-Value Observed: 
  0.244 (Depositor) 

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• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.203 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.181 (DCC) 

Literature

Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design.

Weber, I.T., Waltman, M.J., Mustyakimov, M., Blakeley, M.P., Keen, D.A., Ghosh, A.K., Langan, P., Kovalevsky, A.Y.

(2013) J Med Chem 56: 5631-5635

• PubMed: 23772563 
• DOI: https://doi.org/10.1021/jm400684f
• Primary Citation Related Structures: 
  4JEC


• PubMed Abstract: 
  

  HIV-1 protease is an important target for the development of antiviral inhibitors to treat AIDS. A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined at 2.0 Å resolution. The structure provides direct determination of hydrogen atom positions in the enzyme active site. Analysis of the enzyme-drug interactions suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances. This information may be valuable for the design of improved protease inhibitors.

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Organizational Affiliation: 
• Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.02 kDa 
• Atom Count: 1,679 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
478	D [auth B]	{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER C25 H35 N3 O6 S YMARZQAQMVYCKC-OEMFJLHTSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.261 (Depositor) 
• R-Value Work:  0.244 (Depositor) 
• R-Value Observed: 0.244 (Depositor) 

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.203 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.181 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.186	α = 90
b = 87.431	β = 90
c = 46.405	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
MAATEL	data collection
LAUEGEN	data reduction
LSCALE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Kovalevsky, A.Y., Weber, I.T., Langan, P.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-11-12
  Changes: Data collection, Structure summary