4JEC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.194 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/jm400684f

  • 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 st ...

    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.


    Organizational Affiliation

    Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 5 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
478
Query on 478

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Download CCD File 
B
{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER
Amprenavir
C25 H35 N3 O6 S
YMARZQAQMVYCKC-OEMFJLHTSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
478Kd: 0.4 nM (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.186α = 90.00
b = 87.431β = 90.00
c = 46.405γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.244 
Software Package:
Software NamePurpose
LAUEGENdata reduction
LSCALEdata scaling
nCNSrefinement
MAATELdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Refinement description