1MUI

Crystal structure of HIV-1 protease complexed with Lopinavir.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray Crystallographic Structure of ABT-378 (Lopinavir) Bound to HIV-1 Protease

Stoll, V.Qin, W.Stewart, K.D.Jakob, C.Park, C.Walter, K.Simmer, R.L.Helfrich, R.Bussiere, D.Kao, J.Kempf, D.Sham, H.L.Norbeck, D.W.

(2002) BIOORG.MED.CHEM. 10: 2803-2806


  • PubMed Abstract: 
  • The crystal structure of ABT-378 (lopinavir), bound to the active site of HIV-1 protease is described. A comparison with crystal structures of ritonavir, A-78791, and BILA-2450 shows some analogous features with previous reported compounds. A cyclic ...

    The crystal structure of ABT-378 (lopinavir), bound to the active site of HIV-1 protease is described. A comparison with crystal structures of ritonavir, A-78791, and BILA-2450 shows some analogous features with previous reported compounds. A cyclic urea unit in the P(2) position of ABT-378 is novel and makes two bidentate hydrogen bonds with Asp 29 of HIV-1 protease. In addition, a previously unreported shift in the Gly 48 carbonyl position is observed. A discussion of the structural features responsible for its high potency against wild-type HIV protease is given along with an analysis of the effect of active site mutations on potency in in vitro assays.


    Organizational Affiliation

    Department of Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protease
B, A
99Human immunodeficiency virus 1N/A
Find proteins for Q903J0 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q903J0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB1
Query on AB1

Download SDF File 
Download CCD File 
B
N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
ABT-378, LOPINAVIR
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AB1Ki: 0.0013 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.261 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.264α = 90.00
b = 63.264β = 90.00
c = 83.621γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
CNXphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance