Crystal structure of HIV-1 protease complexed with Lopinavir.

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.309 

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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

  • DOI: https://doi.org/10.1016/s0968-0896(02)00051-2
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
proteaseA [auth B],
B [auth A]
99Human immunodeficiency virus 1Mutation(s): 1 
Find proteins for Q903J0 (Human immunodeficiency virus 1)
Explore Q903J0 
Go to UniProtKB:  Q903J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ903J0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AB1

Download Ideal Coordinates CCD File 
C37 H48 N4 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
AB1 BindingDB:  1MUI Ki: min: 5.00e-3, max: 16 (nM) from 7 assay(s)
Kd: 1.30e-3 (nM) from 1 assay(s)
IC50: min: 2.5, max: 25 (nM) from 2 assay(s)
EC50: 1160 (nM) from 1 assay(s)
PDBBind:  1MUI Ki: 1.30e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.309 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.264α = 90
b = 63.264β = 90
c = 83.621γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-23
    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: 2021-10-27
    Changes: Database references, Derived calculations, Structure summary