1MUI

Crystal structure of HIV-1 protease complexed with Lopinavir.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.309 

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

  • DOI: 10.1016/s0968-0896(02)00051-2
  • Primary Citation of Related Structures:  
    1MUI

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
proteaseB [auth A], A [auth B]99Human immunodeficiency virus 1Mutation(s): 1 
EC: 3.4.23.16
UniProt
Find proteins for Q903J0 (Human immunodeficiency virus 1)
Explore Q903J0 
Go to UniProtKB:  Q903J0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB1 (Subject of Investigation/LOI)
Query on AB1

Download Ideal Coordinates CCD File 
C [auth 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
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
CNXrefinement
HKL-2000data reduction
CNXphasing

Structure Validation

View Full Validation Report




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