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 1UPJ | pdb_00001upj

HIV-1 PROTEASE COMPLEX WITH U095438 [3-[1-(4-BROMOPHENYL) ISOBUTYL]-4-HYDROXYCOUMARIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Work: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1UPJ

This is version 1.5 of the entry. See complete history. 

Literature

Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors.

Thaisrivongs, S., Watenpaugh, K.D., Howe, W.J., Tomich, P.K., Dolak, L.A., Chong, K.T., Tomich, C.C., Tomasselli, A.G., Turner, S.R., Strohbach, J.W., Mulichak, A.M., Janakiraman, M.N., Moon, J.B., Lynn, J.C., Horng, M.M., Hinshaw, R.R., Curry, K.A., Rothroc, D.J.

(1995) J Med Chem 38: 3624-3637

  • DOI: https://doi.org/10.1021/jm00018a023
  • Primary Citation Related Structures: 
    1UPJ, 2UPJ, 3UPJ, 4UPJ

  • PubMed Abstract: 

    The low oral bioavailability and rapid biliary excretion of peptide-derived HIV protease inhibitors have limited their utility as potential therapeutic agents. Our broad screening program to discover nonpeptidic HIV protease inhibitors had previously identified compound II (phenprocoumon, K(i) = 1 muM) as a lead template. Crystal structures of HIV protease complexes containing the peptide-derived inhibitor I (1-(naphthoxyacetyl)-L-histidyl-5(S)-amino-6-cyclohexyl-3 (R),4(R)-dihydroxy-2(R)-isopropylhexanoyl-L-isoleucine N-(2-pyridylmethyl)amide) and nonpeptidic inhibitors, such as phenprocoumon (compound II), provided a rational basis for the structure-based design of more active analogues. This investigation reports on the important finding of a carboxamide functionally appropriately added to the 4-hydroxycoumarin and the 4-hydroxy-2-pyrone templates which resulted in a new promising series of nonpeptidic HIV protease inhibitors with improved enzyme-binding affinity. The most active diastereomer of the carboxamide-containing compound XXIV inhibited HIV-1 protease with a K(i) value of 0.0014 muM. This research provides a new design direction for the discovery of more potent HIV protease inhibitors as potential therapeutic agents for the treatment of HIV infection.


  • Organizational Affiliation: 
    • Upjohn Laboratories, Kalamazoo, Michigan 49001, USA.

Macromolecule Content 

  • Total Structure Weight: 11.18 kDa 
  • Atom Count: 874 
  • Modeled Residue Count: 99 
  • Deposited Residue Count: 99 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 PROTEASE99Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U01

Query on U01



Download:Ideal Coordinates CCD File
B [auth A]3-[1-(4-BROMO-PHENYL)-2-METHYL-PROPYL]-4-HYDROXY-CHROMEN-2-ONE
C19 H17 Br O3
KGDWLSFLMSFPSU-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Work:  0.193 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.475α = 90
b = 63.475β = 90
c = 84.1γ = 120
Software Package:
Software NamePurpose
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Database references
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description