1HPO

HIV-1 PROTEASE TRIPLE MUTANT/U103265 COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


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


Literature

Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyramones.

Skulnick, H.I., Johnson, P.D., Aristoff, P.A., Morris, J.K., Lovasz, K.D., Howe, W.J., Watenpaugh, K.D., Janakiraman, M.N., Anderson, D.J., Reischer, R.J., Schwartz, T.M., Banitt, L.S., Tomich, P.K., Lynn, J.C., Horng, M.M., Chong, K.T., Hinshaw, R.R., Dolak, L.A., Seest, E.P., Schwende, F.J., Rush, B.D., Howard, G.M., Toth, L.N., Wilkinson, K.R., Kakuk, T.J., Johnson, C.W., Cole, S.L., Zaya, R.M., Zipp, G.L., Possert, P.L., Dalga, R.J., Zhong, W.-Z., Williams, M.G., Romines, K.R.

(1997) J Med Chem 40: 1149-1164

  • DOI: https://doi.org/10.1021/jm960441m
  • Primary Citation of Related Structures:  
    1HPO, 7UPJ

  • PubMed Abstract: 

    • Recently, cyclooctylpyranone derivatives with m-carboxamide substituents (e.g. 2c) were identified as potent, nonpeptidic HIV protease inhibitors, but these compounds lacked significant antiviral activity in cell culture. Substitution of a sulfonamide group at the meta position, however, produces compounds with excellent HIV protease binding affinity and antiviral activity ...

    Recently, cyclooctylpyranone derivatives with m-carboxamide substituents (e.g. 2c) were identified as potent, nonpeptidic HIV protease inhibitors, but these compounds lacked significant antiviral activity in cell culture. Substitution of a sulfonamide group at the meta position, however, produces compounds with excellent HIV protease binding affinity and antiviral activity. Guided by an iterative structure-based drug design process, we have prepared and evaluated a number of these derivatives, which are readily available via a seven-step synthesis. A few of the most potent compounds were further evaluated for such characteristics as pharmacokinetics and toxicity in rats and dogs. From this work, the p-cyanophenyl sulfonamide derivative 35k emerged as a promising inhibitor, was selected for further development, and entered phase I clinical trials.

    Related Citations: 
    • Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors.
      Skulnick, H.I., Johnson, P.D., Howe, W.J., Tomich, P.K., Chong, K.T., Watenpaugh, K.D., Janakiraman, M.N., Dolak, L.A., McGrath, J.P., Lynn, J.C., Horng, M.-M., Hinshaw, R.B., Zipp, G.L., Ruwart, M.J., Schwende, F.J., Padbury, G.E., Dalga, R.J., Zhong, W.-Z., Shiou, L., Possert, P.L., Rush, Bob D., Wilkinson, Karen F., Howard, Gina M., Toth, L.N., Williams, M.G., Kakuk, T.J., Cole, S.L., Zaya, R.M., Lovasz, K.D., Morris, J.K., Romines, K.R., Thaisrivongs, S., Aristoff, P.A.
      (1995) J Med Chem 38: 4968
    Organizational Affiliation: 

    Discovery Chemistry Research, Pharmacia and Upjohn, Kalamazoo, Michigan 49001, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 3 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNI
Query on UNI
Download Ideal Coordinates CCD File 
C [auth B]4-CYANO-N-(3-CYCLOPROPYL(5,6,7,8,9,10-HEXAHYDRO-4-HYDROXY-2-OXO-CYCLOOCTA[B]PYRAN-3-YL)METHYL)PHENYL BENZENSULFONAMIDE
C28 H28 N2 O5 S
VCYQENLVFRTJIC-VWLOTQADSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UNI BindingDB:  1HPO Ki: min: 0.8, max: 1 (nM) from 2 assay(s)
IC50: 2000 (nM) from 1 assay(s)
Binding MOAD:  1HPO Ki: 0.6 (nM) from 1 assay(s)
PDBBind:  1HPO Ki: 0.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.543α = 90
b = 88.416β = 90
c = 46.484γ = 90
Software Package:
Software NamePurpose
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-21
    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: 2018-03-07
    Changes: Data collection
  • Version 1.5: 2021-11-03
    Changes: Database references, Derived calculations