1HPX

HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR KNI-272


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine.

Baldwin, E.T.Bhat, T.N.Gulnik, S.Liu, B.Topol, I.A.Kiso, Y.Mimoto, T.Mitsuya, H.Erickson, J.W.

(1995) Structure 3: 581-590

  • DOI: https://doi.org/10.1016/s0969-2126(01)00192-7
  • Primary Citation of Related Structures:  
    1HPX

  • PubMed Abstract: 

    HIV-1 protease (HIV PR), an aspartic protease, cleaves Phe-Pro bonds in the Gag and Gag-Pol viral polyproteins. Substrate-based peptide mimics constitute a major class of inhibitors of HIV PR presently being developed for AIDS treatment. One such compound, KNI-272, which incorporates allophenylnorstatine (Apns)-thioproline (Thp) in place of Phe-Pro, has potent antiviral activity and is undergoing clinical trials. The structure of the enzyme-inhibitor complex should lead to an understanding of the structural basis for its tight binding properties and provide a framework for interpreting the emerging resistance to this drug. The three-dimensional crystal structure of KNI-272 bound to HIV PR has been determined to 2.0 A resolution and used to analyze structure-activity data and drug resistance for the Arg8-->Gln and ILe84-->Val mutations in HIV PR. The conformationally constrained Apns-Thp linkage is favorably recognized in its low energy trans conformation, which results in a symmetric mode of binding to the active-site aspartic acids and also explains the unusual preference of HIV PR for the S, or syn, hydroxyl group of the Apns residue. The inhibitor recognizes the enzyme via hydrogen bonds to three bridging water molecules, including one that is coordinated directly to the catalytic Asp125 residue. The structure of the HIV PR/KNI-272 complex illustrates the importance of limiting the conformational degrees of freedom and of using protein-bound water molecules for building potent inhibitors. The binding mode of HIV PR inhibitors can be predicted from the stereochemical relationship between adjacent hydroxyl-bearing and side chain bearing carbon atoms of the P1 substituent. Our structure also provides a framework for designing analogs targeted to drug-resistant mutant enzymes.


  • Organizational Affiliation

    Frederick Biomedical Supercomputing Center, SAIC-Frederick, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 PROTEASE
A, B
99Human 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KNI
Query on KNI

Download Ideal Coordinates CCD File 
C [auth B](4R)-N-tert-butyl-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-S-methyl-L-cysteinyl}amino)-4-phenylbutanoyl]-1,3-thiazolidine-4-carboxamide
C33 H41 N5 O6 S2
NJBBLOIWMSYVCQ-VZTVMPNDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KNI BindingDB:  1HPX Ki: min: 5.50e-3, max: 1.7 (nM) from 9 assay(s)
IC50: 6.5 (nM) from 1 assay(s)
-TΔS: min: -8.03e+1, max: -3.22e+1 (kJ/mol) from 16 assay(s)
ΔH: min: -2.26e+1, max: 40.13 (kJ/mol) from 16 assay(s)
ΔG: min: -5.64e+1, max: -3.80e+1 (kJ/mol) from 14 assay(s)
PDBBind:  1HPX Ki: 5.50e-3 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_000562 (KNI)
Query on PRD_000562
C [auth B]kynostatin 272Peptide-like / Enzyme inhibitor
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 59.1β = 90
c = 62.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MSIdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary