3A2O

Crystal Structure of HIV-1 Protease Complexed with KNI-1689


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.118 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.101 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket.

Hidaka, K.Kimura, T.Abdel-Rahman, H.M.Nguyen, J.T.McDaniel, K.F.Kohlbrenner, W.E.Molla, A.Adachi, M.Tamada, T.Kuroki, R.Katsuki, N.Tanaka, Y.Matsumoto, H.Wang, J.Hayashi, Y.Kempf, D.J.Kiso, Y.

(2009) J Med Chem 52: 7604-7617

  • DOI: 10.1021/jm9005115
  • Primary Citation of Related Structures:  
    3A2O

  • PubMed Abstract: 
  • A series of HIV protease inhibitor based on the allophenylnorstatine structure with various P(2)' moieties were synthesized. Among these analogues, we discovered that a small allyl group would maintain potent enzyme inhibitory activity compared to th ...

    A series of HIV protease inhibitor based on the allophenylnorstatine structure with various P(2)' moieties were synthesized. Among these analogues, we discovered that a small allyl group would maintain potent enzyme inhibitory activity compared to the o-methylbenzyl moiety in clinical candidate 1 (KNI-764, also known as JE-2147, AG-1776, or SM-319777). Introduction of an anilinic amino group to 2 (KNI-727) improved water-solubility and anti-HIV-1 activity. X-ray crystallographic analysis of 13k (KNI-1689) with a beta-methallyl group at P(2)' position revealed hydrophobic interactions with Ala28, Ile84, and Ile50' similar to that of 1. The presence of an additional methyl group on the allyl group in compound 13k significantly increased anti-HIV activity over 1 while providing a rational drug design for structural minimization and improving membrane permeability.


    Organizational Affiliation

    Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASEAB99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
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)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNJ
Query on KNJ

Download CCD File 
B
(4R)-3-[(2S,3S)-3-{[(4-amino-2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-5,5-dimethyl-N-(2-methylprop -2-en-1-yl)-1,3-thiazolidine-4-carboxamide
C30 H40 N4 O5 S
YCDHYYBDJVMMOY-SCTDOJESSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KNJKi:  0.8299999833106995   nM  Binding MOAD
KNJKi :  0.8299999833106995   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000584 (KNJ)
Query on PRD_000584
BKNI-1689Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.118 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.101 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.223α = 90
b = 85.815β = 90
c = 46.484γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other