5YOK

Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine.

Hidaka, K.Kimura, T.Sankaranarayanan, R.Wang, J.McDaniel, K.F.Kempf, D.J.Kameoka, M.Adachi, M.Kuroki, R.Nguyen, J.T.Hayashi, Y.Kiso, Y.

(2018) J. Med. Chem. 61: 5138-5153


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
100Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8Z0
Query on 8Z0

Download SDF File 
Download CCD File 
A
(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3-yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
KNI-1657
C41 H48 N4 O8 S
ZNVSERMHCCYPMY-JZILQDPNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.250α = 90.00
b = 85.948β = 90.00
c = 46.529γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
SCALAdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release