2PK5

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex with KNI-10075


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 2PK5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22505.65

Macromolecule Entities
Molecule Chains Length Organism Details
Protease A, B 99 Human immunodeficiency virus 1 Mutation: Q7K, L33I, L63I
Gene Name(s): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
075
Query on 075

A (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H- inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin- 5-yloxy)acetyl]-3-(methylsulfonyl)-L-alanyl}amino)- 4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine- 4-carboxamide
KNI-10075 (Synonym)
C40 H45 N5 O9 S2
GNSJNHNIJIEWNZ-SHJYOGRKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
075 N/A in BindingDB
Kd: 0.02 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000576
Query on PRD_000576
A KNI-10075 Peptide-like /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.160
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 58.84 α = 90.00
b = 85.99 β = 90.00
c = 46.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-04-17
  • Released Date: 2007-05-08
  • Deposition author(s): Armstrong, A.A., Lafont, V., Kiso, Y., Freire, E., Amzel, L.M.

Revision History

  • Version 1_0: 2007-05-08

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_3: 2012-12-12

    Type: Other

  • Version 1_4: 2017-10-18

    Type: Refinement description