3KDD

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10265


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How much binding affinity can be gained by filling a cavity?

Kawasaki, Y.Chufan, E.E.Lafont, V.Hidaka, K.Kiso, Y.Mario Amzel, L.Freire, E.

(2010) Chem.Biol.Drug Des. 75: 143-151

  • DOI: 10.1111/j.1747-0285.2009.00921.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding affinity optimization is critical during drug development. Here, we evaluate the thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii (-H, -F, -Cl, and CH(3)) that improve the geometric ...

    Binding affinity optimization is critical during drug development. Here, we evaluate the thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii (-H, -F, -Cl, and CH(3)) that improve the geometric fit without participating in hydrogen bonding or other specific interactions. We observe a binding affinity increase of two orders of magnitude. There appears to be three phases in the process. The first phase is associated with the formation of stable van der Waals interactions. This phase is characterized by a gain in binding enthalpy and a loss in binding entropy, attributed to a loss of conformational degrees of freedom. For the specific case presented in this article, the enthalpy gain amounts to -1.5 kcal/mol while the entropic losses amount to +0.9 kcal/mol resulting in a net 3.5-fold affinity gain. The second phase is characterized by simultaneous enthalpic and entropic gains. This phase improves the binding affinity 25-fold. The third phase represents the collapse of the trend and is triggered by the introduction of chemical functionalities larger than the binding cavity itself [CH(CH(3))(2)]. It is characterized by large enthalpy and affinity losses. The thermodynamic signatures associated with each phase provide guidelines for lead optimization.


    Organizational Affiliation

    Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZQ
Query on JZQ

Download SDF File 
Download CCD File 
A
(4R)-3-[(2S,3S)-3-{[(2,6-difluorophenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
KNI-10265
C33 H35 F2 N3 O6 S
KCNWMHBIZSWXTB-UPZHSWQNSA-N
 Ligand Interaction
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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000583 (JZQ)
Query on PRD_000583
AKNI-10265Peptide-like / Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JZQKd: 3.45 nM BINDINGMOAD
JZQKd: 3.45 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.408α = 90.00
b = 85.916β = 90.00
c = 46.438γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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