3M9F

HIV protease complexed with compound 10b

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Epsilon substituted lysinol derivatives as HIV-1 protease inhibitors.

Jones, K.L., Holloway, M.K., Su, H.P., Carroll, S.S., Burlein, C., Touch, S., DiStefano, D.J., Sanchez, R.I., Williams, T.M., Vacca, J.P., Coburn, C.A.

(2010) Bioorg Med Chem Lett 20: 4065-4068

  • DOI: 10.1016/j.bmcl.2010.05.082
  • Primary Citation of Related Structures:  
    3M9F

  • PubMed Abstract: 

    • A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors ...

    A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors. Modeling studies and synthetic efforts suggest the potency increase is due to both conformational bias and van der Waals interactions with the S2 pocket.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. kristen_jones@merck.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 proteaseA, B99Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q9WFL7 (Human immunodeficiency virus 1)
Explore Q9WFL7 
Go to UniProtKB:  Q9WFL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WFL7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
595
Query on 595
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		N-[(1S,5S)-5-{[(4-aminophenyl)sulfonyl](3-methylbutyl)amino}-1-methyl-6-oxohexyl]-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide
C35 H46 N4 O6 S
JSZGHYRPBNJGPM-ZMAXYJRFSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
595 PDBBind:  3M9F IC50: 7.00e-3 (nM) from 1 assay(s)
Binding MOAD:  3M9F IC50: 7.00e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.173α = 90
b = 85.934β = 90
c = 46.134γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2010-03-22 
  • Released Date: 2010-06-30 
    • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description