1K6C

LACK OF SYNERGY FOR INHIBITORS TARGETING A MULTI-DRUG RESISTANT HIV-1 PROTEASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease.

King, N.M., Melnick, L., Prabu-Jeyabalan, M., Nalivaika, E.A., Yang, S.S., Gao, Y., Nie, X., Zepp, C., Heefner, D.L., Schiffer, C.A.

(2002) Protein Sci 11: 418-429

  • DOI: 10.1110/ps.25502
  • Primary Citation of Related Structures:  
    1K6C, 1K6P, 1K6T, 1K6V

  • PubMed Abstract: 

    • The three-dimensional structures of indinavir and three newly synthesized indinavir analogs in complex with a multi-drug-resistant variant (L63P, V82T, I84V) of HIV-1 protease were determined to approximately 2.2 A resolution. Two of the three analogs have only a single modification of indinavir, and their binding affinities to the variant HIV-1 protease are enhanced over that of indinavir ...

    The three-dimensional structures of indinavir and three newly synthesized indinavir analogs in complex with a multi-drug-resistant variant (L63P, V82T, I84V) of HIV-1 protease were determined to approximately 2.2 A resolution. Two of the three analogs have only a single modification of indinavir, and their binding affinities to the variant HIV-1 protease are enhanced over that of indinavir. However, when both modifications were combined into a single compound, the binding affinity to the protease variant was reduced. On close examination, the structural rearrangements in the protease that occur in the tightest binding inhibitor complex are mutually exclusive with the structural rearrangements seen in the second tightest inhibitor complex. This occurs as adaptations in the S1 pocket of one monomer propagate through the dimer and affect the conformation of the S1 loop near P81 of the other monomer. Therefore, structural rearrangements that occur within the protease when it binds to an inhibitor with a single modification must be accounted for in the design of inhibitors with multiple modifications. This consideration is necessary to develop inhibitors that bind sufficiently tightly to drug-resistant variants of HIV-1 protease to potentially become the next generation of therapeutic agents.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL polyproteinA, B99Human immunodeficiency virus 1Mutation(s): 4 
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)
UniProt
Find proteins for P35963 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35963 
Go to UniProtKB:  P35963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35963
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MK1
Query on MK1
Download Ideal Coordinates CCD File 
H [auth B]N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
C36 H47 N5 O4
CBVCZFGXHXORBI-PXQQMZJSSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B],
G [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MK1 BindingDB:  1K6C Ki: min: 0.05, max: 398 (nM) from 48 assay(s)
Kd: min: 1.07, max: 5.5 (nM) from 4 assay(s)
IC50: min: 0.36, max: 370 (nM) from 23 assay(s)
-TΔS: min: -8.28e+1, max: -2.80e+1 (kJ/mol) from 37 assay(s)
ΔH: min: -3.34e+1, max: 51 (kJ/mol) from 38 assay(s)
ΔG: min: -6.31e+1, max: -3.18e+1 (kJ/mol) from 38 assay(s)
PDBBind:  1K6C Kd: 33 (nM) from 1 assay(s)
Binding MOAD:  1K6C Kd: 33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.45α = 90
b = 59.4β = 90
c = 61.74γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2001-10-15 
  • Released Date: 2002-02-06 
    • Deposition Author(s): Schiffer, C.A.

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations