2R5P

Crystal Structure Analysis of HIV-1 Subtype C Protease Complexed with Indinavir

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 

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


Literature

The Contribution of Naturally Occurring Polymorphisms in Altering the Biochemical and Structural Characteristics of HIV-1 Subtype C Protease

Coman, R.M., Robbins, A.H., Fernandez, M.A., Gilliland, C.T., Sochet, A.A., Goodenow, M.M., McKenna, R., Dunn, B.M.

(2008) Biochemistry 47: 731-743

  • DOI: 10.1021/bi7018332
  • Primary Citation of Related Structures:  
    2R5P, 2R5Q

  • PubMed Abstract: 

    • Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease ...

    Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease. The kinetic studies performed in this work showed that the preexistent polymorphisms in subtype C protease, by themselves, do not provide for a greater level of resistance. Inhibition analysis with eight clinically used protease inhibitors revealed that the natural polymorphisms found in subtype C protease, in combination with drug resistance mutations, can influence enzymatic catalytic efficiency and inhibitor resistance. Structural analyses of the subtype C protease bound to nelfinavir and indinavir showed that these inhibitors form similar interactions with the residues in the active site of subtype B and C proteases. It also revealed that the naturally occurring polymorphisms could alter the position of the outer loops of the subtype C protease, especially the 60's loop.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B, C, D99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
EC: 3.4.23.16 (UniProt), 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 O12158 (Human immunodeficiency virus type 1 group M subtype C (isolate 92BR025))
Explore O12158 
Go to UniProtKB:  O12158
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO12158
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MK1
Query on MK1
Download Ideal Coordinates CCD File 
H [auth B],
K [auth D]		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
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
I [auth C],
J [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
G [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MK1 BindingDB:  2R5P Ki: min: 0.05, max: 108 (nM) from 47 assay(s)
Kd: min: 1.07, max: 5.5 (nM) from 4 assay(s)
IC50: min: 0.36, max: 370 (nM) from 20 assay(s)
-TΔS: min: -8.28e+1, max: -2.80e+1 (kJ/mol) from 38 assay(s)
ΔH: min: -3.34e+1, max: 51 (kJ/mol) from 39 assay(s)
ΔG: min: -6.31e+1, max: -3.18e+1 (kJ/mol) from 36 assay(s)
Binding MOAD:  2R5P Ki: 3.3 (nM) from 1 assay(s)
IDV PDBBind:  2R5P Ki: 3.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.727α = 90
b = 59.526β = 95.56
c = 87.384γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations