6C8Y

D30N HIV-1 protease in complex with a phenylboronic acid (P2') analog of darunavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid.

Windsor, I.W.Palte, M.J.Lukesh 3rd., J.C.Gold, B.Forest, K.T.Raines, R.T.

(2018) J. Am. Chem. Soc. 140: 14015-14018


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: pol
Find proteins for Q5RZ08 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5RZ08
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BVR
Query on BVR

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Download CCD File 
A
[4-[[(2~{R},3~{S})-3-[[(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl]oxycarbonylamino]-2-oxidanyl-4-phenyl-butyl]-(2-methylpropyl)sulfamoyl]phenyl]-oxidanyl-oxidanylidene-boron
C27 H36 B N2 O9 S
QKKZROKMILDVQY-HEXNFIEUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.118α = 90.00
b = 86.410β = 90.00
c = 45.793γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM044783
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008349

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release