3AO2

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1

Wielens, J.Headey, S.J.Deadman, J.J.Rhodes, D.I.Parker, M.W.Chalmers, D.K.Scanlon, M.J.

(2011) ChemMedChem 6: 258-261


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL polyproteinA, B163Human immunodeficiency virus 1Mutation(s): 7 
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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVX (Subject of Investigation/LOI)
Query on AVX

Download Ideal Coordinates CCD File 
I [auth A], Q [auth B]3-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-5-amine
C11 H10 Br N3 O2
CYGCZVZRSOGLAB-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download Ideal Coordinates CCD File 
P [auth B]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
DTV (Subject of Investigation/LOI)
Query on DTV

Download Ideal Coordinates CCD File 
J [auth A](2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], K [auth B], L [auth B]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], N [auth B], O [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], M [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AVX BindingDB:  3AO2 Kd: 1.70e+5 (nM) from 1 assay(s)
Binding MOAD:  3AO2 Kd: 1.70e+5 (nM) from 1 assay(s)
PDBBind:  3AO2 Kd: 1.70e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.16α = 90
b = 49.16β = 90
c = 103.12γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance