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: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL polyprotein
A, B
163Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVX
Query on AVX

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A, 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
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DTV
Query on DTV

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A
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

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B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AVXKd: 170000 nM BINDINGMOAD
AVXKd: 170000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 49.160α = 90.00
b = 49.160β = 90.00
c = 103.120γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AMoREphasing
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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