3AO5

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: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1)
Explore Q72498 
Go to UniProtKB:  Q72498
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBY (Subject of Investigation/LOI)
Query on BBY

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

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], P [auth B], Q [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], H [auth A], I [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
Binding Affinity Annotations 
IDSourceBinding Affinity
BBY Binding MOAD:  3AO5 Kd: 5.90e+6 (nM) from 1 assay(s)
PDBBind:  3AO5 Kd: 5.90e+6 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
CsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.032α = 90
b = 49.032β = 90
c = 103.724γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary