3OVN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POL polyprotein
A, B
163Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: pol
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1)
Explore Q72498 
Go to UniProtKB:  Q72498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72498
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPV
Query on MPV

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine
C8 H9 N3 S
NFTITKUYTQZKIZ-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
MPV PDBBind:  3OVN Kd: 2.80e+6 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.75α = 90
b = 59.704β = 90
c = 81.818γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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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: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary