RCSB PDB - 4CGI: Interrogating HIV integrase for compounds that bind- a SAMPL challenge

 4CGI

Interrogating HIV integrase for compounds that bind- a SAMPL challenge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NZLClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.

Peat, T.S.Dolezal, O.Newman, J.Mobley, D.Deadman, J.J.

(2014) J Comput Aided Mol Des 28: 347


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTEGRASE
A, B
183Human immunodeficiency virus 1Mutation(s): 3 
EC: 2.7.7.7
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NZL
Query on NZL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
5-[[(1S,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid
C24 H28 N2 O5
SSXWUTMSZZTPIE-OALUTQOASA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
NZL PDBBind:  4CGI Kd: 7.52e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.05α = 90
b = 71.05β = 90
c = 66.38γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NZLClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2013-12-04 
  • Deposition Author(s): Peat, T.S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description