4CK3

Interrogating HIV integrase for compounds that bind- a SAMPL challenge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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

  • DOI: 10.1007/s10822-014-9721-7
  • Primary Citation of Related Structures:  
    4CE9, 4CEA, 4CEB, 4CEC, 4CED, 4CEE, 4CEF, 4CEO, 4CEQ, 4CER, 4CES, 4CEZ, 4CF0, 4CF1, 4CF2, 4CF8, 4CF9, 4CFA, 4CFB, 4CFC, 4CFD, 4CGD, 4CGF, 4CGG, 4CGH, 4CGI, 4CGJ, 4CHN, 4CHO, 4CHP, 4CHQ, 4CHY, 4CHZ, 4CIE, 4CIF, 4CIG, 4CJ3, 4CJ4, 4CJ5, 4CJE, 4CJF, 4CJK, 4CJL, 4CJP, 4CJQ, 4CJR, 4CJS, 4CJT, 4CJU, 4CJV

  • PubMed Abstract: 
  • Tremendous gains and novel methods are often developed when people are challenged to do something new or difficult. This process is enhanced when people compete against each other-this can be seen in sport as well as in science and technology (e.g. the space race) ...

    Tremendous gains and novel methods are often developed when people are challenged to do something new or difficult. This process is enhanced when people compete against each other-this can be seen in sport as well as in science and technology (e.g. the space race). The SAMPL challenges, like the CASP challenges, aim to challenge modellers and software developers to develop new ways of looking at molecular interactions so the community as a whole can progress in the accurate prediction of these interactions. In order for this challenge to occur, data must be supplied so the prospective test can be done. We have supplied unpublished data related to a drug discovery program run several years ago on HIV integrase for the SAMPL4 challenge. This paper describes the methods used to obtain these data and the chemistry involved.


    Organizational Affiliation

    CSIRO, Parkville, VIC, Australia, tompeat@hotmail.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRASEA, B183Human immunodeficiency virus 1Mutation(s): 3 
EC: 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K1T (Subject of Investigation/LOI)
Query on K1T

Download Ideal Coordinates CCD File 
G [auth A], O [auth B]5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid
C19 H28 N2 O5
RVKWMXPCIVFAJW-ZDUSSCGKSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
F [auth A], L [auth B], M [auth B], N [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
K1T Binding MOAD:  4CK3 Kd: 2.68e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.58α = 90
b = 71.58β = 90
c = 66.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2013-12-24 
  • Released Date: 2014-01-22 
  • Deposition Author(s): Peat, T.S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references