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- PDB-1uud: NMR structure of a synthetic small molecule, rbt203, bound to HIV... -

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Basic information

Entry
Database: PDB / ID: 1uud
TitleNMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA
ComponentsRNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3')
KeywordsHIV-1 / TAR RNA / DRUG DESIGN / LIGAND-RNA INTERACTION / RNA BULGE
Function / homologyChem-P14 / RNA / RNA (> 10)
Function and homology information
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodSOLUTION NMR / NOE-RESTRAINED DYNAMICS
Model type detailsMINIMIZED AVERAGE
AuthorsDavis, B. / Afshar, M. / Varani, G. / Karn, J. / Murchie, A.I.H. / Lentzen, G. / Drysdale, M.J. / Potter, A.J. / Bower, J. / Aboul-Ela, F.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Rational Design of Inhibitors of HIV-1 Tar RNA Through the Stabilisation of Electrostatic "Hot Spots"
Authors: Davis, B. / Afshar, M. / Varani, G. / Murchie, A.I.H. / Karn, J. / Lentzen, G. / Drysdale, M.J. / Bower, J. / Potter, A.J. / Aboul-Ela, F.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Structure of the Human Immunodeficiency Virus Recognition by Tat Protein
Authors: Aboul-Ela, F. / Jkarn, J. / Varani, G.
History
DepositionDec 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6612
Polymers9,3081
Non-polymers3531
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50LEAST RESTRRAINT VIOLATION ENERGY
RepresentativeModel #1

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Components

#1: RNA chain RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3') / HIV-1 TAR RNA


Mass: 9307.555 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 29 NUCLEOTIDE SEQUENCE COMPRISING PRIMARY BINDING SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA POLYMERASE OFF OF A DNA TEMPLATE
Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 (CLONE 12)
#2: Chemical ChemComp-P14 / N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE / RBT203 INHIBITOR


Mass: 353.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H31N7O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
141ROESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR SPECTRA FOR THE ...Text: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR SPECTRA FOR THE RNA AS ABOUND BY THE LIGAND RBT203 SHOWED SIMILAR NOE AND CHEMICAL SHIFT PATTERNS TO THE LATTER

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Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX6003
Bruker AMXBrukerAMX5004

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
XPLOR/CHARMMstructure solution
RefinementMethod: NOE-RESTRAINED DYNAMICS / Software ordinal: 1
Details: REFINEMENT INCLUDED A NUMBER OF MODELLING CONSTRAINTS BASED UPON PREVIOUSLY PUBLISHED DATA, AS WELL AS FINAL GENTLE REFINEMENT STEP USING CHARMM. DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRRAINT VIOLATION ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 1

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