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- PDB-9pde: Three-dimensional structure of kinase inhibitor Palbociclib-HIV T... -

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Basic information

Entry
Database: PDB / ID: 9pde
TitleThree-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex
ComponentsRNA (29-MER)
KeywordsRNA / Palbociclib / complex / HIV-1 TAR / small molecule-RNA complex
Function / homologyChem-LQQ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsRamireddy, R.R. / Vidadala, V.N. / Chaubey, B. / Olsen, G. / Varani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM126942 United States
CitationJournal: To Be Published
Title: Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex
Authors: Ramireddy, R.R. / Vidadala, V.N. / Chaubey, B. / Olsen, G. / Varani, G.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7882
Polymers9,3411
Non-polymers4481
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (29-MER)


Mass: 9340.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LQQ / 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE / Palbociclib


Mass: 447.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N7O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-1H TOCSY
121isotropic32D 1H-1H NOESY
232isotropic32D 1H-1H TOCSY
242isotropic32D 1H-1H NOESY
353isotropic32D 1H-1H TOCSY
3283isotropic32D 1H-1H NOESY
4274isotropic32D 1H-13C HMQC
4264isotropic32D 1H-13C CT-HSQC aliphatic
4254isotropic32D 1H-13C CT-HSQC aromatic
4244isotropic32D 1H-1H filtered NOESY
5235isotropic32D 1H-15N HSQC
7225isotropic32D 1H-15N HSQC NH2 only
7215isotropic22D 1H-15N HNNCOSY
2206isotropic32D 1H-1H TOCSY
2196isotropic32D 1H-1H NOESY
7187isotropic32D 1H-1H NOESY
8178isotropic32D 1H-1H TOCSY
8168isotropic32D 1H-1H NOESY
9159isotropic32D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.9 mM HIV TAR RNA (29-MER), 90% H2O/10% D2O1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 90%H2O/10%D2OHIV TAR RNA_Palbociclib_H2O complex90% H2O/10% D2O
solution20.9 nM HIV TAR RNA (29-MER), 100% D2O1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 100%D2OHIV TAR RNA_Palbociclib_D2O complex100% D2O
solution30.9 mM HIV TAR RNA (29-MER), 100% D2O1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2OHIV TAR RNA_Palbociclib_D2O complex2100% D2O
solution40.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER), 100% D2O0.5 mM Palbociclib (LQQ), 0.25 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O13C/15N_labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution50.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER), 95% H2O/5% D2O0.5 mM Palbociclib (LQQ), 0.25 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O13C/15N_labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% D2O
solution60.9 mM [U-99% 2H] HIV TAR RNA (29-MER), 100% D2O1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2OSite specific 2H_labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution70.9 mM [U-99% 2H] HIV TAR RNA (29-MER), 90% H2O/10% D2O1.8 mM Palbociclib (LQQ), 0.9 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 90%H2O/10%D2OSite specific 2H_labeled_HIV TAR RNA_Palbociclib_H2O complex90% H2O/10% D2O
solution80.35 mM [U-99% 2H] HIV TAR RNA (29-MER), 90% H2O/10% D2O0.7 mM Palbociclib (LQQ), 0.35 mM RNA (29-MER), 0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 90%H2O/10%D2OUniformly_2H_labeled_HIV TAR RNA_Palbociclib_D2O complex90% H2O/10% D2O
solution90.35 mM [U-99% 2H] HIV TAR RNA (29-MER), 100% D2O0.7 mM Palbociclib (LQQ), 0.35 mM RNA (29-MER), 00.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2OUniformly_2H_labeled_HIV TAR RNA_Palbociclib_H2O complex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMHIV TAR RNA (29-MER)natural abundance1
0.9 nMHIV TAR RNA (29-MER)natural abundance2
0.9 mMHIV TAR RNA (29-MER)natural abundance3
0.25 mMHIV TAR RNA (29-MER)[U-99% 13C; U-99% 15N]4
0.25 mMHIV TAR RNA (29-MER)[U-99% 13C; U-99% 15N]5
0.9 mMHIV TAR RNA (29-MER)[U-99% 2H]6
0.9 mMHIV TAR RNA (29-MER)[U-99% 2H]7
0.35 mMHIV TAR RNA (29-MER)[U-99% 2H]8
0.35 mMHIV TAR RNA (29-MER)[U-99% 2H]9
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Sample conditions to record exchangeable proton distance information (imino, amino)20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
2Sample conditions to record non-exchangeable proton distance information. Same sample as id#1 buffer exchanged with 100% D2O containing d19 buffer20 mM bis tris d19, 50 mM sodium chloride mMhigh temperature5.81 atm298 K
3Sample conditions to record non-exchangeable proton distance information. Same sample as id#1 buffer exchanged with 100% D2O containing sodium acetate buffer20 mM sodium acetate mMhigh temperature51 atm298 K
4Sample conditions to record for identification of 13C of A, C, G and U.20 mM sodium acetate mMhigh temperature51 atm298 K
5Sample conditions to record exchangeable proton distance information. Same sample as id#4 buffer exchanged with 95% H2O containing d19 buffer20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
7Sample conditions to record exchangeable proton distance information and simplify the spectra by deuteration of ribose.20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
8Sample conditions to record non-exchangeable small molecule proton distance information and removal of RNA signals by complete deuteration20 sodium acetate mMhigh temperature51 atm298 K
9Sample conditions to record exchangeable small molecule as well as RNA signals20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO5001
Bruker AVANCE IIBrukerAVANCE II6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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