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

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Basic information

Entry
Database: PDB / ID: 9pdg
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)9,7572
Polymers9,3101
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: 9309.569 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
111isotropic22D 1H-1H TOCSY
121isotropic22D 1H-1H NOESY
232isotropic22D 1H-1H TOCSY
242isotropic22D 1H-1H NOESY
3303isotropic22D 1H-1H TOCSY
3293isotropic22D 1H-1H NOESY
4284isotropic22D 1H-13C HMQC
4274isotropic22D 1H-13C CT-HSQC aliphatic
4264isotropic22D 1H-13C CT-HSQC aromatic
4254isotropic22D filtered/edited NOESY
4244isotropic23D 1H-13C NOESY
5235isotropic22D 1H-15N HSQC
5225isotropic22D 1H-15N HSQC NH2 only
5215isotropic22D 1H-1N HNNCOSY
6206isotropic22D 1H-13C HMQC
6196isotropic22D 1H-13C CT-HSQC aliphatic
6186isotropic22D 1H-13C CT-HSQC aromatic
6176isotropic22D filtered/edited NOESY
7167isotropic22D 1H-15N HSQC NH2 only
8158isotropic22D 1H-13C HMQC
8148isotropic22D 1H-13C CT-HSQC aliphatic
8138isotropic22D 1H-13C CT-HSQC aromatic
8128isotropic22D filtered/edited NOESY
9119isotropic22D 1H-15N HSQC NH2 only
101010isotropic22D 1H-13C HMQC
10910isotropic22D 1H-13C CT-HSQC aliphatic
10810isotropic22D 1H-13C CT-HSQC aromatic
10710isotropic22D filtered/edited NOESY
11611isotropic22D 1H-15N HSQC
11511isotropic22D 1H-15N HSQC NH2 only
123812isotropic22D 1H-1H NOESY
133713isotropic22D 1H-1H NOESY
143614isotropic22D 1H-1H TOCSY
143514isotropic22D 1H-1H NOESY
153415isotropic22D 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 nM 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
solution40.9 nM [U-99% 13C; U-99% 15N] 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% D2O13C/15N_labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution50.9 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER), 95% H2O/5% 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, 95%H2O/5%D2O13C/15N_labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% D2O
solution60.5 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER), 100% D2O1.0 mM Palbociclib (LQQ), 0.5 mM RNA (29-MER), 0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O13C/15N_A only labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution70.45 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER), 95% H2O/5% D2O0.9 mM Palbociclib (LQQ), 0.45 mM RNA (29-MER),0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O13C/15N_A only labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% D2O
solution80.77 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER), 100% D2O1.5 mM Palbociclib (LQQ), 0.77 mM RNA (29-MER),0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O13C/15N_AC only labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution90.75 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER), 95% H2O/5% D2O1.5 mM Palbociclib (LQQ), 0.75 mM RNA (29-MER),0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O13C/15N_AC only labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% D2O
solution100.75 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER), 100% D2O1.5 mM Palbociclib (LQQ), 0.75 mM RNA (29-MER),0.01 mM EDTA, 20 mM sodium acetate buffer, 100% D2O13C/15N_GU only labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution110.7 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER), 95% H2O/5% D2O1.4 mM Palbociclib (LQQ), 0.7 mM RNA (29-MER),0.01 mM EDTA, 20 mM bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2O13C/15N_GU only labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% D2O
solution120.9 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% D2OPartially 2H labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution130.9 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 bis tris D19 buffer, 50 mM sodium chloride, 95%H2O/5%D2OPartially 2H labeled_HIV TAR RNA_Palbociclib_H2O complex100% D2O
solution140.25 mM [U-99% 2H] 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% D2OUniformly 2H labeled_HIV TAR RNA_Palbociclib_D2O complex100% D2O
solution150.25 mM [U-99% 2H] 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%D2OUniformly 2H labeled_HIV TAR RNA_Palbociclib_H2O complex95% H2O/5% 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 nMHIV TAR RNA (29-MER)natural abundance3
0.9 nMHIV TAR RNA (29-MER)[U-99% 13C; U-99% 15N]4
0.9 mMHIV TAR RNA (29-MER)[U-99% 13C; U-99% 15N]5
0.5 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Ade6
0.45 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Ade7
0.77 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Ade, Cyt8
0.75 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Ade, Cyt9
0.75 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Gua, Ura10
0.7 mMHIV TAR RNA (29-MER)[U-13C; U-15N]-Gua, Ura11
0.9 mMHIV TAR RNA (29-MER)[U-99% 2H]12
0.9 mMHIV TAR RNA (29-MER)[U-99% 2H]13
0.25 mMHIV TAR RNA (29-MER)[U-99% 2H]14
0.25 mMHIV TAR RNA (29-MER)[U-99% 2H]15
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 atm310 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 atm310 K
4Sample conditions to record for identification of 13C of A, C, G and U.20 mM sodium acetate mMhigh temperature51 atm310 K
6Sample conditions to record for identification of 13C of A20 mM sodium acetate mMhigh temperature51 atm310 K
8Sample conditions to record for identification of 13C of A and C.20 mM sodium acetate mMhigh temperature51 atm310 K
10Sample conditions to record for identification of 13C of G and U.20 mM sodium acetate mMhigh temperature51 atm310 K
12Sample conditions to record non-exchangeable proton distance information and simplify the spectra by deuteration of ribose.20 mM sodium acetate mMhigh temperature51 atm310 K
14Sample conditions to record non-exchangeable small molecule proton distance information and removal of RNA signals by complete deuteration20 mM sodium acetate mMhigh temperature51 atm310 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
9Sample conditions to record exchangeable proton distance information. Same sample as id#8 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. Same sample as id#6 buffer exchanged with 95% H2O containing d19 buffer20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
11Sample conditions to record exchangeable proton distance information. Same sample as id#10 buffer exchanged with 95% H2O containing d19 buffer20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
13Sample conditions to record exchangeable proton distance information. Same sample as id#12 buffer exchanged with 95% H2O containing d19 buffer20 mM bis tris d19, 50 mM sodium chloride mMlow temperature5.81 atm278 K
15Sample conditions to record exchangeable proton distance information. Same sample as id#14 buffer exchanged with 95% H2O containing d19 buffer20 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 IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: version 3.8
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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