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PDB ID: 9pdg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31259
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Name: Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex
Published: 2026-01-29

Title:

Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

Deposition date:

2025-06-30

Original release date:

2026-01-29

Authors:

Ramireddy, R.; Vidadala, V.; Chaubey, B.; Olsen, G.; Varani, G.

Citation:

Citation: Ramireddy, R.; Vidadala, V.; Chaubey, B.; Olsen, G.; Varani, G.. "Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex" .

Assembly members:

Assembly members:
entity_1, polymer, 29 residues, 9309.569 Da.
entity_LQQ, non-polymer, 447.533 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCAGXUXUGAGCCUGGGAG CUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	146
15N chemical shifts	26
1H chemical shifts	287

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 29 residues - 9309.569 Da.

1

G

C

A

G

AP7

U

CH

U

G

2

A

G

C

U

G

A

G

3

C

U

C

U

C

U

G

C

Entity 2, unit_2 - C24 H29 N7 O2 - 447.533 Da.

1

LQQ

Samples:

sample_1: HIV TAR RNA (29-MER) 0.9 mM

sample_2: HIV TAR RNA (29-MER) 0.9 nM

sample_3: HIV TAR RNA (29-MER) 0.9 nM

sample_4: HIV TAR RNA (29-MER), [U-99% 13C; U-99% 15N], 0.9 nM

sample_5: HIV TAR RNA (29-MER), [U-99% 13C; U-99% 15N], 0.9 mM

sample_6: HIV TAR RNA (29-MER), [U-13C; U-15N]-Ade, 0.5 mM

sample_7: HIV TAR RNA (29-MER), [U-13C; U-15N]-Ade, 0.45 mM

sample_8: HIV TAR RNA (29-MER), [U-13C; U-15N]-Ade, Cyt, 0.77 mM

sample_9: HIV TAR RNA (29-MER), [U-13C; U-15N]-Ade, Cyt, 0.75 mM

sample_10: HIV TAR RNA (29-MER), [U-13C; U-15N]-Gua, Ura, 0.75 mM

sample_11: HIV TAR RNA (29-MER), [U-13C; U-15N]-Gua, Ura, 0.7 mM

sample_12: HIV TAR RNA (29-MER), [U-99% 2H], 0.9 mM

sample_13: HIV TAR RNA (29-MER), [U-99% 2H], 0.9 mM

sample_14: HIV TAR RNA (29-MER), [U-99% 2H], 0.25 mM

sample_15: HIV TAR RNA (29-MER), [U-99% 2H], 0.25 mM

sample_conditions_1: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 310 K

sample_conditions_3: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_4: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_5: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_6: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_7: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_8: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_9: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_10: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_11: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_12: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_13: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

sample_conditions_14: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 310 K

sample_conditions_15: ionic strength: 70 mM; pH: 5.8; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC NH2 only	sample_11	isotropic	sample_conditions_11
2D 1H-15N HSQC	sample_11	isotropic	sample_conditions_11
2D filtered/edited NOESY	sample_10	isotropic	sample_conditions_10
2D 1H-13C CT-HSQC aromatic	sample_10	isotropic	sample_conditions_10
2D 1H-13C CT-HSQC aliphatic	sample_10	isotropic	sample_conditions_10
2D 1H-13C HMQC	sample_10	isotropic	sample_conditions_10
2D 1H-15N HSQC NH2 only	sample_9	isotropic	sample_conditions_9
2D filtered/edited NOESY	sample_8	isotropic	sample_conditions_8
2D 1H-13C CT-HSQC aromatic	sample_8	isotropic	sample_conditions_8
2D 1H-13C CT-HSQC aliphatic	sample_8	isotropic	sample_conditions_8
2D 1H-13C HMQC	sample_8	isotropic	sample_conditions_8
2D 1H-15N HSQC NH2 only	sample_7	isotropic	sample_conditions_7
2D filtered/edited NOESY	sample_6	isotropic	sample_conditions_6
2D 1H-13C CT-HSQC aromatic	sample_6	isotropic	sample_conditions_6
2D 1H-13C CT-HSQC aliphatic	sample_6	isotropic	sample_conditions_6
2D 1H-13C HMQC	sample_6	isotropic	sample_conditions_6
2D 1H-1N HNNCOSY	sample_5	isotropic	sample_conditions_5
2D 1H-15N HSQC NH2 only	sample_5	isotropic	sample_conditions_5
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_5
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_4
2D filtered/edited NOESY	sample_4	isotropic	sample_conditions_4
2D 1H-13C CT-HSQC aromatic	sample_4	isotropic	sample_conditions_4
2D 1H-13C CT-HSQC aliphatic	sample_4	isotropic	sample_conditions_4
2D 1H-13C HMQC	sample_4	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_15	isotropic	sample_conditions_15
2D 1H-1H NOESY	sample_14	isotropic	sample_conditions_14
2D 1H-1H TOCSY	sample_14	isotropic	sample_conditions_14
2D 1H-1H NOESY	sample_13	isotropic	sample_conditions_13
2D 1H-1H NOESY	sample_12	isotropic	sample_conditions_12

Software:

TopSpin, Bruker Biospin - collection, data analysis, processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE II 600 MHz
Bruker AVANCE III 800 MHz

BMRB Entry 31259