9PDG | pdb_00009pdg

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

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	0.9 mM HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
2	2D 1H-1H NOESY	0.9 mM HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
3	2D 1H-1H TOCSY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	310	Bruker AVANCE III 800
4	2D 1H-1H NOESY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	310	Bruker AVANCE III 800
30	2D 1H-1H TOCSY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
29	2D 1H-1H NOESY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
28	2D 1H-13C HMQC	0.9 nM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
27	2D 1H-13C CT-HSQC aliphatic	0.9 nM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
26	2D 1H-13C CT-HSQC aromatic	0.9 nM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
25	2D filtered/edited NOESY	0.9 nM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
24	3D 1H-13C NOESY	0.9 nM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
23	2D 1H-15N HSQC	0.9 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
22	2D 1H-15N HSQC NH2 only	0.9 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
21	2D 1H-1N HNNCOSY	0.9 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
20	2D 1H-13C HMQC	0.5 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
19	2D 1H-13C CT-HSQC aliphatic	0.5 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
18	2D 1H-13C CT-HSQC aromatic	0.5 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
17	2D filtered/edited NOESY	0.5 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
16	2D 1H-15N HSQC NH2 only	0.45 mM [U-13C; U-15N]-Ade HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
15	2D 1H-13C HMQC	0.77 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
14	2D 1H-13C CT-HSQC aliphatic	0.77 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
13	2D 1H-13C CT-HSQC aromatic	0.77 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
12	2D filtered/edited NOESY	0.77 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
11	2D 1H-15N HSQC NH2 only	0.75 mM [U-13C; U-15N]-Ade, Cyt HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
10	2D 1H-13C HMQC	0.75 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
9	2D 1H-13C CT-HSQC aliphatic	0.75 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
8	2D 1H-13C CT-HSQC aromatic	0.75 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
7	2D filtered/edited NOESY	0.75 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
6	2D 1H-15N HSQC	0.7 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
5	2D 1H-15N HSQC NH2 only	0.7 mM [U-13C; U-15N]-Gua, Ura HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
38	2D 1H-1H NOESY	0.9 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
37	2D 1H-1H NOESY	0.9 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
36	2D 1H-1H TOCSY	0.25 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
35	2D 1H-1H NOESY	0.25 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	310	Bruker AVANCE III 800
34	2D 1H-1H NOESY	0.25 mM [U-99% 2H] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	600
2	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing	version 3.8	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
3	data analysis	TopSpin		Bruker Biospin
4	processing	TopSpin		Bruker Biospin
5	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	peak picking	Sparky		Goddard
7	chemical shift assignment	Sparky		Goddard

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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

9PDG | pdb_00009pdg