HEADER RNA 30-JUN-25 9PDE TITLE THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR PALBOCICLIB-HIV TAR TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PALBOCICLIB, COMPLEX, HIV-1 TAR, RNA, SMALL MOLECULE-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.R.RAMIREDDY,V.N.VIDADALA,B.CHAUBEY,G.OLSEN,G.VARANI REVDAT 1 04-FEB-26 9PDE 0 JRNL AUTH R.R.RAMIREDDY,V.N.VIDADALA,B.CHAUBEY,G.OLSEN,G.VARANI JRNL TITL THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR JRNL TITL 2 PALBOCICLIB-HIV TAR COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9PDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000294385. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298; 298; 298; 278; 278; REMARK 210 298; 278 REMARK 210 PH : 5.8; 5.8; 5.0; 5.0; 5.8; 5.8; REMARK 210 5.0; 5.8 REMARK 210 IONIC STRENGTH : 20 MM BIS TRIS D19, 50 MM SODIUM REMARK 210 CHLORIDE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE; 20 MM SODIUM REMARK 210 ACETATE; 20 MM SODIUM ACETATE; REMARK 210 20 MM BIS TRIS D19, 50 MM SODIUM REMARK 210 CHLORIDE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE; 20 SODIUM REMARK 210 ACETATE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM; 1 REMARK 210 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM HIV TAR RNA (29-MER), 90% REMARK 210 H2O/10% D2O; 0.9 NM HIV TAR RNA REMARK 210 (29-MER), 100% D2O; 0.9 MM HIV REMARK 210 TAR RNA (29-MER), 100% D2O; 0.25 REMARK 210 MM [U-99% 13C; U-99% 15N] HIV REMARK 210 TAR RNA (29-MER), 100% D2O; 0.25 REMARK 210 MM [U-99% 13C; U-99% 15N] HIV REMARK 210 TAR RNA (29-MER), 95% H2O/5% D2O; REMARK 210 0.9 MM [U-99% 2H] HIV TAR RNA REMARK 210 (29-MER), 100% D2O; 0.9 MM [U-99% REMARK 210 2H] HIV TAR RNA (29-MER), 90% REMARK 210 H2O/10% D2O; 0.35 MM [U-99% 2H] REMARK 210 HIV TAR RNA (29-MER), 90% H2O/10% REMARK 210 D2O; 0.35 MM [U-99% 2H] HIV TAR REMARK 210 RNA (29-MER), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HMQC; 2D 1H-13C CT- REMARK 210 HSQC ALIPHATIC; 2D 1H-13C CT- REMARK 210 HSQC AROMATIC; 2D 1H-1H FILTERED REMARK 210 NOESY; 2D 1H-15N HSQC; 2D 1H-15N REMARK 210 HSQC NH2 ONLY; 2D 1H-15N HNNCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE II; AVANCE REMARK 210 III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31257 RELATED DB: BMRB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR PALBOCICLIB-HIV TAR REMARK 900 COMPLEX DBREF 9PDE A 17 45 PDB 9PDE 9PDE 17 45 SEQRES 1 A 29 G G C A G G U CH U G A G C SEQRES 2 A 29 C U G G G G G C U C U C U SEQRES 3 A 29 G C C HET CH A 24 32 HET LQQ A 101 62 HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HETNAM LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1- HETNAM 2 LQQ YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE HETSYN LQQ PALBOCICLIB FORMUL 1 CH C9 H15 N3 O8 P 1+ FORMUL 2 LQQ C24 H29 N7 O2 LINK O3' U A 23 P CH A 24 1555 1555 1.63 LINK O3' CH A 24 P U A 25 1555 1555 1.61 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 207 229 CONECT 229 207 230 231 232 CONECT 230 229 CONECT 231 229 CONECT 232 229 233 CONECT 233 232 234 249 250 CONECT 234 233 235 236 251 CONECT 235 234 240 CONECT 236 234 237 238 252 CONECT 237 236 261 CONECT 238 236 239 240 253 CONECT 239 238 254 CONECT 240 235 238 241 255 CONECT 241 240 242 248 CONECT 242 241 243 244 CONECT 243 242 CONECT 244 242 245 256 CONECT 245 244 246 247 CONECT 246 245 257 258 CONECT 247 245 248 259 CONECT 248 241 247 260 CONECT 249 233 CONECT 250 233 CONECT 251 234 CONECT 252 236 CONECT 253 238 CONECT 254 239 CONECT 255 240 CONECT 256 244 CONECT 257 246 CONECT 258 246 CONECT 259 247 CONECT 260 248 CONECT 261 237 CONECT 935 936 CONECT 936 935 937 938 CONECT 937 936 968 969 970 CONECT 938 936 939 953 CONECT 939 938 940 941 CONECT 940 939 971 972 973 CONECT 941 939 942 946 CONECT 942 941 943 974 CONECT 943 942 944 CONECT 944 943 945 955 CONECT 945 944 946 CONECT 946 941 945 947 CONECT 947 946 948 953 CONECT 948 947 949 952 975 CONECT 949 948 950 976 977 CONECT 950 949 951 978 979 CONECT 951 950 952 980 981 CONECT 952 948 951 982 983 CONECT 953 938 947 954 CONECT 954 953 CONECT 955 944 956 984 CONECT 956 955 957 961 CONECT 957 956 958 CONECT 958 957 959 985 CONECT 959 958 960 962 CONECT 960 959 961 986 CONECT 961 956 960 987 CONECT 962 959 963 967 CONECT 963 962 964 988 989 CONECT 964 963 965 990 991 CONECT 965 964 966 992 CONECT 966 965 967 993 994 CONECT 967 962 966 995 996 CONECT 968 937 CONECT 969 937 CONECT 970 937 CONECT 971 940 CONECT 972 940 CONECT 973 940 CONECT 974 942 CONECT 975 948 CONECT 976 949 CONECT 977 949 CONECT 978 950 CONECT 979 950 CONECT 980 951 CONECT 981 951 CONECT 982 952 CONECT 983 952 CONECT 984 955 CONECT 985 958 CONECT 986 960 CONECT 987 961 CONECT 988 963 CONECT 989 963 CONECT 990 964 CONECT 991 964 CONECT 992 965 CONECT 993 966 CONECT 994 966 CONECT 995 967 CONECT 996 967 MASTER 102 0 2 0 0 0 0 6 650 1 96 3 END