1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0009-0008-6780-4384 Ichijo, R. 0000-0003-1480-2840 Kawai, G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C24 H34 F N5 O2 443.557 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide non-polymer C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N C Y 2 N C Y 3 N C N 4 N N N 5 N C Y 6 N C N 7 N C Y 8 N C N 9 N C N 10 N C N 11 N C N 12 N N N 13 N C N 14 N C N 15 N C N 16 N C N 17 N C N 18 N C N 19 N N N 20 N C N 21 N C N 22 N C N 23 N O N 24 N N N 25 N C N 26 N C N 27 N O N 28 N F N 29 N C N 30 N N Y 31 N C Y 32 N C N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N O N 68 N P N 69 N O N 70 N O N 71 N O N 72 N C N 73 R C N 74 N O N 75 S C N 76 N O N 77 R C N 78 N O N 79 R C Y 80 N N Y 81 N C Y 82 N N Y 83 N C Y 84 N C N 85 N N Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N O N 105 N P N 106 N O N 107 N O N 108 N O N 109 N C N 110 R C N 111 N O N 112 S C N 113 N O N 114 R C N 115 N O N 116 R C N 117 N N N 118 N C N 119 N O N 120 N N N 121 N C N 122 N N N 123 N C N 124 N C N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N O N 140 N P N 141 N O N 142 N O N 143 N O N 144 N C N 145 R C N 146 N O N 147 S C N 148 N O N 149 R C N 150 N O N 151 R C Y 152 N N Y 153 N C Y 154 N N Y 155 N C N 156 N C N 157 N O N 158 N N N 159 N C N 160 N N N 161 N N Y 162 N C N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N O N 178 N P N 179 N O N 180 N O N 181 N O N 182 N C N 183 R C N 184 N O N 185 S C N 186 N O N 187 R C N 188 N O N 189 R C N 190 N N N 191 N C N 192 N O N 193 N N N 194 N C N 195 N O N 196 N C N 197 N C N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N doub N 11 N sing N 12 N sing N 13 N sing Y 14 N doub Y 15 N sing N 16 N sing N 17 N doub Y 18 N sing N 19 N sing N 20 N sing Y 21 N doub N 22 N sing Y 23 N doub N 24 N sing Y 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing Y 94 N sing Y 95 N sing Y 96 N doub N 97 N sing Y 98 N sing Y 99 N sing Y 100 N doub N 101 N sing Y 102 N doub N 103 N sing N 104 N sing Y 105 N sing Y 106 N doub N 107 N sing Y 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N doub N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing Y 169 N sing Y 170 N sing Y 171 N doub N 172 N sing Y 173 N sing N 174 N sing Y 175 N doub N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N doub N 212 N sing N 213 N sing N 214 N sing N 215 N doub N 216 N sing N 217 N doub N 218 N sing N 219 N sing US Biochemistry BICHAW 0033 0006-2960 64 2192 2199 10.1021/acs.biochem.4c00669 40067027 Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge. 2025 10.2210/pdb9io0/pdb pdb_00009io0 10.13018/BMR36681 6070.632 RNA (5'-R(*GP*GP*AP*UP*GP*GP*UP*UP*UP*CP*GP*AP*CP*CP*GP*AP*UP*CP*C)-3') 1 syn polymer 443.557 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide 1 syn non-polymer no no GGAUGGUUUCGACCGAUCC GGAUGGUUUCGACCGAUCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n 2.683 1 19 A 1 A 20 -2.754 A_G1:C20_A 1 1.700 0.944 0.027 -0.165 -3.674 1 19 A 2 A 19 -1.763 A_G2:C19_A 2 -2.799 0.047 -0.017 -0.151 1.237 1 20 A 3 A 18 -0.778 A_A3:U18_A 3 -2.098 -0.290 -0.054 -0.081 1.522 1 20 A 4 A 17 -0.159 A_U4:A17_A 4 -0.506 1.105 -0.039 -0.454 2.206 1 19 A 5 A 15 -4.469 A_G5:C15_A 5 0.510 -0.130 -0.060 -0.084 -0.401 1 19 A 6 A 14 -1.008 A_G6:C14_A 6 -2.899 -0.043 0.066 -0.120 0.233 1 20 A 7 A 13 0.011 A_U7:A13_A 7 0.123 1.046 -0.004 -0.406 -0.026 6 A 8 A 11 -86.146 A_U8:G11_A 8 -0.597 1.953 -0.035 -4.249 2.098 31.809 A A 1 2 36.386 A A 20 19 3.361 18.680 0.066 -1.099 AA_G1G2:C19C20_AA 1 3.013 -5.868 25.688 -5.181 0.391 3.715 32.091 A A 2 3 -9.964 A A 19 18 3.628 -5.474 0.146 -1.017 AA_G2A3:U18C19_AA 2 -3.194 5.814 31.475 -0.725 -0.914 3.324 41.602 A A 3 4 2.501 A A 18 17 3.371 1.776 -0.064 -1.071 AA_A3U4:A17U18_AA 3 -0.019 0.027 41.566 -1.701 0.088 2.549 32.566 A A 5 6 28.660 A A 15 14 3.349 15.456 0.359 -0.892 AA_G5G6:C14C15_AA 4 -0.176 0.326 28.752 -4.181 -0.670 3.651 38.897 A A 6 7 1.661 A A 14 13 3.741 1.102 0.187 -1.141 AA_G6U7:A13C14_AA 5 -5.343 8.048 38.527 -1.865 -1.018 3.724 96.566 A A 7 8 3.875 A A 13 11 3.789 5.783 -0.242 -1.392 AA_U7U8:G11A13_AA 6 -0.964 0.646 96.432 -1.046 0.143 citation citation_author repository Initial release Database references 1 0 2025-04-02 1 1 2025-06-04 _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID Not funded gota.kawai@p.chibakoudai.jp 0000-0003-1480-2840 Gota Kawai principal investigator/group leader INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES N PDBJ Y PDBJ 2024-07-08 REL REL 53D 53D SUBJECT OF INVESTIGATION 53D 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide 10090 Mus musculus sample 1 19 Y N structures with the lowest energy 100 11 isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-1H TOCSY 0.42 mM none 0.63 mM none 50 mM condition1 6.5 pH 1 atm 288 K na 1 minimized average structure 0.42 mM RNA (5'-R(*GP*GP*AP*UP*GP*GP*UP*UP*UP*CP*GP*AP*CP*CP*GP*AP*UP*CP*C)-3'), 0.63 mM 53D, 95% H2O/5% D2O sample1 95% H2O/5% D2O solution Goddard chemical shift assignment Sparky 3 Brunger, Adams, Clore, Gros, Nilges and Read structure calculation CNS 1.3 Goddard peak picking Sparky 3 600 Bruker AVANCE NEO 53D 21 2 53D 53D 101 A G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A G 6 n 6 G 6 A U 7 n 7 U 7 A U 8 n 8 U 8 A U 9 n 9 U 9 A C 10 n 10 C 10 A G 11 n 11 G 11 A A 13 n 12 A 13 A C 14 n 13 C 14 A C 15 n 14 C 15 A G 16 n 15 G 16 A A 17 n 16 A 17 A U 18 n 17 U 18 A C 19 n 18 C 19 A C 20 n 19 C 20 A author_and_software_defined_assembly 1 monomeric not applicable NMR Distance Restraints 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 N INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 20 A N3 C 19 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 20 A O2 C 19 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 20 A N4 C 19 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 19 A N3 C 18 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 19 A O2 C 18 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 19 A N4 C 18 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 18 A N3 U 17 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 18 A O4 U 17 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 17 A N1 A 16 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 17 A N6 A 16 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 15 A N3 C 14 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 15 A O2 C 14 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 15 A N4 C 14 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 A C 14 A N3 C 13 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 A C 14 A O2 C 13 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 A C 14 A N4 C 13 1_555 hydrog WATSON-CRICK A U 7 A N3 U 7 1_555 A A 13 A N1 A 12 1_555 hydrog WATSON-CRICK A U 7 A O4 U 7 1_555 A A 13 A N6 A 12 1_555 hydrog U-G MISPAIR A U 8 A O2 U 8 1_555 A G 11 A N1 G 11 1_555 RNA FLUOROQUINOLONE, RNA, INTERACTION, SPECIFICITY 9IO0 PDB 1 1 9IO0 1 20 9IO0 1 20 9IO0 A 1 1 19