1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Sakurabayashi, S. Furuita, K. Yamada, T. Nomura, M. Nakatani, K. Kojima, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C24 H25 N7 O2 443.501 ~{N}-(7-methyl-1,8-naphthyridin-2-yl)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide non-polymer C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking N 1 N O N 2 N C N 3 N N Y 4 N C Y 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N C N 11 N C Y 12 N N Y 13 N C Y 14 N N N 15 N C N 16 N C N 17 N N N 18 N C N 19 N C N 20 N C N 21 N O N 22 N N Y 23 N C Y 24 N C Y 25 N C Y 26 N C Y 27 N C Y 28 N N Y 29 N C Y 30 N C Y 31 N C Y 32 N N N 33 N C 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 O N 60 N P N 61 N O N 62 N O N 63 N O N 64 N C N 65 R C N 66 N O N 67 S C N 68 N O N 69 N C N 70 R C Y 71 N N Y 72 N C Y 73 N N Y 74 N C Y 75 N C N 76 N N Y 77 N N Y 78 N C Y 79 N N Y 80 N C N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N O N 96 N P N 97 N O N 98 N O N 99 N O N 100 N C N 101 R C N 102 N O N 103 S C N 104 N O N 105 N C N 106 R C N 107 N N N 108 N C N 109 N O N 110 N N N 111 N C N 112 N N N 113 N C N 114 N C N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N O N 130 N P N 131 N O N 132 N O N 133 N O N 134 N C N 135 R C N 136 N O N 137 S C N 138 N O N 139 N C N 140 R C Y 141 N N Y 142 N C Y 143 N N Y 144 N C N 145 N C N 146 N O N 147 N N N 148 N C N 149 N N N 150 N N Y 151 N C N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N O N 167 N P N 168 N O N 169 N O N 170 N O N 171 N C N 172 R C N 173 N O N 174 S C N 175 N O N 176 N C N 177 R C N 178 N N N 179 N C N 180 N O N 181 N N N 182 N C N 183 N O N 184 N C N 185 N C N 186 N C N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 1 N sing Y 2 N doub Y 3 N sing Y 4 N sing Y 5 N doub Y 6 N doub Y 7 N sing Y 8 N sing Y 9 N sing Y 10 N doub Y 11 N doub Y 12 N sing N 13 N sing N 14 N sing N 15 N sing Y 16 N sing Y 17 N doub Y 18 N doub Y 19 N sing N 20 N doub N 21 N sing Y 22 N sing Y 23 N doub Y 24 N sing N 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing N 30 N sing Y 31 N doub N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub 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 doub 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 sing 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 Y 85 N sing Y 86 N sing Y 87 N doub N 88 N sing Y 89 N sing Y 90 N sing Y 91 N doub N 92 N sing Y 93 N doub N 94 N sing N 95 N sing Y 96 N sing Y 97 N doub N 98 N sing Y 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing 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 doub N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N doub N 133 N sing N 134 N sing N 135 N sing 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 sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing 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 Y 158 N sing Y 159 N sing Y 160 N doub N 161 N sing Y 162 N sing N 163 N sing Y 164 N doub N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N doub N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing 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 doub N 200 N sing N 201 N sing N 202 N sing N 203 N doub N 204 N sing N 205 N sing N 206 N doub N 207 N sing N 208 N sing N 209 N sing N 210 N sing US J.Am.Chem.Soc. JACSAT 1520-5126 147 14254 14269 10.1021/jacs.4c17538 40245052 NMR-Based Rational Drug Design of G:G Mismatch DNA Binding Ligand Trapping Transient Complex via Disruption of a Key Allosteric Interaction. 2025 0000-0001-6561-2356 0000-0003-3275-415X 0000-0001-6889-5160 0000-0001-7739-3525 0000-0002-1705-5265 0000-0003-2723-8249 10.2210/pdb8zd8/pdb pdb_00008zd8 10.13018/BMR36664 3382.236 DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') 1 syn polymer 3364.208 DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3') 1 syn polymer 443.501 ~{N}-(7-methyl-1,8-naphthyridin-2-yl)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide 1 syn non-polymer no no (DC)(DT)(DA)(DA)(DC)(DG)(DG)(DA)(DA)(DT)(DG) CTAACGGAATG 1 polydeoxyribonucleotide no no (DC)(DA)(DT)(DT)(DC)(DG)(DG)(DT)(DT)(DA)(DG) CATTCGGTTAG 2 polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n 0.794 1 19 1 1 2 22 -2.249 1_DC1:DG22_2 1 -0.591 -0.002 -0.008 -0.223 0.556 1 20 1 2 2 21 -8.585 1_DT2:DA21_2 2 0.314 -0.227 -0.032 -0.127 -1.400 1 20 1 3 2 20 -1.037 1_DA3:DT20_2 3 -0.853 0.146 -0.014 -0.167 -1.707 1 20 1 4 2 19 4.251 1_DA4:DT19_2 4 3.403 0.041 -0.099 -0.099 -1.219 1 19 1 5 2 18 -5.854 1_DC5:DG18_2 5 2.530 -0.057 0.100 -0.212 2.307 1 19 1 7 2 16 -7.505 1_DG7:DC16_2 6 2.564 -0.069 0.151 -0.271 0.458 1 20 1 8 2 15 -7.317 1_DA8:DT15_2 7 0.697 0.098 0.036 -0.053 1.777 1 20 1 9 2 14 -2.965 1_DA9:DT14_2 8 1.161 0.076 0.076 -0.190 -0.196 1 20 1 10 2 13 -3.254 1_DT10:DA13_2 9 0.668 -0.054 0.012 -0.182 -1.688 1 19 1 11 2 12 -2.814 1_DG11:DC12_2 10 0.800 -0.309 -0.059 -0.283 3.711 36.499 1 1 1 2 -6.605 2 2 22 21 3.771 -4.128 -0.663 0.287 11_DC1DT2:DA21DG22_22 1 0.305 -0.488 36.272 1.113 1.107 3.541 40.561 1 1 2 3 12.639 2 2 21 20 3.446 8.691 1.075 0.470 11_DT2DA3:DT20DA21_22 2 3.240 -4.712 39.530 -0.371 -1.160 3.766 41.910 1 1 3 4 -17.396 2 2 20 19 3.793 -12.276 0.298 -0.442 11_DA3DA4:DT19DT20_22 3 0.147 -0.209 40.149 0.897 -0.398 3.038 38.555 1 1 4 5 49.502 2 2 19 18 3.480 29.026 -2.245 0.697 11_DA4DC5:DG18DT19_22 4 -3.569 6.086 25.405 -3.331 2.860 3.511 36.616 1 1 7 8 33.371 2 2 16 15 3.740 19.791 1.643 0.227 11_DG7DA8:DT15DC16_22 5 6.356 -10.718 30.312 -2.964 -1.548 3.363 39.654 1 1 8 9 -5.605 2 2 15 14 3.395 -3.796 0.231 0.071 11_DA8DA9:DT14DT15_22 6 -1.575 2.326 39.449 0.563 -0.531 3.677 39.425 1 1 9 10 -9.474 2 2 14 13 3.688 -6.364 0.016 -0.224 11_DA9DT10:DA13DT14_22 7 1.204 -1.792 38.910 0.520 0.138 3.517 35.923 1 1 10 11 -6.687 2 2 13 12 3.474 -4.116 0.329 -0.541 11_DT10DG11:DC12DA13_22 8 0.565 -0.918 35.690 -0.246 -0.447 atom_site citation citation_author ndb_struct_conf_na ndb_struct_na_base_pair ndb_struct_na_base_pair_step repository Initial release Atomic model Database references Derived calculations 1 0 2025-04-30 2 0 2025-11-12 _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement Japan Japan Society for the Promotion of Science (JSPS) JP22H05536 Japan Japan Society for the Promotion of Science (JSPS) JP23J02416 Japan Japan Agency for Medical Research and Development (AMED) JP23ama121001 Japan Japan Science and Technology JPMJFS2125 Japan Japan Society for the Promotion of Science (JSPS) JP21K06047 kojima-chojiro-xk@ynu.ac.jp 0000-0003-2723-8249 Chojiro Kojima principal investigator/group leader NMR structure of the (CGG-dsDNA:ND=) 1:1 complex N PDBJ N PDBJ 2024-05-01 REL REL A1L1S A1L1S SUBJECT OF INVESTIGATION A1L1S ~{N}-(7-methyl-1,8-naphthyridin-2-yl)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide 32630 synthetic construct sample 1 11 32630 synthetic construct sample 1 11 Y N structures with the lowest energy 50 10 isotropic 1 2D 1H-1H NOESY isotropic 2 2D 1H-1H TOCSY isotropic 3 2D 1H-31P HSQC isotropic 3 2D 1H-15N HSQC isotropic 4 1D 15N isotropic 4 2D 1H-15N HSQC 2.7 mM None 2.7 mM None 2.7 mM None 20 mM None 100 mM None 0.1 mM 10% 13C/15N G6 or G7 0.1 mM 10% 13C/15N G17 or G18 0.1 mM None 20 mM None 100 mM None 2.0 mM None 2.0 mM None 2.0 mM None 20 mM None 100 mM None 120 mM condition 1 6.8 pH 1 atm 293 K simulated annealing 1 closest to the average 2.7 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.7 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.7 mM None ND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 95% H2O/5% D2O CGG-dsDNA-ND 95% H2O/5% D2O solid 0.1 mM 10% 13C/15N G6 or G7 DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 0.1 mM 10% 13C/15N G17 or G18 DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 0.1 mM None ND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 95% H2O/5% D2O G6,G7,G17,G18 residues are site-specifically labeled with 13C and 15N (10% labeling). CGG-dsDNA-ND-labeled 95% H2O/5% D2O solution 2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None 15N4-ND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 95% H2O/5% D2O Using ND labeled with 15N CGG-dsDNA-15N4-ND 95% H2O/5% D2O solution Lee W, Tonelli M, Markley JL chemical shift assignment NMRFAM-SPARKY Brunger, Adams, Clore, Gros, Nilges and Read structure calculation CNS Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS Lee W, Tonelli M, Markley JL peak picking NMRFAM-SPARKY 950 Bruker AVANCE III 800 Bruker AVANCE III HD 600 Bruker AVANCE III HD 500 Bruker AVANCE III HD MOL 23 3 A1L1S A1L1S 101 1 CYT 1 n 1 DC 1 1 THY 2 n 2 DT 2 1 ADE 3 n 3 DA 3 1 ADE 4 n 4 DA 4 1 CYT 5 n 5 DC 5 1 GUA 6 n 6 DG 6 1 GUA 7 n 7 DG 7 1 ADE 8 n 8 DA 8 1 ADE 9 n 9 DA 9 1 THY 10 n 10 DT 10 1 GUA 11 n 11 DG 11 1 CYT 12 n 1 DC 12 2 ADE 13 n 2 DA 13 2 THY 14 n 3 DT 14 2 THY 15 n 4 DT 15 2 CYT 16 n 5 DC 16 2 GUA 17 n 6 DG 17 2 GUA 18 n 7 DG 18 2 THY 19 n 8 DT 19 2 THY 20 n 9 DT 20 2 ADE 21 n 10 DA 21 2 GUA 22 n 11 DG 22 2 author_and_software_defined_assembly 2 dimeric not applicable NMR Distance Restraints 1340 -4 4410 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 1 1 2 O6 H42 DG DC 7 16 1.53 2 1 2 O6 H42 DG DC 7 16 1.53 2 1 2 H42 O6 DC DG 5 18 1.59 3 1 2 O6 H42 DG DC 7 16 1.53 3 1 2 H42 O6 DC DG 5 18 1.59 4 1 2 O6 H42 DG DC 7 16 1.53 5 1 2 O6 H42 DG DC 7 16 1.53 5 1 2 H42 O6 DC DG 5 18 1.60 6 1 2 O6 H42 DG DC 7 16 1.52 8 1 2 H42 O6 DC DG 5 18 1.56 8 1 2 O6 H42 DG DC 7 16 1.58 9 1 2 O6 H42 DG DC 7 16 1.58 9 1 2 H42 O6 DC DG 5 18 1.60 10 1 2 H42 O6 DC DG 5 18 1.52 10 1 2 O6 H42 DG DC 7 16 1.53 N NMR structure of the (CGG-dsDNA:ND=) 1:1 complex 1 N N 2 N N 3 N N hydrog WATSON-CRICK 1 DC 1 A N3 DC 1 1_555 2 DG 22 B N1 DG 11 1_555 hydrog WATSON-CRICK 1 DC 1 A N4 DC 1 1_555 2 DG 22 B O6 DG 11 1_555 hydrog WATSON-CRICK 1 DC 1 A O2 DC 1 1_555 2 DG 22 B N2 DG 11 1_555 hydrog WATSON-CRICK 1 DT 2 A N3 DT 2 1_555 2 DA 21 B N1 DA 10 1_555 hydrog WATSON-CRICK 1 DT 2 A O4 DT 2 1_555 2 DA 21 B N6 DA 10 1_555 hydrog WATSON-CRICK 1 DA 3 A N1 DA 3 1_555 2 DT 20 B N3 DT 9 1_555 hydrog WATSON-CRICK 1 DA 3 A N6 DA 3 1_555 2 DT 20 B O4 DT 9 1_555 hydrog WATSON-CRICK 1 DA 4 A N1 DA 4 1_555 2 DT 19 B N3 DT 8 1_555 hydrog WATSON-CRICK 1 DA 4 A N6 DA 4 1_555 2 DT 19 B O4 DT 8 1_555 hydrog WATSON-CRICK 1 DC 5 A N3 DC 5 1_555 2 DG 18 B N1 DG 7 1_555 hydrog WATSON-CRICK 1 DC 5 A N4 DC 5 1_555 2 DG 18 B O6 DG 7 1_555 hydrog WATSON-CRICK 1 DC 5 A O2 DC 5 1_555 2 DG 18 B N2 DG 7 1_555 hydrog WATSON-CRICK 1 DG 7 A N1 DG 7 1_555 2 DC 16 B N3 DC 5 1_555 hydrog WATSON-CRICK 1 DG 7 A N2 DG 7 1_555 2 DC 16 B O2 DC 5 1_555 hydrog WATSON-CRICK 1 DG 7 A O6 DG 7 1_555 2 DC 16 B N4 DC 5 1_555 hydrog WATSON-CRICK 1 DA 8 A N1 DA 8 1_555 2 DT 15 B N3 DT 4 1_555 hydrog WATSON-CRICK 1 DA 8 A N6 DA 8 1_555 2 DT 15 B O4 DT 4 1_555 hydrog WATSON-CRICK 1 DA 9 A N1 DA 9 1_555 2 DT 14 B N3 DT 3 1_555 hydrog WATSON-CRICK 1 DA 9 A N6 DA 9 1_555 2 DT 14 B O4 DT 3 1_555 hydrog WATSON-CRICK 1 DT 10 A N3 DT 10 1_555 2 DA 13 B N1 DA 2 1_555 hydrog WATSON-CRICK 1 DT 10 A O4 DT 10 1_555 2 DA 13 B N6 DA 2 1_555 hydrog WATSON-CRICK 1 DG 11 A N1 DG 11 1_555 2 DC 12 B N3 DC 1 1_555 hydrog WATSON-CRICK 1 DG 11 A N2 DG 11 1_555 2 DC 12 B O2 DC 1 1_555 hydrog WATSON-CRICK 1 DG 11 A O6 DG 11 1_555 2 DC 12 B N4 DC 1 1_555 DNA mismatched base pair naphthyridine fragile X syndrome CGG repeat repeat expansion diseases, DNA 8ZD8 PDB 1 1 8ZD8 8ZD8 PDB 2 1 8ZD8 1 11 8ZD8 1 11 8ZD8 1 1 1 11 12 22 8ZD8 12 22 8ZD8 2 2 1 11