0.041987 0.000000 0.006560 0.000000 0.024907 0.000000 0.000000 0.000000 0.041621 0.00000 0.00000 0.00000 0000-0001-5617-8447 Wang, S.C. 0000-0003-4170-1527 Hou, M.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 98.88 90.00 23.817 40.150 24.318 C2 H3 O2 -1 59.044 ACETATE ION non-polymer Ca 2 40.078 CALCIUM ION 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 H2 O 18.015 WATER non-polymer C26 H23 N5 O 421.494 N-[4-(acridin-9-ylamino)butyl]quinoxaline-2-carboxamide non-polymer N 1 N C N 2 N O N 3 N O N 4 N C N 5 N H N 6 N H N 7 N H N 8 N CA N 9 N O N 10 N P N 11 N O N 12 N O N 13 N O N 14 N C N 15 R C N 16 N O N 17 S C N 18 N O N 19 N C N 20 R C Y 21 N N Y 22 N C Y 23 N N Y 24 N C Y 25 N C N 26 N N Y 27 N N Y 28 N C Y 29 N N Y 30 N C N 31 N H N 32 N H 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 O N 46 N P N 47 N O N 48 N O N 49 N O N 50 N C N 51 R C N 52 N O N 53 S C N 54 N O N 55 N C N 56 R C N 57 N N N 58 N C N 59 N O N 60 N N N 61 N C N 62 N N N 63 N C N 64 N C N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N O N 80 N P N 81 N O N 82 N O N 83 N O N 84 N C N 85 R C N 86 N O N 87 S C N 88 N O N 89 N C N 90 R C Y 91 N N Y 92 N C Y 93 N N Y 94 N C N 95 N C N 96 N O N 97 N N N 98 N C N 99 N N N 100 N N Y 101 N C N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N O N 117 N P N 118 N O N 119 N O N 120 N O N 121 N C N 122 R C N 123 N O N 124 S C N 125 N O N 126 N C N 127 R C N 128 N N N 129 N C N 130 N O N 131 N N N 132 N C N 133 N O N 134 N C N 135 N C N 136 N C N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N O N 153 N H N 154 N H N 155 N C Y 156 N C Y 157 N C Y 158 N C Y 159 N C Y 160 N C Y 161 N C Y 162 N C Y 163 N C Y 164 N C Y 165 N C Y 166 N C Y 167 N C Y 168 N C N 169 N C N 170 N C N 171 N C N 172 N C Y 173 N C Y 174 N C Y 175 N C Y 176 N C Y 177 N C Y 178 N C Y 179 N C Y 180 N C N 181 N N Y 182 N N N 183 N N Y 184 N N Y 185 N N N 186 N O 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 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 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 doub N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing Y 30 N sing Y 31 N sing Y 32 N doub N 33 N sing Y 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N doub N 39 N sing N 40 N sing Y 41 N sing Y 42 N doub N 43 N sing Y 44 N sing N 45 N sing N 46 N sing N 47 N doub 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 doub 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 doub N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N doub 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 N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing Y 103 N sing Y 104 N sing Y 105 N doub N 106 N sing Y 107 N sing N 108 N sing Y 109 N doub N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N doub 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 sing N 136 N sing N 137 N sing 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 doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N doub 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 doub Y 159 N sing Y 160 N sing Y 161 N doub Y 162 N doub Y 163 N sing Y 164 N sing Y 165 N sing Y 166 N doub N 167 N sing N 168 N sing N 169 N sing Y 170 N doub Y 171 N sing Y 172 N sing N 173 N sing N 174 N sing Y 175 N sing Y 176 N doub Y 177 N sing Y 178 N sing Y 179 N doub Y 180 N doub Y 181 N doub N 182 N sing Y 183 N doub Y 184 N sing Y 185 N sing Y 186 N sing Y 187 N sing Y 188 N doub N 189 N sing N 190 N sing Y 191 N doub Y 192 N sing N 193 N doub 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 sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing UK Nucleic Acids Res. NARHAD 0389 1362-4962 54 10.1093/nar/gkag520 42206361 Structural basis for asymmetric bis-intercalator targeting of DNA triplex junctions enabling dual inhibition of topoisomerase I and oncogene transcription. 2026 0000-0001-5617-8447 0000-0003-4435-8322 0009-0001-5512-8517 0000-0002-7632-9369 0000-0001-9558-3189 0000-0003-4170-1527 10.2210/pdb9v88/pdb pdb_00009v88 100 1 N PIXEL 2023-09-02 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.97626 1.0 TPS 07A NSRRC 0.97626 SYNCHROTRON NSRRC BEAMLINE TPS 07A 2426.617 DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3') 2 syn polymer 59.044 ACETATE ION 2 syn non-polymer 421.494 N-[4-(acridin-9-ylamino)butyl]quinoxaline-2-carboxamide 1 syn non-polymer 40.078 CALCIUM ION 1 nat non-polymer 18.015 water 20 nat water no no (DC)(DG)(DT)(DT)(DA)(DA)(DC)(DG) CGTTAACG A,B polydeoxyribonucleotide n n n n n n n n 1 2.37 48.07 VAPOR DIFFUSION, SITTING DROP 6.5 0.6mM Oligonucleotide, 0.6mM QA4, 100mM Sodium cacodylate pH 6.5, 200mM Calcium acetate hydrate, 18% v/v PEG 8000 293.15 7.220 1 19 A 1 B 8 -2.335 A_DC1:DG8_B 1 -2.163 0.240 -0.216 -0.233 -17.382 1 19 A 2 B 7 -1.986 A_DG2:DC7_B 2 -3.615 -0.306 0.052 -0.285 -9.644 1 20 A 3 B 6 2.781 A_DT3:DA6_B 3 -10.599 -0.585 0.427 -0.222 -0.768 1 20 A 4 B 5 5.432 A_DT4:DA5_B 4 -13.275 -0.042 -0.106 -0.265 1.408 1 20 A 5 B 4 4.989 A_DA5:DT4_B 5 -12.992 0.082 -0.035 -0.193 7.527 1 20 A 6 B 3 3.738 A_DA6:DT3_B 6 -8.746 0.518 0.388 -0.157 29.632 1 19 A 7 B 2 2.048 A_DC7:DG2_B 7 -10.252 0.560 -0.658 -0.258 -2.536 1 19 A 8 B 1 -2.834 A_DG8:DC1_B 8 0.576 -0.106 -0.351 -0.265 3.135 26.478 A A 2 3 10.615 B B 7 6 3.219 4.815 -0.076 -0.016 AA_DG2DT3:DA6DC7_BB 1 -4.267 9.406 25.698 -1.293 -0.950 3.003 32.408 A A 3 4 13.796 B B 6 5 3.068 7.618 -0.072 0.175 AA_DT3DT4:DA5DA6_BB 2 3.392 -6.144 31.345 -0.952 0.693 3.483 39.307 A A 4 5 20.857 B B 5 4 3.325 13.755 0.025 1.048 AA_DT4DA5:DT4DA5_BB 3 -0.436 0.661 36.909 -0.203 -0.093 3.079 32.813 A A 5 6 13.652 B B 4 3 3.156 7.635 0.233 0.168 AA_DA5DA6:DT3DT4_BB 4 -2.951 5.276 31.803 -0.972 -0.903 2.641 28.501 A A 6 7 3.923 B B 3 2 2.808 1.889 0.026 0.163 AA_DA6DC7:DG2DT3_BB 5 10.228 -21.247 26.572 -0.042 1.964 citation citation_author repository Initial release Database references 1 0 2026-06-03 1 1 2026-06-10 _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year Taiwan Ministry of Science and Technology (MoST, Taiwan) 109-2628-M- 005-001-MY4 Taiwan Ministry of Science and Technology (MoST, Taiwan) 109-2311-B-005-007-MY3 mhho@nchu.edu.tw 0000-0003-4170-1527 Ming-Hon Hou principal investigator/group leader N PDBJ Y PDBJ 2025-05-29 REL REL XAU XAU SUBJECT OF INVESTIGATION ACT ACETATE ION XAU N-[4-(acridin-9-ylamino)butyl]quinoxaline-2-carboxamide CA CALCIUM ION HOH water 32630 synthetic construct sample 1 8 Y N BIOVIA Discovery Studio Other experimental model ACT 101 2 ACT ACT 101 A LIG 101 3 XAU XAU 102 A ACT 23 2 ACT ACT 103 A CA 1 4 CA CA 101 B HOH 12 5 HOH HOH 201 A HOH 19 5 HOH HOH 202 A HOH 5 5 HOH HOH 203 A HOH 13 5 HOH HOH 204 A HOH 7 5 HOH HOH 205 A HOH 21 5 HOH HOH 206 A HOH 5 5 HOH HOH 207 A HOH 2 5 HOH HOH 208 A HOH 14 5 HOH HOH 209 A HOH 10 5 HOH HOH 210 A HOH 2 5 HOH HOH 211 A HOH 16 5 HOH HOH 201 B HOH 20 5 HOH HOH 202 B HOH 6 5 HOH HOH 203 B HOH 4 5 HOH HOH 204 B HOH 1 5 HOH HOH 205 B HOH 17 5 HOH HOH 206 B HOH 4 5 HOH HOH 207 B HOH 8 5 HOH HOH 208 B HOH 3 5 HOH HOH 209 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DT 3 n 3 DT 3 A DT 4 n 4 DT 4 A DA 5 n 5 DA 5 A DA 6 n 6 DA 6 A DC 7 n 7 DC 7 A DG 8 n 8 DG 8 A DC 1 n 1 DC 1 B DG 2 n 2 DG 2 B DT 3 n 3 DT 3 B DT 4 n 4 DT 4 B DA 5 n 5 DA 5 B DA 6 n 6 DA 6 B DC 7 n 7 DC 7 B DG 8 n 8 DG 8 B author_and_software_defined_assembly PISA 2 dimeric none 1080 -12 4140 A DG 2 A OP1 DG 2 1_555 B CA 101 F CA CA 1_556 A HOH 202 G O HOH 1_455 51.4 A DG 2 A OP1 DG 2 1_555 B CA 101 F CA CA 1_556 A HOH 206 G O HOH 1_554 47.8 A HOH 202 G O HOH 1_455 B CA 101 F CA CA 1_556 A HOH 206 G O HOH 1_554 4.6 A DG 2 A OP1 DG 2 1_555 B CA 101 F CA CA 1_556 B DG 2 B OP1 DG 2 1_555 44.1 A HOH 202 G O HOH 1_455 B CA 101 F CA CA 1_556 B DG 2 B OP1 DG 2 1_555 7.9 A HOH 206 G O HOH 1_554 B CA 101 F CA CA 1_556 B DG 2 B OP1 DG 2 1_555 6.9 A DG 2 A OP1 DG 2 1_555 B CA 101 F CA CA 1_556 B HOH 202 H O HOH 1_454 44.8 A HOH 202 G O HOH 1_455 B CA 101 F CA CA 1_556 B HOH 202 H O HOH 1_454 7.9 A HOH 206 G O HOH 1_554 B CA 101 F CA CA 1_556 B HOH 202 H O HOH 1_454 3.4 B DG 2 B OP1 DG 2 1_555 B CA 101 F CA CA 1_556 B HOH 202 H O HOH 1_454 7.2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 0.2643 0.2266 0.2303 1.92 15.41 342 3352 10.20 95.72 0.28 1 NONE 1.46 MOLECULAR REPLACEMENT 32.38 0.90 1.10 ML FLAT BULK SOLVENT MODEL 1.92 15.41 20 389 41 328 0 0.009 408 2.019 615 34.375 160 0.231 64 0.006 21 0.3343 0.2798 2.00 172 1517 97.00 0.2461 0.2128 15.41 170 1493 95.00 1.92 30.00 9V88 3366 1.000 1.000 0.041 0.030 0.052 1.049 1 22.7 3.0 95.7 0.138 1.93 2.00 349 0.980 0.995 0.092 0.166 1.069 1 3.2 96.7 0.113 2.00 2.08 313 0.983 0.996 0.076 0.137 1.048 1 3.3 95.7 0.093 2.08 2.17 352 0.993 0.998 0.063 0.113 1.073 1 3.2 97.2 0.083 2.17 2.29 328 0.988 0.997 0.054 0.099 1.094 1 3.2 97.3 0.064 2.29 2.43 358 0.993 0.998 0.045 0.078 1.040 1 3.1 97.8 0.054 2.43 2.62 344 0.994 0.999 0.038 0.066 1.080 1 2.8 98.0 0.048 2.62 2.88 328 0.995 0.999 0.035 0.059 1.016 1 2.9 96.5 0.045 2.88 3.30 332 0.996 0.999 0.035 0.057 1.004 1 2.7 95.7 0.038 3.30 4.15 329 0.996 0.999 0.028 0.048 1.022 1 2.6 91.9 0.033 4.15 30.00 333 0.996 0.999 0.024 0.041 1.014 1 2.6 90.2 refinement PHENIX (1.20.1_4487: ???) data scaling HKL-2000 data reduction HKL-2000 phasing PHENIX (1.20.1_4487) N Crystal structure of d(CGTTAACG)2 with a four-carbon linker containing quinoxaline-acridine asymmetric intercalator compound 1 N N 1 N N 2 N N 3 N N 2 N N 4 N N 5 N N 5 N N metalc 2.336 A DG 2 A OP1 DG 2 1_555 B CA 101 F CA CA 1_556 metalc 2.453 A HOH 202 G O HOH 1_455 B CA 101 F CA CA 1_555 metalc 2.247 A HOH 206 G O HOH 1_554 B CA 101 F CA CA 1_555 metalc 2.156 B DG 2 B OP1 DG 2 1_555 B CA 101 F CA CA 1_555 metalc 2.174 B CA 101 F CA CA 1_555 B HOH 202 H O HOH 1_454 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 8 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 8 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 8 B N2 DG 8 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 7 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 7 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 7 B N4 DC 7 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 6 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 4 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 4 B O4 DT 4 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 3 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 3 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 1 B N4 DC 1 1_555 DNA Ligand-DNA complex, Asymmetric intercalator, Bis-intercalation, Quinoxaline, Acridine, DNA 9V88 PDB 1 1 9V88 1 8 9V88 1 8 9V88 A 1 1 8 1 8 9V88 1 8 9V88 B 1 1 8 4 P 1 21 1