0.042228 0.000000 0.000000 0.000000 0.024221 0.000000 0.000000 0.000000 0.023098 0.00000 0.00000 0.00000 0000-0002-9056-4082 Lee, H.C. 0000-0003-4170-1527 Hou, M.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 23.681 41.286 43.294 C36 H38 N6 554.727 N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine 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 Y 1 N C Y 2 N C N 3 N C N 4 N C N 5 N C N 6 N C N 7 N C Y 8 N C Y 9 N C Y 10 N C Y 11 N C Y 12 N C Y 13 N C Y 14 N C Y 15 N C Y 16 N C Y 17 N C Y 18 N C Y 19 N C Y 20 N C Y 21 N C N 22 N C N 23 N C N 24 N C N 25 N C N 26 N C Y 27 N C Y 28 N C Y 29 N C Y 30 N C Y 31 N C Y 32 N C Y 33 N C Y 34 N C Y 35 N C Y 36 N C Y 37 N N N 38 N N N 39 N N N 40 N N N 41 N N Y 42 N N 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 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 H N 80 N H N 81 N O N 82 N P N 83 N O N 84 N O N 85 N O N 86 N C N 87 R C N 88 N O N 89 S C N 90 N O N 91 N C N 92 R C Y 93 N N Y 94 N C Y 95 N N Y 96 N C Y 97 N C N 98 N N Y 99 N N Y 100 N C Y 101 N N Y 102 N C 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 H N 117 N O N 118 N P N 119 N O N 120 N O N 121 N O N 122 N C N 123 R C N 124 N O N 125 S C N 126 N O N 127 N C N 128 R C N 129 N N N 130 N C N 131 N O N 132 N N N 133 N C N 134 N N 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 O N 152 N P N 153 N O N 154 N O N 155 N O N 156 N C N 157 R C N 158 N O N 159 S C N 160 N O N 161 N C N 162 R C Y 163 N N Y 164 N C Y 165 N N Y 166 N C N 167 N C N 168 N O N 169 N N N 170 N C N 171 N N N 172 N N Y 173 N C N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N O N 189 N P N 190 N O N 191 N O N 192 N O N 193 N C N 194 R C N 195 N O N 196 S C N 197 N O N 198 N C N 199 R C N 200 N N N 201 N C N 202 N O N 203 N N N 204 N C N 205 N O N 206 N C N 207 N C N 208 N C N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N O N 225 N H N 226 N H Y 1 N doub Y 2 N sing Y 3 N sing N 4 N sing N 5 N sing Y 6 N doub N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing Y 14 N doub Y 15 N sing Y 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing Y 22 N doub Y 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N doub Y 30 N doub Y 31 N sing Y 32 N doub Y 33 N sing Y 34 N sing Y 35 N sing Y 36 N sing Y 37 N doub Y 38 N sing Y 39 N doub Y 40 N doub Y 41 N sing Y 42 N sing Y 43 N doub Y 44 N sing Y 45 N sing Y 46 N doub Y 47 N doub Y 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 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 N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub 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 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 Y 110 N sing Y 111 N sing Y 112 N doub N 113 N sing Y 114 N sing Y 115 N sing Y 116 N doub N 117 N sing Y 118 N doub N 119 N sing N 120 N sing Y 121 N sing Y 122 N doub N 123 N sing Y 124 N sing N 125 N sing 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 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 sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N doub N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing Y 183 N sing Y 184 N sing Y 185 N doub N 186 N sing Y 187 N sing N 188 N sing Y 189 N doub N 190 N doub N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N doub N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N doub 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 N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N doub N 229 N sing N 230 N sing N 231 N doub N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing To Be Published 0353 Crystal structure of d(CGTTAACG)2 in complex with N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine 0000-0002-9056-4082 0000-0003-4170-1527 10.2210/pdb21hs/pdb pdb_000021hs 100 1 N PIXEL 2024-12-16 DECTRIS EIGER2 X 9M SINGLE WAVELENGTH M x-ray 1 0.99987 1.0 TPS 05A NSRRC 0.99987 SYNCHROTRON NSRRC BEAMLINE TPS 05A 2426.617 DNA (5'-D(*CP*GP*TP*TP*AP*AP*CP*G)-3') 2 syn polymer 554.727 N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine 1 syn non-polymer 18.015 water 33 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 2.18 43.59 VAPOR DIFFUSION, SITTING DROP 0.004M Potassium chloride, 0.006M Sodium chloride, 0.02M Sodium cacodylate trihydrate pH 7.0, 20% (+/-)-2-Methyl-2,4-pentanediol (MPD), 0.006M Spermine tetrahydrochloride 298.15 1.600 1 19 A 1 B 8 -2.773 A_DC1:DG8_B 1 -4.758 0.235 -0.181 -0.506 -16.121 1 19 A 2 B 7 -0.242 A_DG2:DC7_B 2 3.711 -0.226 0.129 -0.105 -6.968 1 20 A 3 B 6 3.148 A_DT3:DA6_B 3 -7.619 -0.049 0.239 -0.244 -2.934 1 20 A 4 B 5 3.916 A_DT4:DA5_B 4 -19.971 -0.304 -0.062 -0.124 -7.690 1 20 A 5 B 4 3.102 A_DA5:DT4_B 5 -15.714 0.561 -0.151 -0.286 5.564 1 20 A 6 B 3 3.374 A_DA6:DT3_B 6 -6.484 -0.128 0.404 -0.138 6.527 1 19 A 7 B 2 1.269 A_DC7:DG2_B 7 -1.798 -0.043 0.418 -0.272 -3.886 1 19 A 8 B 1 -2.874 A_DG8:DC1_B 8 4.876 -0.343 -0.622 -0.531 6.701 30.731 A A 1 2 -10.514 B B 8 7 6.890 -5.374 -1.817 1.218 AA_DC1DG2:DC7DG8_BB 1 -12.999 25.434 27.392 4.621 -2.190 3.086 25.572 A A 2 3 17.905 B B 7 6 3.255 7.787 0.003 0.005 AA_DG2DT3:DA6DC7_BB 2 -2.844 6.540 24.212 -2.194 -0.812 2.997 34.018 A A 3 4 8.641 B B 6 5 3.100 5.028 -0.292 -0.138 AA_DT3DT4:DA5DA6_BB 3 3.842 -6.603 33.442 -0.990 1.076 3.626 41.333 A A 4 5 14.547 B B 5 4 3.565 10.170 0.161 0.675 AA_DT4DA5:DT4DA5_BB 4 1.110 -1.588 40.101 -0.263 -0.095 2.712 28.755 A A 5 6 16.018 B B 4 3 2.917 7.836 0.588 0.000 AA_DA5DA6:DT3DT4_BB 5 -3.712 7.587 27.443 -1.549 -1.917 3.302 27.176 A A 6 7 5.098 B B 3 2 3.348 2.392 0.078 -0.399 AA_DA6DC7:DG2DT3_BB 6 0.469 -0.999 27.069 -1.461 -0.045 6.136 34.345 A A 7 8 -8.190 B B 2 1 6.582 -4.433 2.041 1.037 AA_DC7DG8:DC1DG2_BB 7 22.619 -41.791 25.636 3.317 4.506 repository Initial release 1 0 2026-05-27 Taiwan Ministry of Science and Technology (MoST, Taiwan) 113-2311-B- 005-006-MY3 Taiwan Ministry of Science and Technology (MoST, Taiwan) 113-2113-M-005-016-MY3 mhho@nchu.edu.tw 0000-0003-4170-1527 Ming-hon Hou principal investigator/group leader 2026-05-27 SPRSDE N PDBJ N PDBJ 2025-12-12 REL REL A1L8R A1L8R SUBJECT OF INVESTIGATION A1L8R N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine HOH water 2853804 DNA molecule sample 1 8 Y N unpublished model Other experimental model LIG 103 2 A1L8R A1L8R 101 A HOH 7 3 HOH HOH 201 A HOH 21 3 HOH HOH 202 A HOH 70 3 HOH HOH 203 A HOH 77 3 HOH HOH 204 A HOH 89 3 HOH HOH 205 A HOH 118 3 HOH HOH 206 A HOH 108 3 HOH HOH 207 A HOH 75 3 HOH HOH 208 A HOH 24 3 HOH HOH 209 A HOH 81 3 HOH HOH 210 A HOH 110 3 HOH HOH 211 A HOH 107 3 HOH HOH 212 A HOH 93 3 HOH HOH 213 A HOH 12 3 HOH HOH 214 A HOH 71 3 HOH HOH 215 A HOH 115 3 HOH HOH 216 A HOH 104 3 HOH HOH 101 B HOH 83 3 HOH HOH 102 B HOH 105 3 HOH HOH 103 B HOH 76 3 HOH HOH 104 B HOH 90 3 HOH HOH 105 B HOH 27 3 HOH HOH 106 B HOH 28 3 HOH HOH 107 B HOH 101 3 HOH HOH 108 B HOH 11 3 HOH HOH 109 B HOH 97 3 HOH HOH 110 B HOH 99 3 HOH HOH 111 B HOH 119 3 HOH HOH 112 B HOH 116 3 HOH HOH 113 B HOH 112 3 HOH HOH 114 B HOH 117 3 HOH HOH 115 B HOH 102 3 HOH HOH 116 B HOH 114 3 HOH HOH 117 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 light scattering 840 -6 3920 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 0.2556 0.2040 0.2090 2.16 21.65 236 2430 9.71 97.51 0.33 1 FREE R-VALUE 1.35 MOLECULAR REPLACEMENT 21.03 0.90 1.11 ML FLAT BULK SOLVENT MODEL 2.16 21.65 33 397 42 322 0 0.004 408 0.748 618 35.044 166 0.028 62 0.003 18 0.4267 0.2743 2.72 119 1070 98.00 0.1998 0.1842 10 117 1124 97.00 2.16 21.65 21HS 2516 0.94 1 13.5 4.4 98.3 0.291 2.16 2.24 2430 1 refinement PHENIX (1.18.2_3874: ???) data extraction PDB_EXTRACT data reduction HKL-2000 data scaling HKL-2000 phasing PHENIX N Crystal structure of d(CGTTAACG)2 in complex with N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine 1 N N 1 N N 2 N N 3 N N 3 N N 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 DNA with a new diacridine intercalator, DNA 21HS PDB 1 1 21HS 1 8 21HS 1 8 21HS A 1 1 8 1 8 21HS 1 8 21HS B 1 1 8 19 P 21 21 21