0.033070 0.019093 0.000000 0.000000 0.038186 0.000000 0.000000 0.000000 0.025419 0.000000 0.000000 0.000000 Adams, A. Guss, J.M. Denny, W.A. Wakelin, L.P.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 30.239 30.239 39.340 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 C20 H22 N4 O2 350.414 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4-ACRIDINECARBOXAMIDE non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H 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 O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C 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 O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N C N 110 N C N 111 N C N 112 N C N 113 N N N 114 N C N 115 N C N 116 N N N 117 N C N 118 N O N 119 N N Y 120 N C Y 121 N C Y 122 N C Y 123 N C Y 124 N C Y 125 N C Y 126 N C Y 127 N C Y 128 N C Y 129 N N Y 130 N C Y 131 N C Y 132 N C Y 133 N C N 134 N H N 135 N H N 136 N H 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 H N 153 N H N 154 N H N 155 N H N 156 N O N 157 N P N 158 N O N 159 N O N 160 N O N 161 N C N 162 R C N 163 N O N 164 S C N 165 N O N 166 N C N 167 R C N 168 N N N 169 N C N 170 N O N 171 N N N 172 N C N 173 N O N 174 N C N 175 N C N 176 N C 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 H N 189 N H N 190 N H N 191 N H N 192 N O N 193 N H N 194 N H N 1 N sing N 2 N sing N 3 N doub 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 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub 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 N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub 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 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 doub N 137 N sing N 138 N sing N 139 N sing N 140 N sing Y 141 N doub Y 142 N sing Y 143 N sing N 144 N sing Y 145 N doub N 146 N sing Y 147 N sing N 148 N sing Y 149 N doub Y 150 N sing Y 151 N sing Y 152 N doub Y 153 N sing Y 154 N sing Y 155 N doub Y 156 N sing Y 157 N doub N 158 N sing Y 159 N sing N 160 N sing Y 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub 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 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 doub N 190 N sing N 191 N sing N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N doub N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 30 719 725 10.1093/nar/30.3.719 11809884 Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide bound to d(CGTACG)2: implications for structure-activity relationships of acridinecarboxamide topoisomerase poisons. 2002 10.2210/pdb1kci/pdb pdb_00001kci 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 110 1 focusing mirror IMAGE PLATE 2000-08-01 RIGAKU RAXIS II SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 1809.217 5'-D(*CP*GP*TP*AP*CP*G)-3' 1 syn polymer 350.414 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4-ACRIDINECARBOXAMIDE 2 syn non-polymer 18.015 water 20 nat water no no (DC)(DG)(DT)(DA)(DC)(DG) CGTACG A polydeoxyribonucleotide n n n n n n 1 2.75 55.25 VAPOR DIFFUSION, SITTING DROP 6.0 cacodylate, spermine, KCl, MgCl2, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K 285 cacodylate 1 spermine 1 KCl 1 MgCl2 1 MPD 1 2.482 1 19 A 1001 A 1006 -2.502 A_DC1001:DG1006_A 1 -12.144 -0.068 0.020 -0.125 -6.840 1 19 A 1002 A 1005 1.355 A_DG1002:DC1005_A 2 -2.296 -0.211 -0.089 -0.102 2.803 1 20 A 1003 A 1004 -3.608 A_DT1003:DA1004_A 3 -11.915 -0.043 -0.027 -0.158 -2.803 1 20 A 1004 A 1003 -3.608 A_DA1004:DT1003_A 4 -11.915 0.043 -0.027 -0.158 6.840 1 19 A 1005 A 1002 1.355 A_DC1005:DG1002_A 5 -2.296 0.211 -0.089 -0.102 -2.482 1 19 A 1006 A 1001 -2.502 A_DG1006:DC1001_A 6 -12.144 0.068 0.020 -0.125 6.953 24.957 A A 1001 1002 7.847 A A 1006 1005 6.958 3.380 0.519 0.576 AA_DC1001DG1002:DC1005DG1006_AA 1 -0.791 1.836 24.718 -0.824 -1.705 3.070 28.579 A A 1002 1003 6.253 A A 1005 1004 3.091 3.081 -0.730 -0.071 AA_DG1002DT1003:DA1004DC1005_AA 2 -0.150 0.304 28.415 -0.804 1.446 3.178 48.040 A A 1003 1004 -5.835 A A 1004 1003 3.352 -4.743 0.000 1.714 AA_DT1003DA1004:DT1003DA1004_AA 3 0.000 0.000 47.819 2.479 0.000 3.070 28.579 A A 1004 1005 6.253 A A 1003 1002 3.091 3.081 0.730 -0.071 AA_DA1004DC1005:DG1002DT1003_AA 4 0.150 -0.304 28.415 -0.804 -1.446 6.953 24.957 A A 1005 1006 7.847 A A 1002 1001 6.958 3.380 -0.519 0.576 AA_DC1005DG1006:DC1001DG1002_AA 5 0.791 -1.836 24.718 -0.824 1.705 chem_comp_atom chem_comp_bond database_2 struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2002-02-01 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 5'-d(CpGpTpApCpG)-3', 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide 5'-d(CpGpTpApCpG)-3', 5-F-9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide 5'-d(CG5BrUACG)-3', 6Br-9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide RCSB Y RCSB 2001-11-08 REL REL DRC 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4-ACRIDINECARBOXAMIDE HOH water 465D NDB entry DD0015 PDB experimental model DRC 3014 2 DRC DRC 3014 A DRC 3015 2 DRC DRC 3015 A HOH 4001 3 HOH HOH 4001 A HOH 4002 3 HOH HOH 4002 A HOH 4003 3 HOH HOH 4003 A HOH 4004 3 HOH HOH 4004 A HOH 4005 3 HOH HOH 4005 A HOH 4006 3 HOH HOH 4006 A HOH 4007 3 HOH HOH 4007 A HOH 4008 3 HOH HOH 4008 A HOH 4009 3 HOH HOH 4009 A HOH 4010 3 HOH HOH 4010 A HOH 4011 3 HOH HOH 4011 A HOH 4012 3 HOH HOH 4012 A HOH 4013 3 HOH HOH 4013 A HOH 4014 3 HOH HOH 4014 A HOH 4015 3 HOH HOH 4015 A HOH 4016 3 HOH HOH 4016 A HOH 4017 3 HOH HOH 4017 A HOH 4018 3 HOH HOH 4018 A HOH 4019 3 HOH HOH 4019 A HOH 4020 3 HOH HOH 4020 A C 1001 n 1 DC 1001 A G 1002 n 2 DG 1002 A T 1003 n 3 DT 1003 A A 1004 n 4 DA 1004 A C 1005 n 5 DC 1005 A G 1006 n 6 DG 1006 A 0.2190000 0.2150000 0.2910000 author_defined_assembly 2 dimeric 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_655 -x+1,-y,z crystal symmetry operation 30.2390000000 0.0000000000 0.0000000000 1 A HOH 4009 D HOH 1 A HOH 4019 D HOH 1 A HOH 4020 D HOH 1 -6.50 0.80 109.40 102.90 A A A O5' C5' C4' DC DC DC 1001 1001 1001 N 1 7.90 1.10 109.80 117.70 A A A C5' C4' O4' DC DC DC 1001 1001 1001 N 1 9.36 0.90 103.10 112.46 A A A C4' C3' C2' DC DC DC 1001 1001 1001 N 1 -6.89 0.80 102.40 95.51 A A A C3' C2' C1' DC DC DC 1001 1001 1001 N 1 4.77 0.50 106.80 111.57 A A A O4' C1' C2' DC DC DC 1001 1001 1001 N 1 -4.79 0.70 108.00 103.21 A A A O4' C1' N1 DC DC DC 1001 1001 1001 N 1 -9.95 0.80 109.40 99.45 A A A O5' C5' C4' DG DG DG 1002 1002 1002 N 1 -11.67 1.60 120.90 109.23 A A A P O5' C5' DG DG DG 1002 1002 1002 N 1 9.32 1.10 109.80 119.12 A A A C5' C4' O4' DG DG DG 1002 1002 1002 N 1 7.86 0.90 103.10 110.96 A A A C4' C3' C2' DG DG DG 1002 1002 1002 N 1 -6.54 0.80 102.40 95.86 A A A C3' C2' C1' DG DG DG 1002 1002 1002 N 1 3.98 0.50 106.80 110.78 A A A O4' C1' C2' DG DG DG 1002 1002 1002 N 1 -10.78 0.80 109.40 98.62 A A A O5' C5' C4' DT DT DT 1003 1003 1003 N 1 -14.97 1.60 120.90 105.93 A A A P O5' C5' DT DT DT 1003 1003 1003 N 1 7.05 1.10 109.80 116.85 A A A C5' C4' O4' DT DT DT 1003 1003 1003 N 1 6.99 0.90 103.10 110.09 A A A C4' C3' C2' DT DT DT 1003 1003 1003 N 1 -11.19 0.80 102.40 91.21 A A A C3' C2' C1' DT DT DT 1003 1003 1003 N 1 3.13 0.50 106.80 109.93 A A A O4' C1' C2' DT DT DT 1003 1003 1003 N 1 11.51 1.20 119.70 131.21 A A A C3' O3' P DT DT DA 1003 1003 1004 Y 1 -9.54 0.80 109.40 99.86 A A A O5' C5' C4' DA DA DA 1004 1004 1004 N 1 7.20 1.10 109.80 117.00 A A A C5' C4' O4' DA DA DA 1004 1004 1004 N 1 8.07 0.90 103.10 111.17 A A A C4' C3' C2' DA DA DA 1004 1004 1004 N 1 -7.43 0.80 102.40 94.97 A A A C3' C2' C1' DA DA DA 1004 1004 1004 N 1 4.95 0.50 106.80 111.75 A A A O4' C1' C2' DA DA DA 1004 1004 1004 N 1 -8.65 0.80 109.40 100.75 A A A O5' C5' C4' DC DC DC 1005 1005 1005 N 1 -10.25 1.60 120.90 110.65 A A A P O5' C5' DC DC DC 1005 1005 1005 N 1 7.44 1.10 109.80 117.24 A A A C5' C4' O4' DC DC DC 1005 1005 1005 N 1 8.08 0.90 103.10 111.18 A A A C4' C3' C2' DC DC DC 1005 1005 1005 N 1 -9.82 0.80 102.40 92.58 A A A C3' C2' C1' DC DC DC 1005 1005 1005 N 1 -9.23 0.80 109.40 100.17 A A A O5' C5' C4' DG DG DG 1006 1006 1006 N 1 -15.44 1.60 120.90 105.46 A A A P O5' C5' DG DG DG 1006 1006 1006 N 1 7.34 0.90 103.10 110.44 A A A C4' C3' C2' DG DG DG 1006 1006 1006 N 1 -8.33 0.80 102.40 94.07 A A A C3' C2' C1' DG DG DG 1006 1006 1006 N 1 6.21 0.50 106.80 113.01 A A A O4' C1' C2' DG DG DG 1006 1006 1006 N 1 A A C2' C1' DC DC 1001 1001 0.119 0.010 1.519 1.638 N 1 A A O4' C1' DC DC 1001 1001 0.077 0.011 1.420 1.497 N 1 A A O3' C3' DC DC 1001 1001 -0.054 0.006 1.419 1.365 N 1 A A O3' P DC DG 1001 1002 0.113 0.012 1.607 1.720 Y 1 A A P O5' DG DG 1002 1002 0.075 0.010 1.593 1.668 N 1 A A C2' C1' DG DG 1002 1002 0.126 0.010 1.519 1.645 N 1 A A O3' C3' DG DG 1002 1002 -0.062 0.006 1.419 1.357 N 1 A A O3' P DG DT 1002 1003 0.118 0.012 1.607 1.725 Y 1 A A P O5' DT DT 1003 1003 0.073 0.010 1.593 1.666 N 1 A A C2' C1' DT DT 1003 1003 0.142 0.010 1.519 1.661 N 1 A A O3' C3' DT DT 1003 1003 -0.070 0.006 1.419 1.349 N 1 A A O3' P DT DA 1003 1004 0.110 0.012 1.607 1.717 Y 1 A A P O5' DA DA 1004 1004 0.080 0.010 1.593 1.673 N 1 A A C2' C1' DA DA 1004 1004 0.122 0.010 1.519 1.641 N 1 A A O3' C3' DA DA 1004 1004 -0.057 0.006 1.419 1.362 N 1 A A O3' P DA DC 1004 1005 0.132 0.012 1.607 1.739 Y 1 A A P O5' DC DC 1005 1005 0.067 0.010 1.593 1.660 N 1 A A C2' C1' DC DC 1005 1005 0.140 0.010 1.519 1.659 N 1 A A O3' C3' DC DC 1005 1005 -0.052 0.006 1.419 1.367 N 1 A A O3' P DC DG 1005 1006 0.130 0.012 1.607 1.737 Y 1 A A P O5' DG DG 1006 1006 0.067 0.010 1.593 1.660 N 1 A A C2' C1' DG DG 1006 1006 0.128 0.010 1.519 1.647 N 1 A A O3' C3' DG DG 1006 1006 -0.056 0.006 1.419 1.363 N 28 0.2910000 0.2150000 0.2190000 0.2190000 1.8 40 143 1931 1931 Random 1 isotropic Rfree 0.0 0.0 ISOMORPHOUS NDB entry DD0015 SHELX 2000 DNA dictioary 1.8 40 20 192 52 120 0 1.8 40 1KCI 1951 1951 0.0 0.0 0.0940000 1 21.5 7.7 99.8 1.80 1.86 5.0 195 0.3500000 6.6 100 refinement SHELXL-97 data reduction DENZO data scaling SCALEPACK Crystal Structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide Bound to d(CGTACG)2 1 N N 2 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1001 A N3 DC 1 1_555 A DG 1006 A N1 DG 6 4_655 hydrog WATSON-CRICK A DC 1001 A N4 DC 1 1_555 A DG 1006 A O6 DG 6 4_655 hydrog WATSON-CRICK A DC 1001 A O2 DC 1 1_555 A DG 1006 A N2 DG 6 4_655 hydrog WATSON-CRICK A DG 1002 A N1 DG 2 1_555 A DC 1005 A N3 DC 5 4_655 hydrog WATSON-CRICK A DG 1002 A N2 DG 2 1_555 A DC 1005 A O2 DC 5 4_655 hydrog WATSON-CRICK A DG 1002 A O6 DG 2 1_555 A DC 1005 A N4 DC 5 4_655 hydrog WATSON-CRICK A DT 1003 A N3 DT 3 1_555 A DA 1004 A N1 DA 4 4_655 hydrog WATSON-CRICK A DT 1003 A O4 DT 3 1_555 A DA 1004 A N6 DA 4 4_655 hydrog WATSON-CRICK A DA 1004 A N1 DA 4 1_555 A DT 1003 A N3 DT 3 4_655 hydrog WATSON-CRICK A DA 1004 A N6 DA 4 1_555 A DT 1003 A O4 DT 3 4_655 hydrog WATSON-CRICK A DC 1005 A N3 DC 5 1_555 A DG 1002 A N1 DG 2 4_655 hydrog WATSON-CRICK A DC 1005 A N4 DC 5 1_555 A DG 1002 A O6 DG 2 4_655 hydrog WATSON-CRICK A DC 1005 A O2 DC 5 1_555 A DG 1002 A N2 DG 2 4_655 hydrog WATSON-CRICK A DG 1006 A N1 DG 6 1_555 A DC 1001 A N3 DC 1 4_655 hydrog WATSON-CRICK A DG 1006 A N2 DG 6 1_555 A DC 1001 A O2 DC 1 4_655 hydrog WATSON-CRICK A DG 1006 A O6 DG 6 1_555 A DC 1001 A N4 DC 1 4_655 DNA DNA, intercalator, aminoacridinecarboxamide 1KCI PDB 1 1KCI 1001 1006 1KCI 1001 1006 1KCI A 1 1 6 BINDING SITE FOR RESIDUE DRC A 3014 A DRC 3014 Software 11 BINDING SITE FOR RESIDUE DRC A 3015 A DRC 3015 Software 6 A DC 1001 A DC 1 11 1_555 A DG 1002 A DG 2 11 1_555 A DG 1002 A DG 2 11 3_664 A DT 1003 A DT 3 11 1_555 A DA 1004 A DA 4 11 2_655 A DC 1005 A DC 5 11 4_655 A DG 1006 A DG 6 11 4_655 A DRC 3015 C DRC 11 4_655 A HOH 4016 D HOH 11 2_655 A HOH 4019 D HOH 11 4_655 A HOH 4019 D HOH 11 1_555 A DC 1001 A DC 1 6 4_655 A DC 1001 A DC 1 6 1_445 A DG 1006 A DG 6 6 4_545 A DG 1006 A DG 6 6 1_555 A DRC 3014 B DRC 6 4_655 A HOH 4011 D HOH 6 1_555 172 P 64