1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yang, X.-L. Kaenzig, C. Lee, M. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C20 H28 N11 O4 1 486.508 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM TRI-IMIDAZOLE DNA MINOR GROOVE BINDER; AR-1-144 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 C N 2 N O N 3 N N Y 4 N C Y 5 N N Y 6 N C Y 7 N N N 8 N C Y 9 N C N 10 N C N 11 N O N 12 N N Y 13 N C Y 14 N N Y 15 N C Y 16 N N N 17 N C Y 18 N C N 19 N C N 20 N O N 21 N N Y 22 N C Y 23 N N Y 24 N C Y 25 N N N 26 N C Y 27 N C N 28 N C N 29 N O N 30 N N N 31 N C N 32 N C N 33 N N N 34 N C N 35 N C 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 O N 65 N P N 66 N O N 67 N O N 68 N O N 69 N C N 70 R C N 71 N O N 72 S C N 73 N O N 74 N C N 75 R C Y 76 N N Y 77 N C Y 78 N N Y 79 N C Y 80 N C N 81 N N Y 82 N N Y 83 N C Y 84 N N Y 85 N C 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 H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N O N 101 N P N 102 N O N 103 N O N 104 N O N 105 N C N 106 R C N 107 N O N 108 S C N 109 N O N 110 N C N 111 R C N 112 N N N 113 N C N 114 N O N 115 N N N 116 N C N 117 N N N 118 N C N 119 N C 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 H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N O N 135 N P N 136 N O N 137 N O N 138 N O N 139 N C N 140 R C N 141 N O N 142 S C N 143 N O N 144 N C N 145 R C Y 146 N N Y 147 N C Y 148 N N Y 149 N C N 150 N C N 151 N O N 152 N N N 153 N C N 154 N N N 155 N N Y 156 N C 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 H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N O N 172 N P N 173 N O N 174 N O N 175 N O N 176 N C N 177 R C N 178 N O N 179 S C N 180 N O N 181 N C N 182 R C N 183 N N N 184 N C N 185 N O N 186 N N N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C 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 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing Y 6 N sing Y 7 N doub Y 8 N doub Y 9 N sing N 10 N sing N 11 N sing Y 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N doub N 18 N sing N 19 N sing N 20 N sing Y 21 N sing Y 22 N doub Y 23 N doub Y 24 N sing N 25 N sing N 26 N sing Y 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N doub N 33 N sing N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub Y 38 N doub Y 39 N sing N 40 N sing N 41 N sing Y 42 N sing N 43 N sing N 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 doub 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 Y 89 N sing Y 90 N sing Y 91 N doub N 92 N sing Y 93 N sing Y 94 N sing Y 95 N doub N 96 N sing Y 97 N doub N 98 N sing N 99 N sing Y 100 N sing Y 101 N doub N 102 N sing Y 103 N sing N 104 N sing N 105 N sing N 106 N doub 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 sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N doub 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 N 141 N doub 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 N 158 N sing N 159 N sing N 160 N sing N 161 N sing Y 162 N sing Y 163 N sing Y 164 N doub N 165 N sing Y 166 N sing N 167 N sing Y 168 N doub N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N doub N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub 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 sing 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 sing N 207 N doub N 208 N sing N 209 N sing N 210 N doub N 211 N sing N 212 N sing N 213 N sing N 214 N sing IX Eur.J.Biochem. EJBCAI 0262 0014-2956 263 646 655 10.1046/j.1432-1327.1999.00515.x 10469127 Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy. 1999 10.2210/pdb1b0s/pdb pdb_00001b0s 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3045.005 DNA (5'-D(*GP*AP*AP*CP*CP*GP*GP*TP*TP*C)-3') 2 syn polymer 486.508 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM 2 syn non-polymer no no (DG)(DA)(DA)(DC)(DC)(DG)(DG)(DT)(DT)(DC) GAACCGGTTC A,B polydeoxyribonucleotide n n n n n n n n n n -21.315 1 19 A 1 B 20 -8.023 A_DG1:DC20_B 1 14.419 0.379 -0.824 -0.205 -0.894 1 20 A 2 B 19 -0.043 A_DA2:DT19_B 2 0.646 -0.034 0.112 -0.163 5.318 1 20 A 3 B 18 -5.164 A_DA3:DT18_B 3 -25.697 -0.205 -0.261 -0.349 -9.620 1 19 A 4 B 17 -5.217 A_DC4:DG17_B 4 -13.372 0.159 0.262 -0.214 -2.132 1 19 A 5 B 16 -5.092 A_DC5:DG16_B 5 -3.059 0.462 0.187 -0.244 2.171 1 19 A 6 B 15 -5.101 A_DG6:DC15_B 6 -3.035 -0.458 0.187 -0.246 9.628 1 19 A 7 B 14 -5.226 A_DG7:DC14_B 7 -13.390 -0.156 0.260 -0.219 -5.299 1 20 A 8 B 13 -5.160 A_DT8:DA13_B 8 -25.708 0.202 -0.263 -0.354 0.892 1 20 A 9 B 12 -0.036 A_DT9:DA12_B 9 0.631 0.028 0.112 -0.166 21.316 1 19 A 10 B 11 -8.033 A_DC10:DG11_B 10 14.390 -0.386 -0.824 -0.204 3.007 29.603 A A 1 2 -1.180 B B 20 19 2.998 -0.603 0.025 -0.659 AA_DG1DA2:DT19DC20_BB 1 -1.360 2.663 29.567 -1.172 -0.314 3.031 29.935 A A 2 3 12.319 B B 19 18 3.218 6.304 0.563 -0.779 AA_DA2DA3:DT18DT19_BB 2 3.487 -6.814 29.075 -2.772 -0.390 3.547 38.872 A A 3 4 7.611 B B 18 17 3.486 5.032 -1.471 -0.768 AA_DA3DC4:DG17DT18_BB 3 -6.169 9.331 38.079 -1.819 1.395 3.067 29.177 A A 4 5 -5.385 B B 17 16 3.104 -2.708 -0.071 0.269 AA_DC4DC5:DG16DG17_BB 4 -1.576 3.133 29.012 1.092 -0.183 2.687 43.752 A A 5 6 -17.182 B B 16 15 3.167 -12.638 0.000 1.296 AA_DC5DG6:DC15DG16_BB 5 -0.006 0.008 41.973 2.844 0.000 3.068 29.183 A A 6 7 -5.373 B B 15 14 3.105 -2.702 0.070 0.269 AA_DG6DG7:DC14DC15_BB 6 1.581 -3.144 29.018 1.091 0.186 3.547 38.865 A A 7 8 7.602 B B 14 13 3.486 5.025 1.471 -0.767 AA_DG7DT8:DA13DC14_BB 7 6.174 -9.340 38.072 -1.818 -1.395 3.031 29.945 A A 8 9 12.331 B B 13 12 3.218 6.312 -0.562 -0.778 AA_DT8DT9:DA12DA13_BB 8 -3.503 6.843 29.081 -2.771 0.386 3.007 29.591 A A 9 10 -1.190 B B 12 11 2.998 -0.608 -0.026 -0.659 AA_DT9DC10:DG11DA12_BB 9 1.363 -2.669 29.555 -1.172 0.315 chem_comp database_2 entity pdbx_entity_nonpoly pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Structure summary Data collection 1 0 1999-08-31 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-16 1 4 2023-12-27 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 1998-11-12 REL REL AR1 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM REFINED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING 1H 2D NMR SPECTROSCOPY REFINED AVERAGE STRUCTURE 11 1 NOESY TOCSY 7.0 1 atm 275 K NOE-RMD BRUNGER refinement X-PLOR 3.1 structure solution X-PLOR 3.1 structure solution SPEDREF 750 Varian UNITY 750 500 Varian VXR 500 AR1 1 2 AR1 AR1 11 A AR1 2 2 AR1 AR1 2 B G 1 n 1 DG 1 A A 2 n 2 DA 2 A A 3 n 3 DA 3 A C 4 n 4 DC 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A T 9 n 9 DT 9 A C 10 n 10 DC 10 A G 11 n 1 DG 11 B A 12 n 2 DA 12 B A 13 n 3 DA 13 B C 14 n 4 DC 14 B C 15 n 5 DC 15 B G 16 n 6 DG 16 B G 17 n 7 DG 17 B T 18 n 8 DT 18 B T 19 n 9 DT 19 B C 20 n 10 DC 20 B 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 A DT 8 0.065 SIDE CHAIN 1 A DT 9 0.069 SIDE CHAIN 1 B DT 19 0.069 SIDE CHAIN 1 3.31 0.30 108.30 111.61 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 -5.14 0.80 105.90 100.76 A A A O4' C1' C2' DA DA DA 3 3 3 N 1 5.93 0.30 108.30 114.23 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 -7.04 0.80 105.90 98.86 A A A O4' C1' C2' DC DC DC 5 5 5 N 1 6.03 0.30 108.30 114.33 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.91 0.60 118.90 122.81 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 7.29 1.20 119.70 126.99 A A A C3' O3' P DG DG DG 6 6 7 Y 1 5.99 0.30 108.30 114.29 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 6.25 0.30 108.30 114.55 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 3.15 0.50 119.90 123.05 A A A C2 N3 C4 DC DC DC 10 10 10 N 1 3.35 0.30 108.30 111.65 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 -5.17 0.80 105.90 100.73 B B B O4' C1' C2' DA DA DA 13 13 13 N 1 6.00 0.30 108.30 114.30 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 -7.02 0.80 105.90 98.88 B B B O4' C1' C2' DC DC DC 15 15 15 N 1 6.02 0.30 108.30 114.32 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.95 0.60 118.90 122.85 B B B N1 C2 O2 DC DC DC 15 15 15 N 1 7.26 1.20 119.70 126.96 B B B C3' O3' P DG DG DG 16 16 17 Y 1 5.99 0.30 108.30 114.29 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 6.26 0.30 108.30 114.56 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 3.20 0.50 119.90 123.10 B B B C2 N3 C4 DC DC DC 20 20 20 N 1 A A C5 C7 DT DT 8 8 0.048 0.006 1.496 1.544 N 1 A A C5 C7 DT DT 9 9 0.050 0.006 1.496 1.546 N 1 A A C5 C6 DC DC 10 10 0.049 0.008 1.339 1.388 N 1 B B C5 C7 DT DT 18 18 0.048 0.006 1.496 1.544 N 1 B B C5 C7 DT DT 19 19 0.049 0.006 1.496 1.545 N 1 B B C5 C6 DC DC 20 20 0.050 0.008 1.339 1.389 N BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 20 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 20 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 20 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 19 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 19 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 17 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 17 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 17 B N2 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 16 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 16 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 16 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 15 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 15 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 15 B N4 DC 5 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 14 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 14 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 14 B N4 DC 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 13 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 13 B N6 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 12 B N1 DA 2 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 12 B N6 DA 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA ANTICANCER DRUG, DRUG DESIGN, DNA STRUCTURE, SEQUENCE SPECIFIC RECOGNITION, DNA 1B0S PDB 1 1B0S 1 10 1B0S 1 10 1B0S A 1 1 10 11 20 1B0S 11 20 1B0S B 1 1 10 BINDING SITE FOR RESIDUE AR1 A 11 A AR1 11 Software 9 BINDING SITE FOR RESIDUE AR1 B 2 B AR1 2 Software 9 A DC 5 A DC 5 9 1_555 A DG 6 A DG 6 9 1_555 A DG 7 A DG 7 9 1_555 A DT 8 A DT 8 9 1_555 A DT 9 A DT 9 9 1_555 B AR1 2 D AR1 9 1_555 B DC 14 B DC 4 9 1_555 B DG 16 B DG 6 9 1_555 B DG 17 B DG 7 9 1_555 A DC 4 A DC 4 9 1_555 A DG 6 A DG 6 9 1_555 A DG 7 A DG 7 9 1_555 A AR1 11 C AR1 9 1_555 B DC 15 B DC 5 9 1_555 B DG 16 B DG 6 9 1_555 B DG 17 B DG 7 9 1_555 B DT 18 B DT 8 9 1_555 B DT 19 B DT 9 9 1_555 1 P 1