0.035486 0.000000 0.000000 0.000000 0.035486 0.000000 0.000000 0.000000 0.018818 0.00000 0.00000 0.00000 Gao, Y.-G. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 28.180 28.180 53.140 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 C26 H27 N O10 513.493 1-O-DEMETHYL-6-DEOXYDOXORUBICIN 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 Y 108 N C Y 109 N C Y 110 N C Y 111 N C N 112 N O Y 113 N C N 114 N C N 115 N O Y 116 N C Y 117 N C N 118 N O Y 119 N C N 120 S C N 121 N O N 122 N C N 123 S C N 124 N O N 125 N C N 126 N O N 127 N C N 128 N O N 129 N C Y 130 N C Y 131 N C Y 132 N C N 133 N C N 134 N O Y 135 N C N 136 R C N 137 N C N 138 S C N 139 N N N 140 S C N 141 N O N 142 S C N 143 N O N 144 N C 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 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 H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N O N 173 N P N 174 N O N 175 N O N 176 N O N 177 N C N 178 R C N 179 N O N 180 S C N 181 N O N 182 N C N 183 R C N 184 N N N 185 N C N 186 N O N 187 N N N 188 N C N 189 N O N 190 N C N 191 N C N 192 N C 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 O N 209 N H N 210 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 Y 113 N doub Y 114 N sing N 115 N sing Y 116 N sing N 117 N sing Y 118 N doub N 119 N sing N 120 N sing Y 121 N sing N 122 N sing N 123 N sing Y 124 N doub N 125 N doub N 126 N sing Y 127 N doub Y 128 N sing N 129 N sing Y 130 N sing N 131 N sing N 132 N sing Y 133 N doub 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 doub 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 Y 154 N sing Y 155 N doub N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing 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 N 183 N doub 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 sing 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 doub N 211 N sing N 212 N sing N 213 N doub N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing UK Anti-Cancer Drug Des. ACDDEA 0807 0266-9536 6 137 149 1872945 Influence of aglycone modifications on the binding of anthracycline drugs to DNA: the molecular structure of idarubicin and 4-O-demethyl-11-deoxydoxorubicin complexed to d(CGATCG). 1991 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 88 4845 4849 Facile Formation of Crosslinked Adduct between DNA and the Daunorubicin Derivative MAR70 Mediated by Formaldehyde: Molecular Structure of the MAR70-d(CGTnACG) Covalent Adduct 1991 10.2210/pdb1d37/pdb pdb_00001d37 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.00 1 DIFFRACTOMETER RIGAKU AFC-5R x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 1809.217 DNA (5'-D(*CP*GP*AP*TP*CP*G)-3') 1 syn polymer 513.493 1-O-DEMETHYL-6-DEOXYDOXORUBICIN 1 syn non-polymer 18.015 water 42 nat water no no (DC)(DG)(DA)(DT)(DC)(DG) CGATCG A polydeoxyribonucleotide n n n n n n 2.92 57.81 VAPOR DIFFUSION 6.00 pH 6.00, VAPOR DIFFUSION, temperature 298.00K 298.00 WATER 1 MPD 1 BACL2 1 NA CACODYLATE 1 SPERMINE 1 WATER 2 MPD 2 5.120 1 19 A 1 A 6 -1.632 A_DC1:DG6_A 1 3.022 0.239 -0.116 -0.302 -15.724 1 19 A 2 A 5 -1.809 A_DG2:DC5_A 2 -0.507 -0.258 -0.381 -0.287 -8.948 1 20 A 3 A 4 -0.891 A_DA3:DT4_A 3 -5.250 0.014 -0.082 -0.205 8.948 1 20 A 4 A 3 -0.891 A_DT4:DA3_A 4 -5.250 -0.014 -0.082 -0.205 15.724 1 19 A 5 A 2 -1.809 A_DC5:DG2_A 5 -0.507 0.258 -0.381 -0.287 -5.120 1 19 A 6 A 1 -1.632 A_DG6:DC1_A 6 3.022 -0.239 -0.116 -0.302 6.986 34.535 A A 1 2 -1.246 A A 6 5 6.970 -0.739 0.898 1.254 AA_DC1DG2:DC5DG6_AA 1 2.300 -3.878 34.452 2.357 -0.753 3.425 31.708 A A 2 3 4.161 A A 5 4 3.239 2.261 -1.216 0.523 AA_DG2DA3:DT4DC5_AA 2 -5.400 9.937 31.176 0.530 1.205 3.035 31.752 A A 3 4 -0.334 A A 4 3 3.033 -0.183 0.000 -0.402 AA_DA3DT4:DA3DT4_AA 3 0.000 0.000 31.752 -0.704 0.000 3.425 31.708 A A 4 5 4.161 A A 3 2 3.239 2.261 1.216 0.523 AA_DT4DC5:DG2DA3_AA 4 5.400 -9.937 31.176 0.530 -1.205 6.986 34.535 A A 5 6 -1.246 A A 2 1 6.970 -0.739 -0.898 1.254 AA_DC5DG6:DC1DG2_AA 5 -2.300 3.878 34.452 2.357 0.753 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1992-04-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _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 BNL Y NDB 1991-04-23 REL DM4 1-O-DEMETHYL-6-DEOXYDOXORUBICIN HOH water DM4 7 2 DM4 DM4 7 A HOH 8 3 HOH HOH 8 A HOH 9 3 HOH HOH 9 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A HOH 45 3 HOH HOH 45 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A 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 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_665 -y+1,-x+1,-z+1/2 crystal symmetry operation 28.1800000000 28.1800000000 26.5700000000 1 18.91 1.20 119.70 138.61 A A A C3' O3' P DC DC DG 1 1 2 Y 1 -7.49 0.80 109.40 101.91 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 -8.10 0.80 102.40 94.30 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 5.91 0.30 108.30 114.21 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 3.83 0.60 123.90 127.73 A A A N1 C2 N3 DG DG DG 2 2 2 N 1 -6.41 0.90 116.20 109.79 A A A N1 C2 N2 DG DG DG 2 2 2 N 1 -4.25 0.60 119.90 115.65 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 6.96 1.10 110.50 117.46 A A A O3' P OP1 DG DA DA 2 3 3 Y 1 -9.37 1.50 119.60 110.23 A A A OP1 P OP2 DA DA DA 3 3 3 N 1 7.69 1.20 110.70 118.39 A A A O5' P OP2 DA DA DA 3 3 3 N 1 -8.73 0.80 109.40 100.67 A A A O5' C5' C4' DA DA DA 3 3 3 N 1 3.56 0.30 108.30 111.86 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 6.90 0.60 118.60 125.50 A A A C6 N1 C2 DA DA DA 3 3 3 N 1 -3.19 0.50 129.30 126.11 A A A N1 C2 N3 DA DA DA 3 3 3 N 1 -4.33 0.50 117.70 113.37 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 4.58 0.60 118.60 123.18 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 7.65 1.20 119.70 127.35 A A A C3' O3' P DA DA DT 3 3 4 Y 1 -5.83 0.80 109.40 103.57 A A A O5' C5' C4' DT DT DT 4 4 4 N 1 4.60 0.60 114.60 119.20 A A A N1 C2 N3 DT DT DT 4 4 4 N 1 -5.25 0.60 127.20 121.95 A A A C2 N3 C4 DT DT DT 4 4 4 N 1 4.42 0.60 115.20 119.62 A A A N3 C4 C5 DT DT DT 4 4 4 N 1 -6.21 0.80 123.10 116.89 A A A N1 C2 O2 DT DT DT 4 4 4 N 1 -5.96 0.80 109.40 103.44 A A A O5' C5' C4' DC DC DC 5 5 5 N 1 9.96 0.30 108.30 118.26 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 4.04 0.50 119.90 123.94 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 5.76 0.70 121.90 127.66 A A A N3 C2 O2 DC DC DC 5 5 5 N 1 7.00 0.70 118.00 125.00 A A A N3 C4 N4 DC DC DC 5 5 5 N 1 -5.87 0.70 120.20 114.33 A A A C5 C4 N4 DC DC DC 5 5 5 N 1 -6.54 0.90 105.70 99.16 A A A O5' P OP1 DG DG DG 6 6 6 N 1 11.91 1.20 110.70 122.61 A A A O5' P OP2 DG DG DG 6 6 6 N 1 3.33 0.40 110.80 114.13 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 -4.66 0.50 104.30 99.64 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 5.95 0.90 116.20 122.15 A A A N1 C2 N2 DG DG DG 6 6 6 N 1 -6.12 0.70 119.90 113.78 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 6.48 0.60 119.90 126.38 A A A N1 C6 O6 DG DG DG 6 6 6 N 1 -8.80 0.60 128.60 119.80 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 A A P O5' DG DG 2 2 0.063 0.010 1.593 1.656 N 1 A A C5' C4' DA DA 3 3 0.043 0.007 1.512 1.555 N 1 A A C2 N3 DT DT 4 4 -0.054 0.008 1.373 1.319 N 1 A A C4 C5 DG DG 6 6 -0.066 0.007 1.379 1.313 N 1 A A C6 N1 DG DG 6 6 -0.082 0.007 1.391 1.309 N 1 A A N7 C8 DG DG 6 6 0.063 0.006 1.305 1.368 N 0.1790000 1.800 1247 1 2.000 TR isotropic TR isotropic 1.800 42 199 37 120 0 0.025 0.179 fix fix 1.800 1D37 1247 2.000 1 refinement NUCLSQ INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLINE DRUGS TO DNA: THE MOLECULAR STRUCTURE OF IDARUBICIN AND 4-O-DEMETHYL-11-DEOXYDOXORUBICIN COMPLEXED TO D(CGATCG) 1 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 8_665 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 8_665 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 4 A N3 DT 4 8_665 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 4 A O4 DT 4 8_665 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 3 A N1 DA 3 8_665 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 3 A N6 DA 3 8_665 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 8_665 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 8_665 DNA RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA 1D37 PDB 1 1D37 1 6 1D37 1 6 1D37 A 1 1 6 BINDING SITE FOR RESIDUE DM4 A 7 A DM4 7 Software 9 A DC 1 A DC 1 9 8_665 A DG 2 A DG 2 9 8_665 A DA 3 A DA 3 9 8_665 A DT 4 A DT 4 9 1_555 A DC 5 A DC 5 9 1_555 A DG 6 A DG 6 9 1_555 A HOH 16 C HOH 9 1_555 A HOH 27 C HOH 9 1_555 A HOH 48 C HOH 9 1_555 92 P 41 21 2