1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gallego, J. Reid, B.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C31 H30 N4 O4 2 522.594 N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE LU-79553 non-polymer US Biochemistry BICHAW 0033 0006-2960 38 15104 15115 10.1021/bi9915869 10563793 Solution structure and dynamics of a complex between DNA and the antitumor bisnaphthalimide LU-79553: intercalated ring flipping on the millisecond time scale. 1999 10.2210/pdb1cx3/pdb pdb_00001cx3 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 DNA DOUBLE HELIX INTERCALATED BY LU-79553 1808.229 DNA (5'-D(*AP*TP*GP*CP*AP*T)-3') 2 syn polymer 522.594 N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE 1 syn non-polymer no no (DA)(DT)(DG)(DC)(DA)(DT) ATGCAT A,B polydeoxyribonucleotide n n n n n n -8.694 1 20 A 1 B 6 0.501 A_DA1:DT6_B 1 -1.686 -0.341 0.186 -0.096 18.791 1 20 A 2 B 5 -2.135 A_DT2:DA5_B 2 2.043 0.311 -0.226 -0.026 -3.043 1 19 A 3 B 4 -2.533 A_DG3:DC4_B 3 -1.545 -0.831 -0.099 -0.256 4.452 1 19 A 4 B 3 -2.607 A_DC4:DG3_B 4 -3.155 0.526 -0.095 -0.127 -17.640 1 20 A 5 B 2 -0.966 A_DA5:DT2_B 5 0.425 -0.336 -0.217 -0.041 8.513 1 20 A 6 B 1 0.944 A_DT6:DA1_B 6 -3.512 0.330 0.155 -0.094 2.435 26.653 A A 1 2 11.226 B B 6 5 2.604 5.125 -0.174 -0.357 AA_DA1DT2:DA5DT6_BB 1 3.981 -8.720 25.865 -1.823 1.193 6.637 22.346 A A 2 3 9.503 B B 5 4 6.766 3.654 -0.461 -0.223 AA_DT2DG3:DC4DA5_BB 2 -3.203 8.331 21.817 -3.403 -1.289 2.967 39.642 A A 3 4 0.426 B B 4 3 2.969 0.289 -0.017 -0.273 AA_DG3DC4:DG3DC4_BB 3 0.087 -0.128 39.641 -0.434 0.034 6.662 22.861 A A 4 5 9.253 B B 3 2 6.785 3.644 0.511 -0.330 AA_DC4DA5:DT2DG3_BB 4 2.611 -6.630 22.423 -3.528 0.642 2.455 27.228 A A 5 6 11.710 B B 2 1 2.625 5.461 0.130 -0.400 AA_DA5DT6:DA1DT2_BB 5 -3.577 7.671 26.448 -1.929 -0.982 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1999-11-19 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 1999-08-27 REL NF N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY 20 15 COSY NOESY ROESY TOCSY HP-HETCOR 20 mM SODIUM PHOSPHATE 7.20 1 atm 275.00 K DISTANCE GEOMETRY, MOLECULAR DYNAMICS SODIUM PHOSPHATE, EDTA ZHU AND REID refinement BIRDER 1995 structure solution DGII structure solution Amber structure solution BIRDER 500 Bruker DRX 750 Bruker DMX NF 1 2 NF NF 7 A A 1 n 1 DA 1 A T 2 n 2 DT 2 A G 3 n 3 DG 3 A C 4 n 4 DC 4 A A 5 n 5 DA 5 A T 6 n 6 DT 6 A A 1 n 1 DA 1 B T 2 n 2 DT 2 B G 3 n 3 DG 3 B C 4 n 4 DC 4 B A 5 n 5 DA 5 B T 6 n 6 DT 6 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 DA 5 0.054 SIDE CHAIN 1 B DA 5 0.053 SIDE CHAIN 2 B DT 2 0.066 SIDE CHAIN 3 A DA 5 0.051 SIDE CHAIN 3 B DA 5 0.052 SIDE CHAIN 4 A DA 5 0.052 SIDE CHAIN 4 B DA 5 0.053 SIDE CHAIN 6 B DA 5 0.052 SIDE CHAIN 8 B DA 5 0.075 SIDE CHAIN 9 A DA 5 0.053 SIDE CHAIN 13 A DA 5 0.053 SIDE CHAIN 13 B DA 5 0.053 SIDE CHAIN 14 A DA 5 0.053 SIDE CHAIN 15 B DA 5 0.074 SIDE CHAIN 1 2.66 0.30 108.30 110.96 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 -3.69 0.60 122.90 119.21 A A A C6 C5 C7 DT DT DT 2 2 2 N 1 3.24 0.30 108.30 111.54 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 2.18 0.30 108.30 110.48 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 2.75 0.30 108.30 111.05 B B B O4' C1' N9 DA DA DA 1 1 1 N 1 -3.77 0.60 122.90 119.13 B B B C6 C5 C7 DT DT DT 2 2 2 N 1 2.99 0.30 108.30 111.29 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 2.14 0.30 108.30 110.44 B B B O4' C1' N1 DT DT DT 6 6 6 N 2 2.76 0.30 108.30 111.06 A A A O4' C1' N9 DA DA DA 1 1 1 N 2 -3.75 0.60 122.90 119.15 A A A C6 C5 C7 DT DT DT 2 2 2 N 2 3.02 0.30 108.30 111.32 A A A O4' C1' N9 DA DA DA 5 5 5 N 2 1.92 0.30 108.30 110.22 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 2.82 0.30 108.30 111.12 B B B O4' C1' N9 DA DA DA 1 1 1 N 2 3.99 0.30 108.30 112.29 B B B O4' C1' N1 DT DT DT 2 2 2 N 2 7.41 1.20 119.70 127.11 B B B C3' O3' P DT DT DG 2 2 3 Y 2 2.67 0.30 108.30 110.97 B B B O4' C1' N9 DA DA DA 5 5 5 N 2 1.92 0.30 108.30 110.22 B B B O4' C1' N1 DT DT DT 6 6 6 N 3 2.72 0.30 108.30 111.02 A A A O4' C1' N9 DA DA DA 1 1 1 N 3 2.86 0.30 108.30 111.16 A A A O4' C1' N9 DA DA DA 5 5 5 N 3 1.96 0.30 108.30 110.26 A A A O4' C1' N1 DT DT DT 6 6 6 N 3 2.67 0.30 108.30 110.97 B B B O4' C1' N9 DA DA DA 1 1 1 N 3 -3.76 0.60 122.90 119.14 B B B C6 C5 C7 DT DT DT 2 2 2 N 3 2.94 0.30 108.30 111.24 B B B O4' C1' N9 DA DA DA 5 5 5 N 3 2.03 0.30 108.30 110.33 B B B O4' C1' N1 DT DT DT 6 6 6 N 4 2.66 0.30 108.30 110.96 A A A O4' C1' N9 DA DA DA 1 1 1 N 4 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 2 2 2 N 4 3.37 0.30 108.30 111.67 A A A O4' C1' N9 DA DA DA 5 5 5 N 4 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DT DT DT 6 6 6 N 4 2.84 0.30 108.30 111.14 B B B O4' C1' N9 DA DA DA 1 1 1 N 4 -3.70 0.60 122.90 119.20 B B B C6 C5 C7 DT DT DT 2 2 2 N 4 2.96 0.30 108.30 111.26 B B B O4' C1' N9 DA DA DA 5 5 5 N 4 2.17 0.30 108.30 110.47 B B B O4' C1' N1 DT DT DT 6 6 6 N 5 2.55 0.30 108.30 110.85 A A A O4' C1' N9 DA DA DA 1 1 1 N 5 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 2 2 2 N 5 2.97 0.30 108.30 111.27 A A A O4' C1' N9 DA DA DA 5 5 5 N 5 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DT DT DT 6 6 6 N 5 2.52 0.30 108.30 110.82 B B B O4' C1' N9 DA DA DA 1 1 1 N 5 3.92 0.30 108.30 112.22 B B B O4' C1' N9 DA DA DA 5 5 5 N 5 1.87 0.30 108.30 110.17 B B B O4' C1' N1 DT DT DT 6 6 6 N 6 2.62 0.30 108.30 110.92 A A A O4' C1' N9 DA DA DA 1 1 1 N 6 2.87 0.30 108.30 111.17 A A A O4' C1' N9 DA DA DA 5 5 5 N 6 1.91 0.30 108.30 110.21 A A A O4' C1' N1 DT DT DT 6 6 6 N 6 2.71 0.30 108.30 111.01 B B B O4' C1' N9 DA DA DA 1 1 1 N 6 -3.81 0.60 122.90 119.09 B B B C6 C5 C7 DT DT DT 2 2 2 N 6 2.91 0.30 108.30 111.21 B B B O4' C1' N9 DA DA DA 5 5 5 N 6 1.97 0.30 108.30 110.27 B B B O4' C1' N1 DT DT DT 6 6 6 N 7 2.75 0.30 108.30 111.05 A A A O4' C1' N9 DA DA DA 1 1 1 N 7 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 2 2 2 N 7 2.93 0.30 108.30 111.23 A A A O4' C1' N9 DA DA DA 5 5 5 N 7 1.90 0.30 108.30 110.20 A A A O4' C1' N1 DT DT DT 6 6 6 N 7 2.79 0.30 108.30 111.09 B B B O4' C1' N9 DA DA DA 1 1 1 N 7 -3.61 0.60 122.90 119.29 B B B C6 C5 C7 DT DT DT 2 2 2 N 7 2.93 0.30 108.30 111.23 B B B O4' C1' N9 DA DA DA 5 5 5 N 7 1.91 0.30 108.30 110.21 B B B O4' C1' N1 DT DT DT 6 6 6 N 8 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DA DA DA 1 1 1 N 8 -3.64 0.60 122.90 119.26 A A A C6 C5 C7 DT DT DT 2 2 2 N 8 4.34 0.30 108.30 112.64 A A A O4' C1' N9 DA DA DA 5 5 5 N 8 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 6 6 6 N 8 2.63 0.30 108.30 110.93 B B B O4' C1' N9 DA DA DA 1 1 1 N 8 -3.70 0.60 122.90 119.20 B B B C6 C5 C7 DT DT DT 2 2 2 N 8 2.43 0.30 108.30 110.73 B B B O4' C1' N1 DC DC DC 4 4 4 N 8 7.68 1.20 119.70 127.38 B B B C3' O3' P DC DC DA 4 4 5 Y 8 3.83 0.30 108.30 112.13 B B B O4' C1' N9 DA DA DA 5 5 5 N 8 2.22 0.30 108.30 110.52 B B B O4' C1' N1 DT DT DT 6 6 6 N 9 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DA DA DA 1 1 1 N 9 3.10 0.30 108.30 111.40 A A A O4' C1' N9 DA DA DA 5 5 5 N 9 2.08 0.30 108.30 110.38 A A A O4' C1' N1 DT DT DT 6 6 6 N 9 2.69 0.30 108.30 110.99 B B B O4' C1' N9 DA DA DA 1 1 1 N 9 -3.71 0.60 122.90 119.19 B B B C6 C5 C7 DT DT DT 2 2 2 N 9 2.79 0.30 108.30 111.09 B B B O4' C1' N9 DA DA DA 5 5 5 N 9 1.87 0.30 108.30 110.17 B B B O4' C1' N1 DT DT DT 6 6 6 N 10 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DA DA DA 1 1 1 N 10 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 2 2 2 N 10 3.01 0.30 108.30 111.31 A A A O4' C1' N9 DA DA DA 5 5 5 N 10 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DT DT DT 6 6 6 N 10 2.66 0.30 108.30 110.96 B B B O4' C1' N9 DA DA DA 1 1 1 N 10 -3.65 0.60 122.90 119.25 B B B C6 C5 C7 DT DT DT 2 2 2 N 10 3.31 0.30 108.30 111.61 B B B O4' C1' N9 DA DA DA 5 5 5 N 10 2.13 0.30 108.30 110.43 B B B O4' C1' N1 DT DT DT 6 6 6 N 11 2.76 0.30 108.30 111.06 A A A O4' C1' N9 DA DA DA 1 1 1 N 11 3.01 0.30 108.30 111.31 A A A O4' C1' N9 DA DA DA 5 5 5 N 11 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DT DT DT 6 6 6 N 11 2.81 0.30 108.30 111.11 B B B O4' C1' N9 DA DA DA 1 1 1 N 11 -3.65 0.60 122.90 119.25 B B B C6 C5 C7 DT DT DT 2 2 2 N 11 2.98 0.30 108.30 111.28 B B B O4' C1' N9 DA DA DA 5 5 5 N 11 1.97 0.30 108.30 110.27 B B B O4' C1' N1 DT DT DT 6 6 6 N 12 3.11 0.30 108.30 111.41 A A A O4' C1' N9 DA DA DA 1 1 1 N 12 -3.74 0.60 122.90 119.16 A A A C6 C5 C7 DT DT DT 2 2 2 N 12 1.86 0.30 108.30 110.16 A A A O4' C1' N9 DG DG DG 3 3 3 N 12 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DA DA DA 5 5 5 N 12 1.91 0.30 108.30 110.21 A A A O4' C1' N1 DT DT DT 6 6 6 N 12 2.83 0.30 108.30 111.13 B B B O4' C1' N9 DA DA DA 1 1 1 N 12 -3.71 0.60 122.90 119.19 B B B C6 C5 C7 DT DT DT 2 2 2 N 12 3.67 0.30 108.30 111.97 B B B O4' C1' N9 DA DA DA 5 5 5 N 12 2.21 0.30 108.30 110.51 B B B O4' C1' N1 DT DT DT 6 6 6 N 13 2.80 0.30 108.30 111.10 A A A O4' C1' N9 DA DA DA 1 1 1 N 13 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 2 2 2 N 13 3.01 0.30 108.30 111.31 A A A O4' C1' N9 DA DA DA 5 5 5 N 13 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DT DT DT 6 6 6 N 13 2.67 0.30 108.30 110.97 B B B O4' C1' N9 DA DA DA 1 1 1 N 13 -3.69 0.60 122.90 119.21 B B B C6 C5 C7 DT DT DT 2 2 2 N 13 3.32 0.30 108.30 111.62 B B B O4' C1' N9 DA DA DA 5 5 5 N 13 2.14 0.30 108.30 110.44 B B B O4' C1' N1 DT DT DT 6 6 6 N 14 2.68 0.30 108.30 110.98 A A A O4' C1' N9 DA DA DA 1 1 1 N 14 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 2 2 2 N 14 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DA DA DA 5 5 5 N 14 2.13 0.30 108.30 110.43 A A A O4' C1' N1 DT DT DT 6 6 6 N 14 2.70 0.30 108.30 111.00 B B B O4' C1' N9 DA DA DA 1 1 1 N 14 -3.76 0.60 122.90 119.14 B B B C6 C5 C7 DT DT DT 2 2 2 N 14 2.99 0.30 108.30 111.29 B B B O4' C1' N9 DA DA DA 5 5 5 N 14 2.17 0.30 108.30 110.47 B B B O4' C1' N1 DT DT DT 6 6 6 N 15 2.72 0.30 108.30 111.02 A A A O4' C1' N9 DA DA DA 1 1 1 N 15 -3.78 0.60 122.90 119.12 A A A C6 C5 C7 DT DT DT 2 2 2 N 15 2.87 0.30 108.30 111.17 A A A O4' C1' N9 DA DA DA 5 5 5 N 15 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DT DT DT 6 6 6 N 15 2.84 0.30 108.30 111.14 B B B O4' C1' N9 DA DA DA 1 1 1 N 15 7.62 1.20 119.70 127.32 B B B C3' O3' P DC DC DA 4 4 5 Y 15 3.77 0.30 108.30 112.07 B B B O4' C1' N9 DA DA DA 5 5 5 N 15 2.22 0.30 108.30 110.52 B B B O4' C1' N1 DT DT DT 6 6 6 N SOLUTION STRUCTURE OF A COMPLEX BETWEEN D(ATGCAT)2 AND THE ANTITUMOR BISNAPHTHALIMIDE LU-79553 1 N N 1 N N 2 N N hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 6 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 6 B O4 DT 6 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 4 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 4 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 4 B N4 DC 4 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 3 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 3 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 3 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 2 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 2 B O4 DT 2 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 1 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 1 B N6 DA 1 1_555 DNA TOPOISOMERASE, ANTICANCER, DNA, NAPHTHALIMIDE, INTERCALATION, DEOXYRIBONUCLEIC ACID 1CX3 PDB 1 1CX3 1 6 1CX3 1 6 1CX3 A 1 1 6 1 6 1CX3 1 6 1CX3 B 1 1 6 BINDING SITE FOR RESIDUE NF A 7 A NF 7 Software 8 A DT 2 A DT 2 8 1_555 A DG 3 A DG 3 8 1_555 A DC 4 A DC 4 8 1_555 A DA 5 A DA 5 8 1_555 B DT 2 B DT 2 8 1_555 B DG 3 B DG 3 8 1_555 B DC 4 B DC 4 8 1_555 B DA 5 B DA 5 8 1_555 1 P 1