1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chung, W.J. Heddi, B. Tera, M. Iida, K. Nagasawa, K. Phan, A.T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-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 C32 H34 N10 O8 686.675 (12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione Telomestatin derivative non-polymer US J.Am.Chem.Soc. JACSAT 0004 0002-7863 135 13495 13501 10.1021/ja405843r 23909929 Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative. 2013 10.2210/pdb2mb3/pdb pdb_00002mb3 7591.883 DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') 1 syn polymer 686.675 (12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione 1 syn non-polymer no no (DT)(DT)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DA) TTGGGTTAGGGTTAGGGTTAGGGA A polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n chem_comp database_2 entity pdbx_database_status pdbx_entity_nonpoly pdbx_nmr_software struct_site repository Initial release Database references Data collection Database references Derived calculations Other Structure summary 1 0 2013-08-28 1 1 2013-09-25 1 2 2023-06-14 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_database_status.status_code_nmr_data _pdbx_entity_nonpoly.name _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BMRB Y RCSB 2013-07-24 REL REL REL REL L2H (12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione 579 279 structures with the lowest energy 100 10 2D 1H-1H TOCSY 2D 1H-1H TOCSY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-13C HSQC aromatic 2D 1H-13C HSQC aromatic 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 1D JRHMBC 2D 1H-31P HSQC 0.2-2 mM 0.2-2 mM 0.2-2 mM 0.2-2 mM 0.2 mM [U-99% 13C; U-99% 15N] 0.2 mM 0.2 mM [U-99% 13C; U-99% 15N] 0.2 mM 0.2-1 mM [U-4% 13C] 0.2-1 mM 90 7 ambient atm 310 K 90 7 298 K 40 7 298 K DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics 1 lowest energy 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O 90% H2O/10% D2O 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O 100% D2O 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O 90% H2O/10% D2O 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O 100% D2O 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O 90% H2O/10% D2O Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman refinement Amber Goddard data analysis Sparky Goddard chemical shift assignment Sparky Goddard peak picking Sparky Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore structure solution X-PLOR NIH Bruker Biospin collection TopSpin 600 Bruker AMX Bruker AMX 700 Bruker AMX Bruker AMX 400 Bruker AMX Bruker AMX L2H 25 2 L2H L2H 25 A DT 1 n 1 DT 1 A DT 2 n 2 DT 2 A DG 3 n 3 DG 3 A DG 4 n 4 DG 4 A DG 5 n 5 DG 5 A DT 6 n 6 DT 6 A DT 7 n 7 DT 7 A DA 8 n 8 DA 8 A DG 9 n 9 DG 9 A DG 10 n 10 DG 10 A DG 11 n 11 DG 11 A DT 12 n 12 DT 12 A DT 13 n 13 DT 13 A DA 14 n 14 DA 14 A DG 15 n 15 DG 15 A DG 16 n 16 DG 16 A DG 17 n 17 DG 17 A DT 18 n 18 DT 18 A DT 19 n 19 DT 19 A DA 20 n 20 DA 20 A DG 21 n 21 DG 21 A DG 22 n 22 DG 22 A DG 23 n 23 DG 23 A DA 24 n 24 DA 24 A author_defined_assembly 1 monomeric 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 A HO5' OP1 DT DT 1 2 1.54 1 -3.61 0.60 122.90 119.29 A A A C6 C5 C7 DT DT DT 2 2 2 N 1 -3.63 0.60 122.90 119.27 A A A C6 C5 C7 DT DT DT 6 6 6 N 2 -3.83 0.60 122.90 119.07 A A A C6 C5 C7 DT DT DT 6 6 6 N 3 -3.69 0.60 122.90 119.21 A A A C6 C5 C7 DT DT DT 6 6 6 N 4 -3.64 0.60 122.90 119.26 A A A C6 C5 C7 DT DT DT 1 1 1 N 6 -3.63 0.60 122.90 119.27 A A A C6 C5 C7 DT DT DT 6 6 6 N 8 -3.73 0.60 122.90 119.17 A A A C6 C5 C7 DT DT DT 6 6 6 N 9 -3.66 0.60 122.90 119.24 A A A C6 C5 C7 DT DT DT 1 1 1 N 10 -3.71 0.60 122.90 119.19 A A A C6 C5 C7 DT DT DT 6 6 6 N 10 -3.64 0.60 122.90 119.26 A A A C6 C5 C7 DT DT DT 18 18 18 N lowest energy, model1 Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative 1 N N 2 N N hydrog TYPE_6_PAIR A DG 3 A N7 DG 3 1_555 A DG 9 A N2 DG 9 1_555 hydrog TYPE_6_PAIR A DG 3 A O6 DG 3 1_555 A DG 9 A N1 DG 9 1_555 hydrog TYPE_6_PAIR A DG 3 A N1 DG 3 1_555 A DG 21 A O6 DG 21 1_555 hydrog TYPE_6_PAIR A DG 3 A N2 DG 3 1_555 A DG 21 A N7 DG 21 1_555 hydrog TYPE_6_PAIR A DG 4 A N1 DG 4 1_555 A DG 10 A O6 DG 10 1_555 hydrog TYPE_6_PAIR A DG 4 A N2 DG 4 1_555 A DG 10 A N7 DG 10 1_555 hydrog TYPE_6_PAIR A DG 4 A N7 DG 4 1_555 A DG 22 A N2 DG 22 1_555 hydrog TYPE_6_PAIR A DG 4 A O6 DG 4 1_555 A DG 22 A N1 DG 22 1_555 hydrog TYPE_6_PAIR A DG 5 A N1 DG 5 1_555 A DG 11 A O6 DG 11 1_555 hydrog TYPE_6_PAIR A DG 5 A N2 DG 5 1_555 A DG 11 A N7 DG 11 1_555 hydrog TYPE_27_PAIR A DG 5 A N1 DG 5 1_555 A DT 13 A O4 DT 13 1_555 hydrog TYPE_27_PAIR A DG 5 A O6 DG 5 1_555 A DT 13 A N3 DT 13 1_555 hydrog TYPE_6_PAIR A DG 5 A N7 DG 5 1_555 A DG 23 A N2 DG 23 1_555 hydrog TYPE_6_PAIR A DG 5 A O6 DG 5 1_555 A DG 23 A N1 DG 23 1_555 hydrog TYPE_6_PAIR A DG 9 A N7 DG 9 1_555 A DG 17 A N2 DG 17 1_555 hydrog TYPE_6_PAIR A DG 9 A O6 DG 9 1_555 A DG 17 A N1 DG 17 1_555 hydrog TYPE_6_PAIR A DG 10 A N1 DG 10 1_555 A DG 16 A O6 DG 16 1_555 hydrog TYPE_6_PAIR A DG 10 A N2 DG 10 1_555 A DG 16 A N7 DG 16 1_555 hydrog TYPE_6_PAIR A DG 11 A N1 DG 11 1_555 A DG 15 A O6 DG 15 1_555 hydrog TYPE_6_PAIR A DG 11 A N2 DG 11 1_555 A DG 15 A N7 DG 15 1_555 hydrog DT-DG MISPAIR A DT 13 A O2 DT 13 1_555 A DG 15 A N1 DG 15 1_555 hydrog REVERSED WATSON-CRICK A DT 13 A N3 DT 13 1_555 A DA 24 A N1 DA 24 1_555 hydrog REVERSED WATSON-CRICK A DT 13 A O2 DT 13 1_555 A DA 24 A N6 DA 24 1_555 hydrog TYPE_6_PAIR A DG 15 A N1 DG 15 1_555 A DG 23 A O6 DG 23 1_555 hydrog TYPE_6_PAIR A DG 15 A N2 DG 15 1_555 A DG 23 A N7 DG 23 1_555 hydrog TYPE_6_PAIR A DG 16 A N1 DG 16 1_555 A DG 22 A O6 DG 22 1_555 hydrog TYPE_6_PAIR A DG 16 A N2 DG 16 1_555 A DG 22 A N7 DG 22 1_555 hydrog TYPE_6_PAIR A DG 17 A N7 DG 17 1_555 A DG 21 A N2 DG 21 1_555 hydrog TYPE_6_PAIR A DG 17 A O6 DG 17 1_555 A DG 21 A N1 DG 21 1_555 DNA/DNA INHIBITOR intramolecular G-quadruplex, human telomere, anticancer targets, macrocyclic hexaoxazole, telomestatin derivative, DNA-DNA INHIBITOR complex 2MB3 PDB 1 2MB3 TTGGGTTAGGGTTAGGGTTAGGGA 1 24 2MB3 1 24 2MB3 A 1 1 24 BINDING SITE FOR RESIDUE L2H A 25 A L2H 25 Software 9 A DT 2 A DT 2 9 1_555 A DG 3 A DG 3 9 1_555 A DA 8 A DA 8 9 1_555 A DG 9 A DG 9 9 1_555 A DG 17 A DG 17 9 1_555 A DT 18 A DT 18 9 1_555 A DT 19 A DT 19 9 1_555 A DA 20 A DA 20 9 1_555 A DG 21 A DG 21 9 1_555