data_ABT # _chem_comp.id ABT _chem_comp.name ;3'-AZIDO-3'-DEOXY-THYMIDINE-5'-ALPHA BORANO TRIPHOSPHATE ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 B N5 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-09-10 _chem_comp.pdbx_modified_date 2012-01-05 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 503.001 _chem_comp.one_letter_code N _chem_comp.three_letter_code ABT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1MN7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal ABT PG PG P 0 1 N N N 28.349 39.216 6.032 -6.425 -1.519 0.727 PG ABT 1 ABT O1G O1G O 0 1 N N N 27.652 39.931 7.142 -7.549 -0.754 0.143 O1G ABT 2 ABT O2G O2G O 0 1 N N N 29.063 40.030 5.018 -6.778 -1.917 2.247 O2G ABT 3 ABT O3G O3G O 0 1 N N N 27.420 38.151 5.552 -6.182 -2.858 -0.135 O3G ABT 4 ABT O3B O3B O 0 1 N N N 29.497 38.382 6.757 -5.092 -0.617 0.704 O3B ABT 5 ABT PB PB P 0 1 N N S 29.643 37.956 8.283 -4.452 0.406 -0.362 PB ABT 6 ABT O1B O1B O 0 1 N N N 28.294 38.043 8.914 -4.625 -0.134 -1.729 O1B ABT 7 ABT O2B O2B O 0 1 N N N 30.398 36.683 8.341 -5.194 1.831 -0.250 O2B ABT 8 ABT O3A O3A O 0 1 N N N 30.546 39.091 8.941 -2.883 0.592 -0.052 O3A ABT 9 ABT PA PA P 0 1 N N N 30.102 40.463 9.620 -1.644 1.200 -0.881 PA ABT 10 ABT B1A B1A B 0 1 N N N 30.627 40.466 11.007 -1.939 2.758 -1.230 B1A ABT 11 ABT O2A O2A O 0 1 N N N 28.640 40.660 9.391 -1.454 0.371 -2.248 O2A ABT 12 ABT "O5'" O5* O 0 1 N N N 30.910 41.530 8.747 -0.303 1.093 0.003 "O5'" ABT 13 ABT "C5'" C5* C 0 1 N N N 30.330 42.105 7.572 0.892 1.812 -0.306 "C5'" ABT 14 ABT "C4'" C4* C 0 1 N N S 31.397 42.732 6.689 1.968 1.483 0.730 "C4'" ABT 15 ABT "O4'" O4* O 0 1 N N N 32.030 43.844 7.374 2.368 0.100 0.626 "O4'" ABT 16 ABT "C1'" C1* C 0 1 N N R 33.391 43.944 6.978 3.669 -0.008 1.227 "C1'" ABT 17 ABT N1 N1 N 0 1 N N N 34.235 43.914 8.191 4.463 -1.016 0.521 N1 ABT 18 ABT C6 C6 C 0 1 N N N 33.789 43.255 9.314 5.042 -2.037 1.224 C6 ABT 19 ABT C2 C2 C 0 1 N N N 35.465 44.552 8.176 4.611 -0.933 -0.814 C2 ABT 20 ABT O2 O2 O 0 1 N N N 35.906 45.152 7.210 4.083 -0.020 -1.419 O2 ABT 21 ABT N3 N3 N 0 1 N N N 36.164 44.465 9.352 5.335 -1.846 -1.488 N3 ABT 22 ABT C4 C4 C 0 1 N N N 35.773 43.825 10.510 5.926 -2.864 -0.831 C4 ABT 23 ABT O4 O4 O 0 1 N N N 36.507 43.840 11.491 6.581 -3.690 -1.441 O4 ABT 24 ABT C5 C5 C 0 1 N N N 34.484 43.177 10.454 5.774 -2.967 0.573 C5 ABT 25 ABT C5A C5A C 0 1 N N N 33.984 42.450 11.663 6.420 -4.098 1.330 C5A ABT 26 ABT "C2'" C2* C 0 1 N N N 33.686 42.811 5.989 4.346 1.371 1.105 "C2'" ABT 27 ABT "C3'" C3* C 0 1 N N S 32.543 41.832 6.256 3.274 2.260 0.428 "C3'" ABT 28 ABT "N3'" N3* N 0 1 N N N 32.363 40.473 5.592 3.242 3.594 1.034 "N3'" ABT 29 ABT "N4'" N4* N 1 1 N N N 32.836 39.427 6.040 4.077 4.320 0.840 "N4'" ABT 30 ABT "N5'" N5* N -1 1 N N N 33.187 38.383 6.288 4.913 5.046 0.645 "N5'" ABT 31 ABT HOG2 2HOG H 0 0 N N N 29.507 39.575 4.312 -7.572 -2.462 2.336 HOG2 ABT 32 ABT HOG3 3HOG H 0 0 N N N 27.864 37.696 4.846 -5.458 -3.409 0.191 HOG3 ABT 33 ABT HOB2 2HOB H 0 0 N N N 30.485 36.429 9.252 -5.122 2.245 0.621 HOB2 ABT 34 ABT HBA HBA H 0 1 N N N 30.263 41.515 11.461 -2.152 3.881 -1.482 HBA ABT 35 ABT HOA2 2HOA H 0 0 N N N 28.375 41.478 9.796 -1.274 -0.570 -2.115 HOA2 ABT 36 ABT "H5'1" 1H5* H 0 0 N N N 29.525 42.834 7.825 1.243 1.525 -1.298 "H5'1" ABT 37 ABT "H5'2" 2H5* H 0 0 N N N 29.716 41.363 7.011 0.687 2.883 -0.289 "H5'2" ABT 38 ABT "H4'" H4* H 0 1 N N N 30.818 43.015 5.779 1.611 1.705 1.736 "H4'" ABT 39 ABT "H1'" H1* H 0 1 N N N 33.615 44.902 6.454 3.571 -0.283 2.278 "H1'" ABT 40 ABT H6 H6 H 0 1 N N N 32.806 42.755 9.299 4.915 -2.099 2.295 H6 ABT 41 ABT HN3 HN3 H 0 1 N N N 37.074 44.926 9.367 5.431 -1.770 -2.450 HN3 ABT 42 ABT H51 1H5 H 0 1 N N N 33.739 41.409 11.349 5.732 -4.942 1.380 H51 ABT 43 ABT H52 2H5 H 0 1 N N N 34.563 42.385 12.613 7.333 -4.403 0.818 H52 ABT 44 ABT H53 3H5 H 0 1 N N N 32.980 42.866 11.912 6.663 -3.767 2.340 H53 ABT 45 ABT "H2'1" 1H2* H 0 0 N N N 34.708 42.372 6.071 4.597 1.762 2.091 "H2'1" ABT 46 ABT "H2'2" 2H2* H 0 0 N N N 33.790 43.132 4.926 5.237 1.305 0.481 "H2'2" ABT 47 ABT "H3'" H3* H 0 1 N N N 32.827 41.053 7.002 3.447 2.327 -0.647 "H3'" ABT 48 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ABT PG O1G DOUB N N 1 ABT PG O2G SING N N 2 ABT PG O3G SING N N 3 ABT PG O3B SING N N 4 ABT O2G HOG2 SING N N 5 ABT O3G HOG3 SING N N 6 ABT O3B PB SING N N 7 ABT PB O1B DOUB N N 8 ABT PB O2B SING N N 9 ABT PB O3A SING N N 10 ABT O2B HOB2 SING N N 11 ABT O3A PA SING N N 12 ABT PA B1A DOUB N N 13 ABT PA O2A SING N N 14 ABT PA "O5'" SING N N 15 ABT B1A HBA SING N N 16 ABT O2A HOA2 SING N N 17 ABT "O5'" "C5'" SING N N 18 ABT "C5'" "C4'" SING N N 19 ABT "C5'" "H5'1" SING N N 20 ABT "C5'" "H5'2" SING N N 21 ABT "C4'" "O4'" SING N N 22 ABT "C4'" "C3'" SING N N 23 ABT "C4'" "H4'" SING N N 24 ABT "O4'" "C1'" SING N N 25 ABT "C1'" N1 SING N N 26 ABT "C1'" "C2'" SING N N 27 ABT "C1'" "H1'" SING N N 28 ABT N1 C6 SING N N 29 ABT N1 C2 SING N N 30 ABT C6 C5 DOUB N N 31 ABT C6 H6 SING N N 32 ABT C2 O2 DOUB N N 33 ABT C2 N3 SING N N 34 ABT N3 C4 SING N N 35 ABT N3 HN3 SING N N 36 ABT C4 O4 DOUB N N 37 ABT C4 C5 SING N N 38 ABT C5 C5A SING N N 39 ABT C5A H51 SING N N 40 ABT C5A H52 SING N N 41 ABT C5A H53 SING N N 42 ABT "C2'" "C3'" SING N N 43 ABT "C2'" "H2'1" SING N N 44 ABT "C2'" "H2'2" SING N N 45 ABT "C3'" "N3'" SING N N 46 ABT "C3'" "H3'" SING N N 47 ABT "N3'" "N4'" DOUB N N 48 ABT "N4'" "N5'" DOUB N N 49 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor ABT SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OP(=B)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2\N=[N+]=[N-]" ABT InChI InChI 1.03 "InChI=1S/C10H17BN5O12P3/c1-5-3-16(10(18)13-9(5)17)8-2-6(14-15-12)7(26-8)4-25-29(11,19)27-31(23,24)28-30(20,21)22/h3,6-8,11,19H,2,4H2,1H3,(H,23,24)(H,13,17,18)(H2,20,21,22)/t6-,7+,8+,29+/m0/s1" ABT InChIKey InChI 1.03 YRFDNFJEDDBNDW-NYNRLPRQSA-N ABT SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@](O)(=B)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" ABT SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(=B)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" ABT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "B=P(O)(OC[C@@H]1[C@H](C[C@@H](O1)N2C=C(C(=O)NC2=O)C)N=[N+]=[N-])O[P@](=O)(O)OP(=O)(O)O" ABT SMILES "OpenEye OEToolkits" 1.7.5 "B=P(O)(OCC1C(CC(O1)N2C=C(C(=O)NC2=O)C)N=[N+]=[N-])OP(=O)(O)OP(=O)(O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier ABT "SYSTEMATIC NAME" ACDLabs 10.04 "3'-azido-5'-O-[(1E,3S)-1-boranylidene-1,3,5,5-tetrahydroxy-3,5-dioxido-1lambda~5~-triphosphoxanyl]-3'-deoxythymidine" ABT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy-boranylidene-hydroxy-phosphoranyl] phosphono hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ABT "Create component" 2002-09-10 RCSB ABT "Modify descriptor" 2011-06-04 RCSB ABT "Modify descriptor" 2012-01-05 RCSB ABT "Modify coordinates" 2012-01-05 RCSB #