data_AZD # _chem_comp.id AZD _chem_comp.name "3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 427.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AZD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag Y _chem_comp.pdbx_model_coordinates_db_code 1LWX _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 AZD PA PA P 0 1 N N S 49.464 2.366 9.093 -3.098 -0.213 -0.139 PA AZD 1 AZD O1A O1A O 0 1 N N N 48.175 1.901 9.636 -2.807 0.457 1.148 O1A AZD 2 AZD O2A O2A O 0 1 N N N 49.695 2.417 7.638 -3.799 -1.635 0.142 O2A AZD 3 AZD O3A O3A O 0 1 N N N 49.826 3.852 9.689 -4.088 0.710 -1.012 O3A AZD 4 AZD PB PB P 0 1 N N N 49.011 5.020 10.486 -5.165 1.333 0.010 PB AZD 5 AZD O1B O1B O 0 1 N N N 47.580 4.771 10.331 -5.934 2.556 -0.701 O1B AZD 6 AZD O2B O2B O 0 1 N N N 49.310 6.278 9.770 -6.229 0.199 0.425 O2B AZD 7 AZD O3B O3B O 0 1 N N N 49.347 4.858 11.936 -4.470 1.824 1.220 O3B AZD 8 AZD "O5'" O5* O 0 1 N N N 50.550 1.426 9.800 -1.725 -0.442 -0.948 "O5'" AZD 9 AZD "C5'" C5* C 0 1 N N N 50.239 1.142 11.225 -0.849 -1.163 -0.079 "C5'" AZD 10 AZD "C4'" C4* C 0 1 N N S 51.437 1.182 12.176 0.481 -1.415 -0.791 "C4'" AZD 11 AZD "O4'" O4* O 0 1 N N N 52.265 0.465 11.266 1.228 -0.185 -0.933 "O4'" AZD 12 AZD "C3'" C3* C 0 1 N N S 52.134 2.532 12.433 1.406 -2.303 0.080 "C3'" AZD 13 AZD "N3'" N3* N 0 1 N N N 52.484 2.804 13.889 1.129 -3.724 -0.144 "N3'" AZD 14 AZD "N4'" N4* N 1 1 N N N 51.749 3.648 14.396 1.725 -4.506 0.402 "N4'" AZD 15 AZD "N5'" N5* N -1 1 N N N 50.937 4.304 14.766 2.320 -5.287 0.948 "N5'" AZD 16 AZD "C2'" C2* C 0 1 N N N 53.295 2.578 11.466 2.811 -1.924 -0.449 "C2'" AZD 17 AZD "C1'" C1* C 0 1 N N R 53.526 1.100 11.053 2.605 -0.552 -1.119 "C1'" AZD 18 AZD N1 N1 N 0 1 N N N 54.005 0.716 9.642 3.475 0.445 -0.490 N1 AZD 19 AZD C2 C2 C 0 1 N N N 55.371 0.391 9.448 3.288 0.774 0.801 C2 AZD 20 AZD O2 O2 O 0 1 N N N 56.167 0.131 10.347 2.397 0.239 1.432 O2 AZD 21 AZD N3 N3 N 0 1 N N N 55.836 0.396 8.149 4.073 1.686 1.404 N3 AZD 22 AZD C4 C4 C 0 1 N N N 55.080 0.680 7.065 5.068 2.284 0.719 C4 AZD 23 AZD O4 O4 O 0 1 N N N 55.615 0.702 5.992 5.779 3.110 1.263 O4 AZD 24 AZD C5 C5 C 0 1 N N N 53.722 0.964 7.297 5.273 1.951 -0.642 C5 AZD 25 AZD C5A C5A C 0 1 N N N 52.785 1.108 6.112 6.376 2.609 -1.431 C5A AZD 26 AZD C6 C6 C 0 1 N N N 53.237 0.985 8.542 4.471 1.033 -1.222 C6 AZD 27 AZD HOA2 2HOA H 0 0 N N N 50.525 2.716 7.288 -3.972 -2.037 -0.720 HOA2 AZD 28 AZD HOB2 2HOB H 0 0 N N N 48.835 6.957 10.233 -6.659 -0.094 -0.391 HOB2 AZD 29 AZD HOB3 3HOB H 0 0 N N N 48.872 5.537 12.399 ? ? ? HOB3 AZD 30 AZD "H5'1" 1H5* H 0 0 N N N 49.439 1.829 11.587 -1.305 -2.117 0.187 "H5'1" AZD 31 AZD "H5'2" 2H5* H 0 0 N N N 49.711 0.163 11.314 -0.673 -0.580 0.825 "H5'2" AZD 32 AZD "H4'" H4* H 0 1 N N N 51.198 0.853 13.214 0.313 -1.875 -1.765 "H4'" AZD 33 AZD "H3'" H3* H 0 1 N N N 51.438 3.382 12.241 1.307 -2.051 1.135 "H3'" AZD 34 AZD "H2'1" 1H2* H 0 0 N N N 53.140 3.269 10.605 3.155 -2.658 -1.179 "H2'1" AZD 35 AZD "H2'2" 2H2* H 0 0 N N N 54.202 3.082 11.872 3.520 -1.844 0.375 "H2'2" AZD 36 AZD "H1'" H1* H 0 1 N N N 54.404 0.785 11.664 2.830 -0.622 -2.183 "H1'" AZD 37 AZD HN3 HN3 H 0 1 N N N 56.816 0.172 7.976 3.924 1.911 2.335 HN3 AZD 38 AZD H51 1H5 H 0 1 N N N 51.708 1.333 6.295 5.993 3.513 -1.906 H51 AZD 39 AZD H52 2H5 H 0 1 N N N 53.198 1.877 5.419 7.196 2.869 -0.762 H52 AZD 40 AZD H53 3H5 H 0 1 N N N 52.856 0.189 5.484 6.735 1.921 -2.196 H53 AZD 41 AZD H6 H6 H 0 1 N N N 52.169 1.232 8.665 4.615 0.763 -2.257 H6 AZD 42 # 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 AZD PA O1A DOUB N N 1 AZD PA O2A SING N N 2 AZD PA O3A SING N N 3 AZD PA "O5'" SING N N 4 AZD O2A HOA2 SING N N 5 AZD O3A PB SING N N 6 AZD PB O1B DOUB N N 7 AZD PB O2B SING N N 8 AZD PB O3B SING N N 9 AZD O2B HOB2 SING N N 10 AZD O3B HOB3 SING N N 11 AZD "O5'" "C5'" SING N N 12 AZD "C5'" "C4'" SING N N 13 AZD "C5'" "H5'1" SING N N 14 AZD "C5'" "H5'2" SING N N 15 AZD "C4'" "O4'" SING N N 16 AZD "C4'" "C3'" SING N N 17 AZD "C4'" "H4'" SING N N 18 AZD "O4'" "C1'" SING N N 19 AZD "C3'" "N3'" SING N N 20 AZD "C3'" "C2'" SING N N 21 AZD "C3'" "H3'" SING N N 22 AZD "N3'" "N4'" DOUB N N 23 AZD "N4'" "N5'" DOUB N N 24 AZD "C2'" "C1'" SING N N 25 AZD "C2'" "H2'1" SING N N 26 AZD "C2'" "H2'2" SING N N 27 AZD "C1'" N1 SING N N 28 AZD "C1'" "H1'" SING N N 29 AZD N1 C2 SING N N 30 AZD N1 C6 SING N N 31 AZD C2 O2 DOUB N N 32 AZD C2 N3 SING N N 33 AZD N3 C4 SING N N 34 AZD N3 HN3 SING N N 35 AZD C4 O4 DOUB N N 36 AZD C4 C5 SING N N 37 AZD C5 C5A SING N N 38 AZD C5 C6 DOUB N N 39 AZD C5A H51 SING N N 40 AZD C5A H52 SING N N 41 AZD C5A H53 SING N N 42 AZD C6 H6 SING N N 43 # 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 AZD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2/N=[N+]=[N-]" AZD SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" AZD SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" AZD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)N=[N+]=[N-]" AZD SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)N=[N+]=[N-]" AZD InChI InChI 1.03 "InChI=1S/C10H15N5O10P2/c1-5-3-15(10(17)12-9(5)16)8-2-6(13-14-11)7(24-8)4-23-27(21,22)25-26(18,19)20/h3,6-8H,2,4H2,1H3,(H,21,22)(H,12,16,17)(H2,18,19,20)/t6-,7+,8+/m0/s1" AZD InChIKey InChI 1.03 QOYVAFWJURKBJG-XLPZGREQSA-N # 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 AZD "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-azido-3'-deoxythymidine 5'-(trihydrogen diphosphate) ; AZD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl 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 AZD "Create component" 1999-07-08 RCSB AZD "Modify descriptor" 2011-06-04 RCSB #