data_6AZ # _chem_comp.id 6AZ _chem_comp.name ;6-azidouridine 5'-(dihydrogen phosphate) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 N5 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 6-AZIDO-UMP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-02-16 _chem_comp.pdbx_modified_date 2024-09-27 _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 365.193 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6AZ _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 2ZZ6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 6AZ O3P O3P O 0 1 N N N N N N 24.527 -17.212 7.698 -5.719 0.106 0.030 O3P 6AZ 1 6AZ P P P 0 1 N N N N N N 24.409 -16.297 8.898 -4.685 -0.835 0.519 P 6AZ 2 6AZ O1P O1P O 0 1 N N N N N N 25.712 -15.508 9.122 -5.106 -1.386 1.972 O1P 6AZ 3 6AZ O2P O2P O 0 1 N N N N N N 23.240 -15.320 8.753 -4.556 -2.069 -0.506 O2P 6AZ 4 6AZ "O5'" "O5'" O 0 1 N N N N N N 24.084 -17.192 10.162 -3.271 -0.072 0.623 "O5'" 6AZ 5 6AZ "C5'" "C5'" C 0 1 N N N N N N 25.137 -17.654 11.023 -2.678 0.620 -0.478 "C5'" 6AZ 6 6AZ "C4'" "C4'" C 0 1 N N R N N N 24.414 -18.277 12.219 -1.344 1.228 -0.038 "C4'" 6AZ 7 6AZ "C3'" "C3'" C 0 1 N N S N N N 23.725 -17.331 13.167 -0.744 2.086 -1.174 "C3'" 6AZ 8 6AZ "O3'" "O3'" O 0 1 N N N N N N 22.635 -17.988 13.809 -1.031 3.470 -0.962 "O3'" 6AZ 9 6AZ "C2'" "C2'" C 0 1 N N R N N N 24.835 -16.969 14.171 0.776 1.827 -1.077 "C2'" 6AZ 10 6AZ "O2'" "O2'" O 0 1 N N N N N N 24.321 -16.452 15.355 1.474 3.043 -0.802 "O2'" 6AZ 11 6AZ "O4'" "O4'" O 0 1 N N N N N N 25.373 -18.965 13.084 -0.369 0.188 0.193 "O4'" 6AZ 12 6AZ "C1'" "C1'" C 0 1 N N R N N N 25.521 -18.267 14.363 0.914 0.844 0.106 "C1'" 6AZ 13 6AZ N1 N1 N 0 1 N N N N N N 26.982 -18.314 14.721 1.970 -0.135 -0.165 N1 6AZ 14 6AZ C6 C6 C 0 1 N N N N N N 27.447 -18.991 15.916 3.113 -0.154 0.622 C6 6AZ 15 6AZ C5 C5 C 0 1 N N N N N N 28.777 -19.208 16.081 4.115 -1.109 0.338 C5 6AZ 16 6AZ C4 C4 C 0 1 N N N N N N 29.721 -18.806 15.109 3.904 -2.007 -0.741 C4 6AZ 17 6AZ O4 O4 O 0 1 N N N N N N 30.928 -19.011 15.124 4.744 -2.844 -1.016 O4 6AZ 18 6AZ N3 N3 N 0 1 N N N N N N 29.205 -18.102 13.994 2.768 -1.926 -1.459 N3 6AZ 19 6AZ C2 C2 C 0 1 N N N N N N 27.906 -17.816 13.755 1.824 -1.014 -1.172 C2 6AZ 20 6AZ O2 O2 O 0 1 N N N N N N 27.532 -17.207 12.800 0.811 -0.981 -1.844 O2 6AZ 21 6AZ N7 N7 N 0 1 N N N N N N 26.478 -19.093 16.944 3.261 0.699 1.610 N7 6AZ 22 6AZ "H5'" "H5'" H 0 1 N N N N N N 25.770 -18.395 10.513 -2.506 -0.079 -1.296 "H5'" 6AZ 23 6AZ "H5'A" "H5'A" H 0 0 N N N N N N 25.813 -16.840 11.325 -3.347 1.413 -0.812 "H5'A" 6AZ 24 6AZ "H4'" "H4'" H 0 1 N N N N N N 23.662 -18.911 11.727 -1.480 1.830 0.860 "H4'" 6AZ 25 6AZ "H3'" "H3'" H 0 1 N N N N N N 23.296 -16.445 12.676 -1.128 1.761 -2.142 "H3'" 6AZ 26 6AZ "HO3'" "HO3'" H 0 0 N N N N N N 22.847 -18.134 14.723 -0.678 4.054 -1.647 "HO3'" 6AZ 27 6AZ "H2'" "H2'" H 0 1 N N N N N N 25.509 -16.174 13.817 1.146 1.375 -1.997 "H2'" 6AZ 28 6AZ "HO2'" "HO2'" H 0 0 N N N N N N 24.204 -17.155 15.983 1.371 3.720 -1.486 "HO2'" 6AZ 29 6AZ "H1'" "H1'" H 0 1 N N N N N N 25.046 -18.698 15.257 1.127 1.386 1.027 "H1'" 6AZ 30 6AZ H5 H5 H 0 1 N N N N N N 29.122 -19.700 16.978 5.019 -1.155 0.928 H5 6AZ 31 6AZ HN3 HN3 H 0 1 N N N N N N 29.868 -17.785 13.316 2.627 -2.540 -2.196 HN3 6AZ 32 6AZ N8 N8 N 1 1 N N N N N N 26.157 -20.291 16.944 4.192 0.673 2.240 N8 6AZ 33 6AZ N9 N9 N -1 1 N N N N N N 25.836 -21.489 16.944 5.122 0.648 2.870 N9 6AZ 34 6AZ H11 H11 H 0 1 N N N N N N 26.132 -15.345 8.286 -5.950 -1.857 1.985 H11 6AZ 35 6AZ H12 H12 H 0 1 N N N N N N 22.888 -15.118 9.612 -3.895 -2.727 -0.248 H12 6AZ 36 # 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 6AZ O3P P DOUB N N 1 6AZ P O1P SING N N 2 6AZ P O2P SING N N 3 6AZ P "O5'" SING N N 4 6AZ "O5'" "C5'" SING N N 5 6AZ "C5'" "C4'" SING N N 6 6AZ "C5'" "H5'" SING N N 7 6AZ "C5'" "H5'A" SING N N 8 6AZ "C4'" "C3'" SING N N 9 6AZ "C4'" "O4'" SING N N 10 6AZ "C4'" "H4'" SING N N 11 6AZ "C3'" "O3'" SING N N 12 6AZ "C3'" "C2'" SING N N 13 6AZ "C3'" "H3'" SING N N 14 6AZ "O3'" "HO3'" SING N N 15 6AZ "C2'" "O2'" SING N N 16 6AZ "C2'" "C1'" SING N N 17 6AZ "C2'" "H2'" SING N N 18 6AZ "O2'" "HO2'" SING N N 19 6AZ "O4'" "C1'" SING N N 20 6AZ "C1'" N1 SING N N 21 6AZ "C1'" "H1'" SING N N 22 6AZ N1 C6 SING N N 23 6AZ N1 C2 SING N N 24 6AZ C6 C5 DOUB N N 25 6AZ C6 N7 SING N N 26 6AZ C5 C4 SING N N 27 6AZ C5 H5 SING N N 28 6AZ C4 O4 DOUB N N 29 6AZ C4 N3 SING N N 30 6AZ N3 C2 SING N N 31 6AZ N3 HN3 SING N N 32 6AZ C2 O2 DOUB N N 33 6AZ N7 N8 DOUB N N 34 6AZ N8 N9 DOUB N N 35 6AZ O1P H11 SING N N 36 6AZ O2P H12 SING N N 37 # 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 6AZ SMILES ACDLabs 10.04 "[N-]=[N+]=N\C=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O" 6AZ SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2N=[N+]=[N-]" 6AZ SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2N=[N+]=[N-]" 6AZ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N=[N+]=[N-]" 6AZ SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)N=[N+]=[N-]" 6AZ InChI InChI 1.03 "InChI=1S/C9H12N5O9P/c10-13-12-4-1-5(15)11-9(18)14(4)8-7(17)6(16)3(23-8)2-22-24(19,20)21/h1,3,6-8,16-17H,2H2,(H,11,15,18)(H2,19,20,21)/t3-,6-,7-,8-/m1/s1" 6AZ InChIKey InChI 1.03 GBBWDDPNGBRVEX-YXZULKJRSA-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 6AZ "SYSTEMATIC NAME" ACDLabs 10.04 ;6-azidouridine 5'-(dihydrogen phosphate) ; 6AZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-azido-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen 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 6AZ "Create component" 2009-02-16 PDBJ 6AZ "Modify descriptor" 2011-06-04 RCSB 6AZ "Modify synonyms" 2020-06-05 PDBE 6AZ "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 6AZ _pdbx_chem_comp_synonyms.name 6-AZIDO-UMP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 6AZ _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C6 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #