data_EDV # _chem_comp.id EDV _chem_comp.name "1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H14 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2'S)-2'-DEOXY-2'-METHYL-5-ETHYNYLURIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-02-12 _chem_comp.pdbx_modified_date 2021-03-01 _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 266.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EDV _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 4OQX _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 EDV O01 O01 O 0 1 N N N 51.215 23.252 53.490 -3.720 -2.443 1.225 O01 EDV 1 EDV C03 C03 C 0 1 N N N 50.233 24.086 52.875 -3.572 -1.658 0.040 C03 EDV 2 EDV C06 C06 C 0 1 N N R 50.172 25.489 53.525 -2.880 -0.338 0.385 C06 EDV 3 EDV O08 O08 O 0 1 N N N 48.882 25.939 53.086 -1.499 -0.571 0.738 O08 EDV 4 EDV C09 C09 C 0 1 N N S 50.118 25.617 55.113 -2.821 0.579 -0.857 C09 EDV 5 EDV O11 O11 O 0 1 N N N 50.420 26.959 55.480 -3.878 1.540 -0.820 O11 EDV 6 EDV C13 C13 C 0 1 N N S 48.660 25.369 55.495 -1.448 1.278 -0.742 C13 EDV 7 EDV C15 C15 C 0 1 N N N 48.395 23.884 55.598 -0.569 0.933 -1.946 C15 EDV 8 EDV C16 C16 C 0 1 N N R 47.992 26.080 54.265 -0.840 0.701 0.555 C16 EDV 9 EDV N18 N18 N 0 1 N N N 46.602 25.674 53.825 0.604 0.509 0.400 N18 EDV 10 EDV C19 C19 C 0 1 N N N 45.512 26.352 54.257 1.433 1.539 0.637 C19 EDV 11 EDV O20 O20 O 0 1 N N N 45.622 27.286 55.049 0.964 2.609 0.975 O20 EDV 12 EDV N21 N21 N 0 1 N N N 44.221 25.998 53.813 2.766 1.421 0.512 N21 EDV 13 EDV C23 C23 C 0 1 N N N 44.043 24.941 52.900 3.314 0.246 0.139 C23 EDV 14 EDV O24 O24 O 0 1 N N N 42.918 24.616 52.504 4.521 0.132 0.024 O24 EDV 15 EDV C25 C25 C 0 1 N N N 45.155 24.259 52.452 2.425 -0.894 -0.126 C25 EDV 16 EDV C26 C26 C 0 1 N N N 46.433 24.614 52.893 1.079 -0.714 0.024 C26 EDV 17 EDV C28 C28 C 0 1 N N N 44.927 23.219 51.555 2.956 -2.165 -0.520 C28 EDV 18 EDV C29 C29 C 0 1 N N N 44.725 22.393 50.839 3.391 -3.206 -0.843 C29 EDV 19 EDV H1 H1 H 0 1 N N N 51.221 22.403 53.064 -4.152 -3.296 1.081 H1 EDV 20 EDV H2 H2 H 0 1 N N N 50.481 24.199 51.809 -2.969 -2.206 -0.684 H2 EDV 21 EDV H3 H3 H 0 1 N N N 49.248 23.606 52.973 -4.554 -1.454 -0.385 H3 EDV 22 EDV H4 H4 H 0 1 N N N 50.981 26.123 53.133 -3.403 0.161 1.201 H4 EDV 23 EDV H5 H5 H 0 1 N N N 50.787 24.881 55.582 -2.876 -0.013 -1.771 H5 EDV 24 EDV H6 H6 H 0 1 N N N 50.390 27.044 56.426 -4.763 1.152 -0.828 H6 EDV 25 EDV H7 H7 H 0 1 N N N 48.400 25.888 56.429 -1.575 2.357 -0.660 H7 EDV 26 EDV H8 H8 H 0 1 N N N 48.903 23.481 56.487 -1.057 1.270 -2.861 H8 EDV 27 EDV H9 H9 H 0 1 N N N 47.312 23.710 55.684 0.396 1.429 -1.845 H9 EDV 28 EDV H10 H10 H 0 1 N N N 48.777 23.380 54.698 -0.420 -0.146 -1.990 H10 EDV 29 EDV H11 H11 H 0 1 N N N 47.948 27.150 54.514 -1.048 1.360 1.398 H11 EDV 30 EDV H12 H12 H 0 1 N N N 43.425 26.502 54.149 3.337 2.185 0.691 H12 EDV 31 EDV H13 H13 H 0 1 N N N 47.296 24.080 52.524 0.396 -1.529 -0.162 H13 EDV 32 EDV H14 H14 H 0 1 N N N 44.532 21.605 50.156 3.781 -4.137 -1.132 H14 EDV 33 # # 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 EDV C29 C28 TRIP N N 1 EDV C28 C25 SING N N 2 EDV C25 C26 DOUB N N 3 EDV C25 C23 SING N N 4 EDV O24 C23 DOUB N N 5 EDV C03 O01 SING N N 6 EDV C03 C06 SING N N 7 EDV C26 N18 SING N N 8 EDV C23 N21 SING N N 9 EDV O08 C06 SING N N 10 EDV O08 C16 SING N N 11 EDV C06 C09 SING N N 12 EDV N21 C19 SING N N 13 EDV N18 C19 SING N N 14 EDV N18 C16 SING N N 15 EDV C19 O20 DOUB N N 16 EDV C16 C13 SING N N 17 EDV C09 O11 SING N N 18 EDV C09 C13 SING N N 19 EDV C13 C15 SING N N 20 EDV O01 H1 SING N N 21 EDV C03 H2 SING N N 22 EDV C03 H3 SING N N 23 EDV C06 H4 SING N N 24 EDV C09 H5 SING N N 25 EDV O11 H6 SING N N 26 EDV C13 H7 SING N N 27 EDV C15 H8 SING N N 28 EDV C15 H9 SING N N 29 EDV C15 H10 SING N N 30 EDV C16 H11 SING N N 31 EDV N21 H12 SING N N 32 EDV C26 H13 SING N N 33 EDV C29 H14 SING N N 34 # # 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 EDV SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2C)CO" EDV InChI InChI 1.03 "InChI=1S/C12H14N2O5/c1-3-7-4-14(12(18)13-10(7)17)11-6(2)9(16)8(5-15)19-11/h1,4,6,8-9,11,15-16H,5H2,2H3,(H,13,17,18)/t6-,8+,9-,11+/m0/s1" EDV InChIKey InChI 1.03 HBALXYGFMJGYHQ-GTQWGBSQSA-N EDV SMILES_CANONICAL CACTVS 3.385 "C[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N2C=C(C#C)C(=O)NC2=O" EDV SMILES CACTVS 3.385 "C[CH]1[CH](O)[CH](CO)O[CH]1N2C=C(C#C)C(=O)NC2=O" EDV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C#C)CO)O" EDV SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(OC1N2C=C(C(=O)NC2=O)C#C)CO)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 EDV "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione" EDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-ethynyl-1-[(2R,3S,4S,5R)-5-(hydroxymethyl)-3-methyl-4-oxidanyl-oxolan-2-yl]pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EDV "Create component" 2014-02-12 RCSB EDV "Modify synonyms" 2014-02-18 RCSB EDV "Initial release" 2014-08-13 RCSB EDV "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EDV _pdbx_chem_comp_synonyms.name "(2'S)-2'-DEOXY-2'-METHYL-5-ETHYNYLURIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##