data_LDC # _chem_comp.id LDC _chem_comp.name "4-AMINO-1-(2-DEOXY-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDIN-2(1H)-ONE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "L-2'-DEOXYCYTIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-10-26 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 227.217 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LDC _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 N _chem_comp.pdbx_model_coordinates_db_code ? _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 LDC O1 O1 O 0 1 N N N 38.728 93.370 92.876 2.997 1.560 -2.050 O1 LDC 1 LDC C2 C2 C 0 1 Y N N 37.572 93.058 92.935 2.460 0.527 -2.454 C2 LDC 2 LDC N3 N3 N 0 1 Y N N 37.251 91.686 92.558 3.220 -0.464 -3.051 N3 LDC 3 LDC C3 C3 C 0 1 Y N N 36.037 91.240 92.599 2.668 -1.566 -3.487 C3 LDC 4 LDC N4 N4 N 0 1 N N N 35.695 89.997 92.252 3.441 -2.539 -4.077 N4 LDC 5 LDC C4 C4 C 0 1 Y N N 34.996 92.227 93.000 1.207 -1.809 -3.364 C4 LDC 6 LDC C5 C5 C 0 1 Y N N 35.385 93.478 93.339 0.494 -0.843 -2.787 C5 LDC 7 LDC N2 N2 N 0 1 Y N N 36.622 93.918 93.289 1.064 0.330 -2.320 N2 LDC 8 LDC C8 C8 C 0 1 N N S 36.947 95.295 93.675 0.213 1.312 -1.713 C8 LDC 9 LDC C9 C9 C 0 1 N N N 37.637 95.375 95.100 -0.005 1.073 -0.228 C9 LDC 10 LDC C10 C10 C 0 1 N N R 37.228 96.723 95.745 -1.391 1.636 -0.017 C10 LDC 11 LDC O3 O3 O 0 1 N N N 38.236 97.743 95.493 -1.286 3.051 0.123 O3 LDC 12 LDC C11 C11 C 0 1 N N S 35.885 96.997 94.968 -2.097 1.303 -1.324 C11 LDC 13 LDC O4 O4 O 0 1 N N N 35.830 96.175 93.779 -1.076 1.280 -2.341 O4 LDC 14 LDC C12 C12 C 0 1 N N N 34.575 96.690 95.740 -2.768 -0.064 -1.304 C12 LDC 15 LDC O5 O5 O 0 1 N N N 33.459 96.943 94.834 -3.405 -0.281 -2.552 O5 LDC 16 LDC HN41 1HN4 H 0 0 N N N 36.487 89.461 91.960 3.312 -3.478 -3.785 HN41 LDC 17 LDC HN42 2HN4 H 0 0 N N N 34.760 89.645 92.281 4.093 -2.260 -4.770 HN42 LDC 18 LDC H4 H4 H 0 1 N N N 33.952 91.950 93.020 0.770 -2.728 -3.731 H4 LDC 19 LDC H5 H5 H 0 1 N N N 34.623 94.165 93.675 -0.579 -0.939 -2.658 H5 LDC 20 LDC H8 H8 H 0 1 N N N 37.608 95.609 92.854 0.655 2.297 -1.899 H8 LDC 21 LDC H91 1H9 H 0 1 N N N 37.301 94.538 95.730 0.771 1.551 0.377 H91 LDC 22 LDC H92 2H9 H 0 1 N N N 38.731 95.311 95.002 -0.004 -0.002 -0.006 H92 LDC 23 LDC H10 H10 H 0 1 N N N 37.123 96.719 96.840 -1.894 1.247 0.871 H10 LDC 24 LDC HO3 HO3 H 0 1 N N N 38.456 98.180 96.307 -0.629 3.358 -0.526 HO3 LDC 25 LDC H11 H11 H 0 1 N N N 35.920 98.079 94.774 -2.831 2.066 -1.603 H11 LDC 26 LDC H121 1H12 H 0 0 N N N 34.497 97.338 96.625 -3.518 -0.106 -0.510 H121 LDC 27 LDC H122 2H12 H 0 0 N N N 34.565 95.644 96.081 -2.025 -0.849 -1.142 H122 LDC 28 LDC HO5 HO5 H 0 1 N N N 32.652 96.998 95.332 -3.001 -1.074 -2.942 HO5 LDC 29 # # 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 LDC O1 C2 DOUB N N 1 LDC C2 N3 SING Y N 2 LDC C2 N2 SING Y N 3 LDC N3 C3 DOUB Y N 4 LDC C3 N4 SING N N 5 LDC C3 C4 SING Y N 6 LDC N4 HN41 SING N N 7 LDC N4 HN42 SING N N 8 LDC C4 C5 DOUB Y N 9 LDC C4 H4 SING N N 10 LDC C5 N2 SING Y N 11 LDC C5 H5 SING N N 12 LDC N2 C8 SING N N 13 LDC C8 O4 SING N N 14 LDC C8 C9 SING N N 15 LDC C8 H8 SING N N 16 LDC C9 C10 SING N N 17 LDC C9 H91 SING N N 18 LDC C9 H92 SING N N 19 LDC C10 C11 SING N N 20 LDC C10 O3 SING N N 21 LDC C10 H10 SING N N 22 LDC O3 HO3 SING N N 23 LDC C11 O4 SING N N 24 LDC C11 C12 SING N N 25 LDC C11 H11 SING N N 26 LDC C12 O5 SING N N 27 LDC C12 H121 SING N N 28 LDC C12 H122 SING N N 29 LDC O5 HO5 SING N N 30 # # 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 LDC SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)CO" LDC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO)O2" LDC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO)O2" LDC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)CO)O" LDC SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)CO)O" LDC InChI InChI 1.03 "InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m1/s1" LDC InChIKey InChI 1.03 CKTSBUTUHBMZGZ-CHKWXVPMSA-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 LDC "SYSTEMATIC NAME" ACDLabs 10.04 "4-amino-1-(2-deoxy-beta-L-erythro-pentofuranosyl)pyrimidin-2(1H)-one" LDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site LDC "Create component" 2006-10-26 RCSB LDC "Modify descriptor" 2011-06-04 RCSB LDC "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id LDC _pdbx_chem_comp_synonyms.name "L-2'-DEOXYCYTIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##