data_DC # _chem_comp.id DC _chem_comp.name "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-01 _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 307.197 _chem_comp.one_letter_code C _chem_comp.three_letter_code DC _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 _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 DC OP3 O3P O 0 1 N Y N N N N 4.521 -6.081 1.748 1.941 -1.055 -4.672 OP3 DC 1 DC P P P 0 1 N N N N N N 5.008 -7.323 0.810 0.987 -0.017 -3.894 P DC 2 DC OP1 O1P O 0 1 N N N N N N 4.362 -8.553 1.260 1.802 1.099 -3.365 OP1 DC 3 DC OP2 O2P O 0 1 N N N N N N 6.422 -7.269 0.587 -0.119 0.560 -4.910 OP2 DC 4 DC "O5'" O5* O 0 1 N N N N N N 4.417 -6.922 -0.639 0.255 -0.772 -2.674 "O5'" DC 5 DC "C5'" C5* C 0 1 N N N N N N 3.027 -6.960 -0.848 -0.571 0.196 -2.027 "C5'" DC 6 DC "C4'" C4* C 0 1 N N R N N N 2.755 -6.252 -2.153 -1.300 -0.459 -0.852 "C4'" DC 7 DC "O4'" O4* O 0 1 N N N N N N 3.079 -4.851 -2.018 -0.363 -0.863 0.171 "O4'" DC 8 DC "C3'" C3* C 0 1 N N S N N N 3.612 -6.699 -3.352 -2.206 0.569 -0.129 "C3'" DC 9 DC "O3'" O3* O 0 1 N N N N N N 2.853 -7.769 -3.975 -3.488 0.649 -0.756 "O3'" DC 10 DC "C2'" C2* C 0 1 N N N N N N 3.748 -5.461 -4.207 -2.322 -0.040 1.288 "C2'" DC 11 DC "C1'" C1* C 0 1 N N R N N N 3.043 -4.367 -3.370 -1.106 -0.981 1.395 "C1'" DC 12 DC N1 N1 N 0 1 N N N N N N 3.699 -3.066 -3.385 -0.267 -0.584 2.528 N1 DC 13 DC C2 C2 C 0 1 N N N N N N 3.037 -1.974 -3.937 0.270 0.648 2.563 C2 DC 14 DC O2 O2 O 0 1 N N N N N N 1.958 -2.147 -4.515 0.052 1.424 1.647 O2 DC 15 DC N3 N3 N 0 1 N N N N N N 3.565 -0.741 -3.770 1.037 1.035 3.581 N3 DC 16 DC C4 C4 C 0 1 N N N N N N 4.751 -0.588 -3.153 1.291 0.212 4.589 C4 DC 17 DC N4 N4 N 0 1 N N N N N N 5.196 0.651 -3.008 2.085 0.622 5.635 N4 DC 18 DC C5 C5 C 0 1 N N N N N N 5.473 -1.715 -2.681 0.746 -1.088 4.580 C5 DC 19 DC C6 C6 C 0 1 N N N N N N 4.933 -2.915 -2.787 -0.035 -1.465 3.541 C6 DC 20 DC HOP3 3HOP H 0 0 N N N N N N 4.941 -5.280 1.455 2.359 -0.564 -5.392 HOP3 DC 21 DC HOP2 2HOP H 0 0 N N N N N N 6.842 -6.468 0.294 -0.626 -0.198 -5.231 HOP2 DC 22 DC "H5'" 1H5* H 0 1 N N N N N N 2.607 -7.992 -0.815 -1.302 0.583 -2.737 "H5'" DC 23 DC "H5''" 2H5* H 0 0 N N N N N N 2.444 -6.542 0.006 0.046 1.015 -1.659 "H5''" DC 24 DC "H4'" H4* H 0 1 N N N N N N 1.683 -6.486 -2.353 -1.885 -1.313 -1.193 "H4'" DC 25 DC "H3'" H3* H 0 1 N N N N N N 4.634 -7.084 -3.128 -1.731 1.549 -0.094 "H3'" DC 26 DC "HO3'" H3T H 0 0 N Y N N N N 3.381 -8.044 -4.714 -4.031 1.232 -0.207 "HO3'" DC 27 DC "H2'" 1H2* H 0 1 N N N N N N 4.794 -5.215 -4.501 -3.250 -0.602 1.387 "H2'" DC 28 DC "H2''" 2H2* H 0 0 N N N N N N 3.358 -5.571 -5.245 -2.266 0.742 2.046 "H2''" DC 29 DC "H1'" H1* H 0 1 N N N N N N 2.025 -4.201 -3.796 -1.444 -2.009 1.526 "H1'" DC 30 DC H41 1H4 H 0 1 N N N N N N 4.677 1.461 -3.347 2.461 1.516 5.636 H41 DC 31 DC H42 2H4 H 0 1 N N N N N N 6.131 0.692 -3.412 2.265 0.019 6.373 H42 DC 32 DC H5 H5 H 0 1 N N N N N N 6.474 -1.657 -2.222 0.943 -1.771 5.394 H5 DC 33 DC H6 H6 H 0 1 N N N N N N 5.499 -3.771 -2.385 -0.467 -2.454 3.514 H6 DC 34 # 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 DC OP3 P SING N N 1 DC OP3 HOP3 SING N N 2 DC P OP1 DOUB N N 3 DC P OP2 SING N N 4 DC P "O5'" SING N N 5 DC OP2 HOP2 SING N N 6 DC "O5'" "C5'" SING N N 7 DC "C5'" "C4'" SING N N 8 DC "C5'" "H5'" SING N N 9 DC "C5'" "H5''" SING N N 10 DC "C4'" "O4'" SING N N 11 DC "C4'" "C3'" SING N N 12 DC "C4'" "H4'" SING N N 13 DC "O4'" "C1'" SING N N 14 DC "C3'" "O3'" SING N N 15 DC "C3'" "C2'" SING N N 16 DC "C3'" "H3'" SING N N 17 DC "O3'" "HO3'" SING N N 18 DC "C2'" "C1'" SING N N 19 DC "C2'" "H2'" SING N N 20 DC "C2'" "H2''" SING N N 21 DC "C1'" N1 SING N N 22 DC "C1'" "H1'" SING N N 23 DC N1 C2 SING N N 24 DC N1 C6 SING N N 25 DC C2 O2 DOUB N N 26 DC C2 N3 SING N N 27 DC N3 C4 DOUB N N 28 DC C4 N4 SING N N 29 DC C4 C5 SING N N 30 DC N4 H41 SING N N 31 DC N4 H42 SING N N 32 DC C5 C6 DOUB N N 33 DC C5 H5 SING N N 34 DC C6 H6 SING N N 35 # 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 DC SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O" DC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" DC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" DC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" DC SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" DC InChI InChI 1.03 "InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" DC InChIKey InChI 1.03 NCMVOABPESMRCP-SHYZEUOFSA-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 DC "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-cytidylic acid ; DC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 DC "Create component" 2001-06-01 RCSB DC "Modify descriptor" 2011-06-04 RCSB DC "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 DC PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O1P ? ? 2 DC PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O3P ? ? 3 DC PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "O3'" P ? ? 4 DC SER None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OG ? ? 5 DC TYR None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OH ? ? #