data_DNR # _chem_comp.id DNR _chem_comp.name ;2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2002-04-04 _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 308.205 _chem_comp.one_letter_code C _chem_comp.three_letter_code DNR _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1LAQ _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 DNR P P P 0 1 N N N -0.684 -7.446 15.813 -3.968 -1.665 3.118 P DNR 1 DNR OP1 O1P O 0 1 N N N 0.421 -7.036 14.917 -4.406 -2.599 4.208 OP1 DNR 2 DNR OP2 O2P O 0 1 N N N -1.407 -8.711 15.556 -3.912 -2.311 1.636 OP2 DNR 3 DNR "O5'" O5* O 0 1 N N N -1.767 -6.248 15.855 -2.493 -1.028 3.315 "O5'" DNR 4 DNR "C5'" C5* C 0 1 N N N -2.936 -6.352 16.678 -2.005 -0.136 2.327 "C5'" DNR 5 DNR "C4'" C4* C 0 1 N N R -3.852 -5.142 16.542 -0.611 0.328 2.728 "C4'" DNR 6 DNR "O4'" O4* O 0 1 N N N -3.125 -3.913 16.795 0.247 -0.829 2.764 "O4'" DNR 7 DNR "C1'" C1* C 0 1 N N R -3.181 -3.066 15.625 1.157 -0.778 1.657 "C1'" DNR 8 DNR N1 N1 N 0 1 N N N -1.853 -2.469 15.339 1.164 -2.047 0.989 N1 DNR 9 DNR C6 C6 C 0 1 N N N -0.754 -3.262 15.217 -0.015 -2.783 0.959 C6 DNR 10 DNR C2 C2 C 0 1 N N N -1.760 -1.079 15.249 2.335 -2.532 0.381 C2 DNR 11 DNR O2 O2 O 0 1 N N N -2.767 -0.382 15.363 3.425 -1.977 0.342 O2 DNR 12 DNR N3 N3 N 1 1 N N N -0.527 -0.524 15.041 2.203 -3.824 -0.257 N3 DNR 13 DNR C4 C4 C 0 1 N N N 0.561 -1.305 14.927 1.089 -4.548 -0.301 C4 DNR 14 DNR N4 N4 N 0 1 N N N 1.753 -0.747 14.733 0.968 -5.729 -0.886 N4 DNR 15 DNR C5 C5 C 0 1 N N N 0.463 -2.728 15.014 -0.107 -3.974 0.362 C5 DNR 16 DNR "C2'" C2* C 0 1 N N N -3.671 -3.939 14.490 0.710 0.360 0.754 "C2'" DNR 17 DNR "C3'" C3* C 0 1 N N S -4.447 -5.040 15.147 0.008 1.286 1.720 "C3'" DNR 18 DNR "O3'" O3* O 0 1 N N N -5.846 -4.728 15.206 0.965 2.121 2.368 "O3'" DNR 19 DNR OP3 O3P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 OP3 DNR 20 DNR HOP2 2HOP H 0 0 N N N -2.116 -8.974 16.130 -4.684 -2.823 1.313 HOP2 DNR 21 DNR "H5'" 1H5* H 0 1 N N N -2.630 -6.429 17.716 -1.971 -0.654 1.366 "H5'" DNR 22 DNR "H5''" 2H5* H 0 0 N N N -3.489 -7.251 16.403 -2.683 0.718 2.254 "H5''" DNR 23 DNR "H4'" H4* H 0 1 N N N -4.660 -5.225 17.266 -0.644 0.753 3.736 "H4'" DNR 24 DNR "H1'" H1* H 0 1 N N N -3.901 -2.280 15.793 2.163 -0.604 2.054 "H1'" DNR 25 DNR H6 H6 H 0 1 N N N -0.864 -4.341 15.274 -0.871 -2.335 1.453 H6 DNR 26 DNR HN3 HN3 H 0 1 N N N -0.421 0.491 15.056 3.017 -4.226 -0.715 HN3 DNR 27 DNR H41 H41 H 0 1 N N N 1.833 0.257 14.671 0.511 -5.815 -1.789 H41 DNR 28 DNR H42 H42 H 0 1 N N N 2.576 -1.326 14.649 1.332 -6.567 -0.439 H42 DNR 29 DNR H5 H5 H 0 1 N N N 1.346 -3.360 14.919 -1.040 -4.526 0.354 H5 DNR 30 DNR "H2'" 1H2* H 0 1 N N N -2.839 -4.348 13.921 -0.003 -0.001 0.003 "H2'" DNR 31 DNR "H2''" 2H2* H 0 0 N N N -4.322 -3.365 13.847 1.556 0.818 0.232 "H2''" DNR 32 DNR "H3'" H3* H 0 1 N N N -4.291 -5.978 14.608 -0.722 1.941 1.236 "H3'" DNR 33 DNR "HO3'" H3T H 0 0 N Y N -6.217 -4.664 14.334 0.743 3.042 2.146 "HO3'" DNR 34 DNR HOP3 3HOP H 0 0 N N N -0.709 -0.263 0.574 -5.874 -0.475 2.871 HOP3 DNR 35 # 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 DNR P OP1 DOUB N N 1 DNR P OP2 SING N N 2 DNR P "O5'" SING N N 3 DNR P OP3 SING N N 4 DNR OP2 HOP2 SING N N 5 DNR "O5'" "C5'" SING N N 6 DNR "C5'" "C4'" SING N N 7 DNR "C5'" "H5'" SING N N 8 DNR "C5'" "H5''" SING N N 9 DNR "C4'" "O4'" SING N N 10 DNR "C4'" "C3'" SING N N 11 DNR "C4'" "H4'" SING N N 12 DNR "O4'" "C1'" SING N N 13 DNR "C1'" N1 SING N N 14 DNR "C1'" "C2'" SING N N 15 DNR "C1'" "H1'" SING N N 16 DNR N1 C6 SING N N 17 DNR N1 C2 SING N N 18 DNR C6 C5 DOUB N N 19 DNR C6 H6 SING N N 20 DNR C2 O2 DOUB N N 21 DNR C2 N3 SING N N 22 DNR N3 C4 DOUB N N 23 DNR N3 HN3 SING N N 24 DNR C4 N4 SING N N 25 DNR C4 C5 SING N N 26 DNR N4 H41 SING N N 27 DNR N4 H42 SING N N 28 DNR C5 H5 SING N N 29 DNR "C2'" "C3'" SING N N 30 DNR "C2'" "H2'" SING N N 31 DNR "C2'" "H2''" SING N N 32 DNR "C3'" "O3'" SING N N 33 DNR "C3'" "H3'" SING N N 34 DNR "O3'" "HO3'" SING N N 35 DNR OP3 HOP3 SING N N 36 # 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 DNR SMILES ACDLabs 10.04 "O=C1[NH+]=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O" DNR SMILES_CANONICAL CACTVS 3.341 "NC1=[NH+]C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" DNR SMILES CACTVS 3.341 "NC1=[NH+]C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" DNR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O" DNR SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O" DNR 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)/p+1/t5-,6+,8+/m0/s1" DNR InChIKey InChI 1.03 NCMVOABPESMRCP-SHYZEUOFSA-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 DNR "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-cytidylic acid ; DNR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-3-ium-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 DNR "Create component" 2002-04-04 RCSB DNR "Modify descriptor" 2011-06-04 RCSB #