data_N5C # _chem_comp.id N5C _chem_comp.name ;5-nitrocytidine 5'-(tetrahydrogen triphosphate) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N4 O16 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-12-28 _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 528.154 _chem_comp.one_letter_code ? _chem_comp.three_letter_code N5C _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 3BSN _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 N5C O4 O4 O 0 1 N N N 31.643 -1.335 -3.673 6.494 2.852 -2.127 O4 N5C 1 N5C N5 N5 N 1 1 N N N 30.710 -1.975 -3.216 6.439 2.908 -0.911 N5 N5C 2 N5C O3 O3 O -1 1 N N N 30.907 -3.135 -2.885 7.025 3.794 -0.315 O3 N5C 3 N5C C5 C5 C 0 1 N N N 29.398 -1.372 -3.088 5.655 1.903 -0.159 C5 N5C 4 N5C C4 C4 C 0 1 N N N 28.230 -2.161 -2.837 5.675 1.887 1.251 C4 N5C 5 N5C N4 N4 N 0 1 N N N 28.300 -3.487 -2.702 6.426 2.810 1.942 N4 N5C 6 N5C N3 N3 N 0 1 N N N 27.021 -1.604 -2.726 4.966 0.978 1.907 N3 N5C 7 N5C C2 C2 C 0 1 N N N 26.856 -0.262 -2.847 4.236 0.080 1.248 C2 N5C 8 N5C O2 O2 O 0 1 N N N 25.725 0.252 -2.746 3.592 -0.745 1.874 O2 N5C 9 N5C C6 C6 C 0 1 N N N 29.220 -0.040 -3.209 4.903 0.987 -0.814 C6 N5C 10 N5C N1 N1 N 0 1 N N N 27.979 0.548 -3.092 4.196 0.069 -0.097 N1 N5C 11 N5C "C1'" "C1'" C 0 1 N N R 27.787 2.008 -3.223 3.383 -0.931 -0.793 "C1'" N5C 12 N5C "O4'" "O4'" O 0 1 N N N 28.920 2.607 -3.829 2.024 -0.903 -0.305 "O4'" N5C 13 N5C "C2'" "C2'" C 0 1 N N R 27.572 2.707 -1.874 3.888 -2.354 -0.471 "C2'" N5C 14 N5C "O2'" "O2'" O 0 1 N N N 26.677 3.789 -2.052 4.730 -2.836 -1.521 "O2'" N5C 15 N5C "C3'" "C3'" C 0 1 N N S 28.994 3.167 -1.546 2.598 -3.200 -0.381 "C3'" N5C 16 N5C "O3'" "O3'" O 0 1 N N N 29.104 4.216 -0.578 2.604 -4.229 -1.371 "O3'" N5C 17 N5C "C4'" "C4'" C 0 1 N N R 29.541 3.553 -2.919 1.466 -2.187 -0.659 "C4'" N5C 18 N5C "C5'" "C5'" C 0 1 N N N 31.035 3.471 -3.075 0.248 -2.497 0.213 "C5'" N5C 19 N5C "O5'" "O5'" O 0 1 N N N 31.538 2.186 -2.719 -0.802 -1.576 -0.090 "O5'" N5C 20 N5C PA PA P 0 1 N N R 33.028 1.961 -2.204 -2.236 -1.609 0.642 PA N5C 21 N5C O1A O1A O 0 1 N N N 33.950 2.986 -2.843 -2.049 -1.263 2.204 O1A N5C 22 N5C O2A O2A O 0 1 N N N 33.381 0.512 -2.443 -2.830 -2.957 0.503 O2A N5C 23 N5C O3A O3A O 0 1 N N N 32.811 2.160 -0.614 -3.210 -0.520 -0.036 O3A N5C 24 N5C PB PB P 0 1 N N R 32.590 3.496 0.274 -4.798 -0.262 0.004 PB N5C 25 N5C O1B O1B O 0 1 N N N 31.204 3.456 0.867 -5.280 -0.368 1.400 O1B N5C 26 N5C O2B O2B O 0 1 N N N 32.946 4.715 -0.546 -5.543 -1.362 -0.905 O2B N5C 27 N5C O3B O3B O 0 1 N N N 33.653 3.404 1.478 -5.117 1.210 -0.564 O3B N5C 28 N5C PG PG P 0 1 N N N 35.230 3.135 1.278 -6.368 2.214 -0.429 PG N5C 29 N5C O1G O1G O 0 1 N N N 36.004 3.884 2.339 -7.630 1.444 -0.508 O1G N5C 30 N5C O2G O2G O 0 1 N N N 35.498 1.649 1.417 -6.293 2.977 0.987 O2G N5C 31 N5C O3G O3G O 0 1 N N N 35.665 3.604 -0.098 -6.322 3.293 -1.623 O3G N5C 32 N5C HN4 HN4 H 0 1 N N N 27.385 -3.854 -2.533 6.880 3.522 1.464 HN4 N5C 33 N5C HN4A HN4A H 0 0 N N N 29.138 -4.030 -2.761 6.501 2.750 2.907 HN4A N5C 34 N5C H6 H6 H 0 1 N N N 30.078 0.586 -3.404 4.868 0.981 -1.894 H6 N5C 35 N5C "H1'" "H1'" H 0 1 N N N 26.885 2.133 -3.840 3.403 -0.753 -1.869 "H1'" N5C 36 N5C "H2'" "H2'" H 0 1 N N N 27.131 2.092 -1.076 4.422 -2.364 0.480 "H2'" N5C 37 N5C "HO2'" "HO2'" H 0 0 N N N 26.476 4.177 -1.208 5.076 -3.727 -1.370 "HO2'" N5C 38 N5C "H3'" "H3'" H 0 1 N N N 29.566 2.375 -1.040 2.493 -3.630 0.615 "H3'" N5C 39 N5C "HO3'" "HO3'" H 0 0 N N N 29.128 3.841 0.295 3.332 -4.859 -1.280 "HO3'" N5C 40 N5C "H4'" "H4'" H 0 1 N N N 29.312 4.613 -3.105 1.192 -2.204 -1.714 "H4'" N5C 41 N5C "H5'" "H5'" H 0 1 N N N 31.290 3.670 -4.126 -0.092 -3.513 0.015 "H5'" N5C 42 N5C "H5'A" "H5'A" H 0 0 N N N 31.490 4.214 -2.403 0.520 -2.403 1.265 "H5'A" N5C 43 N5C HO1A HO1A H 0 0 N N N 34.142 3.674 -2.216 -1.664 -0.392 2.370 HO1A N5C 44 N5C HO2B HO2B H 0 0 N N N 33.021 5.471 0.025 -5.276 -1.351 -1.835 HO2B N5C 45 N5C HO2G HO2G H 0 0 N N N 35.554 1.255 0.554 -5.491 3.503 1.108 HO2G N5C 46 N5C HO3G HO3G H 0 0 N N N 35.756 4.550 -0.097 -7.048 3.931 -1.605 HO3G N5C 47 # 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 N5C O4 N5 DOUB N N 1 N5C N5 O3 SING N N 2 N5C N5 C5 SING N N 3 N5C C5 C4 SING N N 4 N5C C5 C6 DOUB N N 5 N5C C4 N4 SING N N 6 N5C C4 N3 DOUB N N 7 N5C N3 C2 SING N N 8 N5C C2 O2 DOUB N N 9 N5C C2 N1 SING N N 10 N5C C6 N1 SING N N 11 N5C N1 "C1'" SING N N 12 N5C "C1'" "O4'" SING N N 13 N5C "C1'" "C2'" SING N N 14 N5C "O4'" "C4'" SING N N 15 N5C "C2'" "O2'" SING N N 16 N5C "C2'" "C3'" SING N N 17 N5C "C3'" "O3'" SING N N 18 N5C "C3'" "C4'" SING N N 19 N5C "C4'" "C5'" SING N N 20 N5C "C5'" "O5'" SING N N 21 N5C "O5'" PA SING N N 22 N5C PA O1A SING N N 23 N5C PA O2A DOUB N N 24 N5C PA O3A SING N N 25 N5C O3A PB SING N N 26 N5C PB O1B DOUB N N 27 N5C PB O2B SING N N 28 N5C PB O3B SING N N 29 N5C O3B PG SING N N 30 N5C PG O1G DOUB N N 31 N5C PG O2G SING N N 32 N5C PG O3G SING N N 33 N5C N4 HN4 SING N N 34 N5C N4 HN4A SING N N 35 N5C C6 H6 SING N N 36 N5C "C1'" "H1'" SING N N 37 N5C "C2'" "H2'" SING N N 38 N5C "O2'" "HO2'" SING N N 39 N5C "C3'" "H3'" SING N N 40 N5C "O3'" "HO3'" SING N N 41 N5C "C4'" "H4'" SING N N 42 N5C "C5'" "H5'" SING N N 43 N5C "C5'" "H5'A" SING N N 44 N5C O1A HO1A SING N N 45 N5C O2B HO2B SING N N 46 N5C O2G HO2G SING N N 47 N5C O3G HO3G SING N N 48 # 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 N5C SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C([N+]([O-])=O)=C1)C(O)C2O" N5C SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1[N+]([O-])=O)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O" N5C SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1[N+]([O-])=O)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O" N5C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N)[N+](=O)[O-]" N5C SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N)[N+](=O)[O-]" N5C InChI InChI 1.03 "InChI=1S/C9H15N4O16P3/c10-7-3(13(17)18)1-12(9(16)11-7)8-6(15)5(14)4(27-8)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h1,4-6,8,14-15H,2H2,(H,22,23)(H,24,25)(H2,10,11,16)(H2,19,20,21)/t4-,5-,6-,8-/m1/s1" N5C InChIKey InChI 1.03 FDSJHYVWUMETJX-UAKXSSHOSA-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 N5C "SYSTEMATIC NAME" ACDLabs 10.04 ;5-nitrocytidine 5'-(tetrahydrogen triphosphate) ; N5C "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-5-nitro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl (hydroxy-phosphonooxy-phosphoryl) hydrogen 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 N5C "Create component" 2007-12-28 RCSB N5C "Modify descriptor" 2011-06-04 RCSB #