data_0RC # _chem_comp.id 0RC _chem_comp.name "5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H20 N4 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-08-13 _chem_comp.pdbx_modified_date 2019-08-02 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 430.245 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 0RC _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 2QQX _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 0RC O3B O3B O 0 1 N N N -22.562 -8.435 23.343 -4.458 -1.407 -1.349 O3B 0RC 1 0RC PB PB P 0 1 N N R -21.604 -9.131 22.894 -4.705 -0.514 -0.195 PB 0RC 2 0RC O2B O2B O 0 1 N N N -21.085 -9.936 23.752 -5.825 0.574 -0.588 O2B 0RC 3 0RC C1B C1B C 0 1 N N N -22.136 -10.157 21.470 -5.288 -1.501 1.223 C1B 0RC 4 0RC C14 C14 C 0 1 N N N -21.055 -11.063 20.824 -6.515 -2.315 0.807 C14 0RC 5 0RC N15 N15 N 0 1 N N N -21.400 -11.866 19.729 -6.984 -3.111 1.950 N15 0RC 6 0RC O3A O3A O 0 1 N N N -20.455 -8.182 22.429 -3.340 0.241 0.202 O3A 0RC 7 0RC PA PA P 0 1 N N S -19.281 -7.410 23.147 -2.346 1.238 -0.579 PA 0RC 8 0RC O1A O1A O 0 1 N N N -19.999 -6.104 23.652 -2.191 0.785 -1.979 O1A 0RC 9 0RC O2A O2A O 0 1 N N N -18.723 -8.189 24.081 -2.958 2.728 -0.562 O2A 0RC 10 0RC "O5'" "O5'" O 0 1 N N N -18.653 -6.792 22.177 -0.909 1.241 0.147 "O5'" 0RC 11 0RC "C5'" "C5'" C 0 1 N N N -18.088 -7.453 21.036 0.222 1.947 -0.367 "C5'" 0RC 12 0RC "C4'" "C4'" C 0 1 N N R -16.611 -7.434 20.709 1.419 1.739 0.562 "C4'" 0RC 13 0RC "C3'" "C3'" C 0 1 N N S -15.509 -7.447 21.828 2.618 2.593 0.094 "C3'" 0RC 14 0RC "O3'" "O3'" O 0 1 N N N -14.486 -8.215 21.378 2.699 3.801 0.854 "O3'" 0RC 15 0RC "C2'" "C2'" C 0 1 N N R -15.261 -5.925 21.960 3.847 1.698 0.367 "C2'" 0RC 16 0RC "O2'" "O2'" O 0 1 N N N -14.174 -5.508 22.525 4.725 2.325 1.304 "O2'" 0RC 17 0RC "O4'" "O4'" O 0 1 N N N -16.382 -6.409 19.891 1.886 0.374 0.482 "O4'" 0RC 18 0RC "C1'" "C1'" C 0 1 N N R -15.623 -5.564 20.470 3.246 0.408 0.968 "C1'" 0RC 19 0RC N1 N1 N 0 1 N N N -15.980 -4.196 20.371 3.984 -0.766 0.498 N1 0RC 20 0RC C6 C6 C 0 1 N N N -17.041 -3.661 21.030 4.634 -1.562 1.393 C6 0RC 21 0RC C5 C5 C 0 1 N N N -17.393 -2.315 20.944 5.314 -2.644 0.946 C5 0RC 22 0RC C4 C4 C 0 1 N N N -16.617 -1.479 20.123 5.329 -2.918 -0.437 C4 0RC 23 0RC N4 N4 N 0 1 N N N -16.858 -0.239 19.982 6.011 -4.012 -0.918 N4 0RC 24 0RC N3 N3 N 0 1 N N N -15.557 -2.077 19.476 4.681 -2.116 -1.271 N3 0RC 25 0RC C2 C2 C 0 1 N N N -15.231 -3.371 19.564 4.013 -1.057 -0.816 C2 0RC 26 0RC O2 O2 O 0 1 N N N -14.336 -3.672 18.968 3.425 -0.334 -1.604 O2 0RC 27 0RC HO2B HO2B H 0 0 N N N -20.957 -10.788 23.351 -6.038 1.194 0.123 HO2B 0RC 28 0RC H1B1 1H1B H 0 0 N N N -22.492 -9.469 20.689 -4.496 -2.177 1.545 H1B1 0RC 29 0RC H1B2 2H1B H 0 0 N N N -22.895 -10.845 21.870 -5.555 -0.836 2.044 H1B2 0RC 30 0RC H141 1H14 H 0 0 N N N -20.713 -11.748 21.614 -7.307 -1.640 0.485 H141 0RC 31 0RC H142 2H14 H 0 0 N N N -20.321 -10.353 20.414 -6.248 -2.981 -0.014 H142 0RC 32 0RC H151 1H15 H 0 0 N N N -21.482 -11.297 18.911 -7.177 -2.522 2.746 H151 0RC 33 0RC H152 2H15 H 0 0 N N N -20.691 -12.556 19.585 -7.795 -3.658 1.701 H152 0RC 34 0RC HO2A HO2A H 0 0 N N N -18.591 -9.061 23.729 -3.087 3.090 0.325 HO2A 0RC 35 0RC "H5'1" "1H5'" H 0 0 N N N -18.579 -6.992 20.166 0.463 1.571 -1.362 "H5'1" 0RC 36 0RC "H5'2" "2H5'" H 0 0 N N N -18.249 -8.512 21.287 -0.011 3.010 -0.428 "H5'2" 0RC 37 0RC "H4'" "H4'" H 0 1 N N N -16.473 -8.440 20.287 1.151 1.991 1.588 "H4'" 0RC 38 0RC "H3'" "H3'" H 0 1 N N N -15.728 -7.884 22.813 2.537 2.816 -0.970 "H3'" 0RC 39 0RC "HO3'" "HO3'" H 0 0 N N N -14.607 -8.395 20.453 3.435 4.376 0.602 "HO3'" 0RC 40 0RC "H2'" "H2'" H 0 1 N N N -15.835 -5.374 22.719 4.374 1.479 -0.561 "H2'" 0RC 41 0RC "HO2'" "HO2'" H 0 0 N N N -13.495 -5.406 21.869 5.084 3.170 1.002 "HO2'" 0RC 42 0RC "H1'" "H1'" H 0 1 N N N -14.719 -5.671 19.852 3.259 0.454 2.057 "H1'" 0RC 43 0RC H6 H6 H 0 1 N N N -17.641 -4.310 21.651 4.608 -1.331 2.448 H6 0RC 44 0RC H5 H5 H 0 1 N N N -18.238 -1.926 21.493 5.836 -3.288 1.638 H5 0RC 45 0RC HN41 1HN4 H 0 0 N N N -17.658 0.035 20.516 6.483 -4.597 -0.306 HN41 0RC 46 0RC HN42 2HN4 H 0 0 N N N -16.319 0.381 19.412 6.019 -4.198 -1.870 HN42 0RC 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 0RC O2 C2 DOUB N N 1 0RC N3 C2 SING N N 2 0RC N3 C4 DOUB N N 3 0RC C2 N1 SING N N 4 0RC N15 C14 SING N N 5 0RC "O4'" "C1'" SING N N 6 0RC "O4'" "C4'" SING N N 7 0RC N4 C4 SING N N 8 0RC C4 C5 SING N N 9 0RC N1 "C1'" SING N N 10 0RC N1 C6 SING N N 11 0RC "C1'" "C2'" SING N N 12 0RC "C4'" "C5'" SING N N 13 0RC "C4'" "C3'" SING N N 14 0RC C14 C1B SING N N 15 0RC C5 C6 DOUB N N 16 0RC "C5'" "O5'" SING N N 17 0RC "O3'" "C3'" SING N N 18 0RC C1B PB SING N N 19 0RC "C3'" "C2'" SING N N 20 0RC "C2'" "O2'" SING N N 21 0RC "O5'" PA SING N N 22 0RC O3A PB SING N N 23 0RC O3A PA SING N N 24 0RC PB O3B DOUB N N 25 0RC PB O2B SING N N 26 0RC PA O1A DOUB N N 27 0RC PA O2A SING N N 28 0RC O2B HO2B SING N N 29 0RC C1B H1B1 SING N N 30 0RC C1B H1B2 SING N N 31 0RC C14 H141 SING N N 32 0RC C14 H142 SING N N 33 0RC N15 H151 SING N N 34 0RC N15 H152 SING N N 35 0RC O2A HO2A SING N N 36 0RC "C5'" "H5'1" SING N N 37 0RC "C5'" "H5'2" SING N N 38 0RC "C4'" "H4'" SING N N 39 0RC "C3'" "H3'" SING N N 40 0RC "O3'" "HO3'" SING N N 41 0RC "C2'" "H2'" SING N N 42 0RC "O2'" "HO2'" SING N N 43 0RC "C1'" "H1'" SING N N 44 0RC C6 H6 SING N N 45 0RC C5 H5 SING N N 46 0RC N4 HN41 SING N N 47 0RC N4 HN42 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 0RC SMILES ACDLabs 10.04 "O=P(O)(OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O)CCN" 0RC SMILES_CANONICAL CACTVS 3.341 "NCC[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N" 0RC SMILES CACTVS 3.341 "NCC[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N" 0RC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(CCN)O)O)O" 0RC SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(CCN)O)O)O" 0RC InChI InChI 1.03 "InChI=1S/C11H20N4O10P2/c12-2-4-26(19,20)25-27(21,22)23-5-6-8(16)9(17)10(24-6)15-3-1-7(13)14-11(15)18/h1,3,6,8-10,16-17H,2,4-5,12H2,(H,19,20)(H,21,22)(H2,13,14,18)/t6-,8-,9-,10-/m1/s1" 0RC InChIKey InChI 1.03 FBADRUOBFLBKJQ-PEBGCTIMSA-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 0RC "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine" 0RC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-aminoethyl-[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 0RC "Create component" 2007-08-13 RCSB 0RC "Modify descriptor" 2011-06-04 RCSB 0RC "Initial release" 2019-08-07 RCSB ##