data_5HC # _chem_comp.id 5HC _chem_comp.name ;2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-08-22 _chem_comp.pdbx_modified_date 2013-01-11 _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 337.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5HC _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 4GLC _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 5HC P P P 0 1 N N N -12.034 5.599 -19.575 -4.516 1.030 -0.276 P 5HC 1 5HC OP1 OP1 O 0 1 N N N -13.504 5.422 -19.477 -5.616 0.094 0.048 OP1 5HC 2 5HC OP2 OP2 O 0 1 N N N -11.289 6.307 -18.501 -4.258 2.009 0.975 OP2 5HC 3 5HC "O5'" "O5'" O 0 1 N N N -11.381 4.165 -19.775 -3.176 0.194 -0.590 "O5'" 5HC 4 5HC "C5'" "C5'" C 0 1 N N N -12.022 3.221 -20.643 -2.621 -0.757 0.319 "C5'" 5HC 5 5HC "C4'" "C4'" C 0 1 N N R -11.100 2.054 -20.896 -1.355 -1.365 -0.288 "C4'" 5HC 6 5HC "O4'" "O4'" O 0 1 N N N -9.797 2.476 -21.343 -0.299 -0.382 -0.338 "O4'" 5HC 7 5HC "C3'" "C3'" C 0 1 N N S -10.855 1.230 -19.635 -0.807 -2.487 0.623 "C3'" 5HC 8 5HC "O3'" "O3'" O 0 1 N N N -11.810 0.167 -19.574 -1.218 -3.768 0.141 "O3'" 5HC 9 5HC "C2'" "C2'" C 0 1 N N N -9.442 0.743 -19.755 0.727 -2.336 0.521 "C2'" 5HC 10 5HC "C1'" "C1'" C 0 1 N N R -8.788 1.626 -20.790 0.924 -1.142 -0.439 "C1'" 5HC 11 5HC N1 N1 N 0 1 N N N -7.749 2.536 -20.273 2.066 -0.329 -0.013 N1 5HC 12 5HC C2 C2 C 0 1 N N N -6.417 2.142 -20.350 2.050 0.269 1.192 C2 5HC 13 5HC O2 O2 O 0 1 N N N -6.154 1.046 -20.846 1.081 0.128 1.919 O2 5HC 14 5HC N3 N3 N 0 1 N N N -5.449 2.970 -19.880 3.075 1.013 1.604 N3 5HC 15 5HC C4 C4 C 0 1 N N N -5.769 4.144 -19.352 4.141 1.184 0.834 C4 5HC 16 5HC N4 N4 N 0 1 N N N -4.780 4.930 -18.900 5.194 1.954 1.271 N4 5HC 17 5HC C5 C5 C 0 1 N N N -7.127 4.577 -19.259 4.190 0.570 -0.435 C5 5HC 18 5HC C5M C5M C 0 1 N N N -7.456 5.904 -18.663 5.391 0.751 -1.326 C5M 5HC 19 5HC O5 O5 O 0 1 N N N -6.932 6.095 -17.352 5.192 0.032 -2.546 O5 5HC 20 5HC C6 C6 C 0 1 N N N -8.069 3.750 -19.728 3.142 -0.187 -0.837 C6 5HC 21 5HC OP3 OP3 O 0 1 N Y N -11.730 6.385 -20.943 -4.919 1.904 -1.567 O1 5HC 22 5HC HOP2 H1 H 0 0 N N N -11.895 6.584 -17.824 -3.548 2.650 0.833 H1 5HC 23 5HC "H5'" H2 H 0 1 N N N -12.264 3.709 -21.599 -2.372 -0.261 1.257 H2 5HC 24 5HC "H5''" H3 H 0 0 N N N -12.947 2.860 -20.171 -3.349 -1.546 0.509 H3 5HC 25 5HC H4 H4 H 0 1 N N N -11.557 1.402 -21.655 -1.563 -1.754 -1.285 H4 5HC 26 5HC "H3'" H5 H 0 1 N N N -10.946 1.882 -18.754 -1.140 -2.341 1.650 H5 5HC 27 5HC "HO3'" H6 H 0 0 N Y N -11.661 -0.349 -18.790 -0.901 -4.509 0.676 H6 5HC 28 5HC "H2'" H7 H 0 1 N N N -9.425 -0.307 -20.082 1.155 -2.115 1.499 H7 5HC 29 5HC "H2''" H8 H 0 0 N N N -8.922 0.835 -18.790 1.173 -3.240 0.106 H8 5HC 30 5HC "H1'" H9 H 0 1 N N N -8.357 0.992 -21.579 1.070 -1.494 -1.460 H9 5HC 31 5HC HN41 H10 H 0 0 N N N -3.830 4.626 -18.966 5.158 2.374 2.144 H10 5HC 32 5HC HN42 H11 H 0 0 N N N -4.993 5.820 -18.497 5.973 2.077 0.705 H11 5HC 33 5HC H5M2 H12 H 0 0 N N N -7.047 6.688 -19.317 5.525 1.810 -1.546 H12 5HC 34 5HC H5M1 H13 H 0 0 N N N -8.551 6.000 -18.616 6.279 0.369 -0.821 H13 5HC 35 5HC HO5 H14 H 0 1 N N N -7.178 6.956 -17.035 5.928 0.104 -3.169 H14 5HC 36 5HC H6 H15 H 0 1 N N N -9.106 4.048 -19.675 3.158 -0.671 -1.803 H15 5HC 37 5HC HOP3 H16 H 0 0 N N N -12.547 6.567 -21.393 -5.719 2.434 -1.449 H16 5HC 38 # 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 5HC "O4'" "C4'" SING N N 1 5HC "O4'" "C1'" SING N N 2 5HC "C4'" "C5'" SING N N 3 5HC "C4'" "C3'" SING N N 4 5HC O2 C2 DOUB N N 5 5HC "C1'" N1 SING N N 6 5HC "C1'" "C2'" SING N N 7 5HC "C5'" "O5'" SING N N 8 5HC C2 N1 SING N N 9 5HC C2 N3 SING N N 10 5HC N1 C6 SING N N 11 5HC N3 C4 DOUB N N 12 5HC "O5'" P SING N N 13 5HC "C2'" "C3'" SING N N 14 5HC C6 C5 DOUB N N 15 5HC "C3'" "O3'" SING N N 16 5HC P OP1 DOUB N N 17 5HC P OP2 SING N N 18 5HC C4 C5 SING N N 19 5HC C4 N4 SING N N 20 5HC C5 C5M SING N N 21 5HC C5M O5 SING N N 22 5HC P OP3 SING N N 23 5HC OP2 HOP2 SING N N 24 5HC "C5'" "H5'" SING N N 25 5HC "C5'" "H5''" SING N N 26 5HC "C4'" H4 SING N N 27 5HC "C3'" "H3'" SING N N 28 5HC "O3'" "HO3'" SING N N 29 5HC "C2'" "H2'" SING N N 30 5HC "C2'" "H2''" SING N N 31 5HC "C1'" "H1'" SING N N 32 5HC N4 HN41 SING N N 33 5HC N4 HN42 SING N N 34 5HC C5M H5M2 SING N N 35 5HC C5M H5M1 SING N N 36 5HC O5 HO5 SING N N 37 5HC C6 H6 SING N N 38 5HC OP3 HOP3 SING N N 39 # 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 5HC SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)CC2O" 5HC InChI InChI 1.03 "InChI=1S/C10H16N3O8P/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(21-8)4-20-22(17,18)19/h2,6-8,14-15H,1,3-4H2,(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" 5HC InChIKey InChI 1.03 BTIWPBKNTZFNRI-XLPZGREQSA-N 5HC SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1CO)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 5HC SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1CO)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 5HC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)O)O" 5HC SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)O)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 5HC "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) ; 5HC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-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 5HC "Create component" 2012-08-22 RCSB 5HC "Initial release" 2013-01-11 RCSB #