data_5HM # _chem_comp.id 5HM _chem_comp.name "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms "5-hydroxymethylcytidine 5'-monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-22 _chem_comp.pdbx_modified_date 2020-06-17 _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 353.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5HM _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 4OHB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 5HM OP3 OP3 O 0 1 N Y N 3.773 -7.235 -3.234 -4.862 2.213 -1.412 OP3 5HM 1 5HM P P P 0 1 N N N 2.904 -6.901 -4.454 -4.584 1.141 -0.243 P 5HM 2 5HM OP1 OP1 O 0 1 N N N 3.120 -7.865 -5.629 -4.436 1.848 1.049 OP1 5HM 3 5HM OP2 OP2 O 0 1 N N N 2.791 -5.438 -4.819 -5.820 0.113 -0.153 OP2 5HM 4 5HM "O5'" "O5'" O 0 1 N N N 1.413 -7.204 -3.967 -3.233 0.329 -0.568 "O5'" 5HM 5 5HM "C5'" "C5'" C 0 1 N N N 1.126 -8.577 -3.730 -2.660 -0.622 0.331 "C5'" 5HM 6 5HM "C4'" "C4'" C 0 1 N N R -0.371 -8.722 -3.582 -1.387 -1.205 -0.285 "C4'" 5HM 7 5HM "O4'" "O4'" O 0 1 N N N -1.043 -8.225 -4.754 -0.346 -0.205 -0.331 "O4'" 5HM 8 5HM "C3'" "C3'" C 0 1 N N S -0.720 -10.182 -3.369 -0.819 -2.326 0.613 "C3'" 5HM 9 5HM "O3'" "O3'" O 0 1 N N N -1.304 -10.430 -2.073 -1.212 -3.609 0.123 "O3'" 5HM 10 5HM "C2'" "C2'" C 0 1 N N R -1.674 -10.496 -4.502 0.713 -2.151 0.508 "C2'" 5HM 11 5HM "O2'" "O2'" O 0 1 N N N -2.961 -10.787 -3.971 1.313 -3.321 -0.051 "O2'" 5HM 12 5HM "C1'" "C1'" C 0 1 N N R -1.699 -9.304 -5.447 0.889 -0.946 -0.442 "C1'" 5HM 13 5HM N1 N1 N 0 1 N N N -0.982 -9.669 -6.701 2.020 -0.119 -0.013 N1 5HM 14 5HM C2 C2 C 0 1 N N N -1.560 -10.511 -7.562 1.996 0.473 1.195 C2 5HM 15 5HM O2 O2 O 0 1 N N N -2.784 -11.010 -7.269 1.029 0.315 1.921 O2 5HM 16 5HM C6 C6 C 0 1 N N N 0.242 -9.138 -6.953 3.093 0.041 -0.838 C6 5HM 17 5HM C5 C5 C 0 1 N N N 0.945 -9.462 -8.088 4.132 0.807 -0.430 C5 5HM 18 5HM CM5 CM5 C 0 1 N N N 2.286 -8.817 -8.298 5.333 1.004 -1.319 CM5 5HM 19 5HM OM5 OM5 O 0 1 N N N 2.116 -7.403 -8.093 5.144 0.285 -2.540 OM5 5HM 20 5HM C4 C4 C 0 1 N N N 0.284 -10.413 -9.033 4.074 1.419 0.839 C4 5HM 21 5HM N3 N3 N 0 1 N N N -0.944 -10.893 -8.700 3.011 1.229 1.610 N3 5HM 22 5HM N4 N4 N 0 1 N N N 0.837 -10.802 -10.214 5.116 2.201 1.279 N4 5HM 23 5HM H1 H1 H 0 1 N N N 4.306 -7.998 -3.424 -5.662 2.739 -1.281 H1 5HM 24 5HM H2 H2 H 0 1 N N N 2.875 -5.339 -5.760 -5.976 -0.386 -0.966 H2 5HM 25 5HM H3 H3 H 0 1 N N N 1.478 -9.184 -4.577 -2.415 -0.129 1.273 H3 5HM 26 5HM H4 H4 H 0 1 N N N 1.626 -8.909 -2.808 -3.375 -1.423 0.516 H4 5HM 27 5HM H5 H5 H 0 1 N N N -0.695 -8.151 -2.699 -1.592 -1.588 -1.285 H5 5HM 28 5HM H6 H6 H 0 1 N N N 0.190 -10.787 -3.491 -1.150 -2.194 1.643 H6 5HM 29 5HM "HO3'" "HO3'" H 0 0 N Y N -0.672 -10.220 -1.395 -0.882 -4.349 0.650 H7 5HM 30 5HM H8 H8 H 0 1 N N N -1.291 -11.369 -5.051 1.141 -1.934 1.487 H8 5HM 31 5HM H9 H9 H 0 1 N N N -2.902 -11.535 -3.388 1.180 -4.121 0.476 H9 5HM 32 5HM H10 H10 H 0 1 N N N -2.742 -9.040 -5.676 1.035 -1.288 -1.467 H10 5HM 33 5HM H11 H11 H 0 1 N N N 0.673 -8.445 -6.245 3.114 -0.438 -1.806 H11 5HM 34 5HM H12 H12 H 0 1 N N N 2.640 -9.009 -9.321 5.453 2.065 -1.538 H12 5HM 35 5HM H13 H13 H 0 1 N N N 3.014 -9.217 -7.577 6.224 0.634 -0.813 H13 5HM 36 5HM H14 H14 H 0 1 N N N 2.404 -7.173 -7.217 5.880 0.367 -3.162 H14 5HM 37 5HM H15 H15 H 0 1 N N N 0.341 -11.428 -10.816 5.075 2.616 2.155 H15 5HM 38 5HM H16 H16 H 0 1 N N N 1.739 -10.462 -10.480 5.892 2.338 0.713 H16 5HM 39 # # 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 5HM N4 C4 SING N N 1 5HM C4 N3 DOUB N N 2 5HM C4 C5 SING N N 3 5HM N3 C2 SING N N 4 5HM CM5 OM5 SING N N 5 5HM CM5 C5 SING N N 6 5HM C5 C6 DOUB N N 7 5HM C2 O2 DOUB N N 8 5HM C2 N1 SING N N 9 5HM C6 N1 SING N N 10 5HM N1 "C1'" SING N N 11 5HM OP1 P DOUB N N 12 5HM "C1'" "O4'" SING N N 13 5HM "C1'" "C2'" SING N N 14 5HM OP2 P SING N N 15 5HM "O4'" "C4'" SING N N 16 5HM "C2'" "O2'" SING N N 17 5HM "C2'" "C3'" SING N N 18 5HM P "O5'" SING N N 19 5HM P OP3 SING N N 20 5HM "O5'" "C5'" SING N N 21 5HM "C5'" "C4'" SING N N 22 5HM "C4'" "C3'" SING N N 23 5HM "C3'" "O3'" SING N N 24 5HM OP3 H1 SING N N 25 5HM OP2 H2 SING N N 26 5HM "C5'" H3 SING N N 27 5HM "C5'" H4 SING N N 28 5HM "C4'" H5 SING N N 29 5HM "C3'" H6 SING N N 30 5HM "O3'" "HO3'" SING N N 31 5HM "C2'" H8 SING N N 32 5HM "O2'" H9 SING N N 33 5HM "C1'" H10 SING N N 34 5HM C6 H11 SING N N 35 5HM CM5 H12 SING N N 36 5HM CM5 H13 SING N N 37 5HM OM5 H14 SING N N 38 5HM N4 H15 SING N N 39 5HM N4 H16 SING N N 40 # # 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 5HM SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)C(O)C2O" 5HM InChI InChI 1.03 "InChI=1S/C10H16N3O9P/c11-8-4(2-14)1-13(10(17)12-8)9-7(16)6(15)5(22-9)3-21-23(18,19)20/h1,5-7,9,14-16H,2-3H2,(H2,11,12,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1" 5HM InChIKey InChI 1.03 KPUOHXMVCZBWQC-JXOAFFINSA-N 5HM SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1CO)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" 5HM SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1CO)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 5HM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)CO" 5HM SMILES "OpenEye OEToolkits" 1.7.6 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)CO" # # 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 5HM "SYSTEMATIC NAME" ACDLabs 12.01 "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" 5HM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(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 5HM "Create component" 2014-01-22 PDBJ 5HM "Initial release" 2014-06-25 RCSB 5HM "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5HM _pdbx_chem_comp_synonyms.name "5-hydroxymethylcytidine 5'-monophosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##