data_5MD # _chem_comp.id 5MD _chem_comp.name "2'-deoxy-1-methyl-pseudouridine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-METHYL-2'-DEOXYPSEUDOURIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-07-26 _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 242.229 _chem_comp.one_letter_code N _chem_comp.three_letter_code 5MD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1F8Y _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 5MD "O5'" "O5'" O 0 1 N N N 56.676 -7.839 -22.105 2.029 -1.350 -3.670 "O5'" 5MD 1 5MD "C5'" "C5'" C 0 1 N N N 55.930 -6.833 -22.853 1.212 -0.178 -3.643 "C5'" 5MD 2 5MD "C4'" "C4'" C 0 1 N N R 56.276 -5.429 -22.312 -0.069 -0.467 -2.860 "C4'" 5MD 3 5MD "O4'" "O4'" O 0 1 N N N 57.683 -5.311 -22.274 0.249 -0.806 -1.498 "O4'" 5MD 4 5MD "C1'" "C1'" C 0 1 N N R 58.215 -4.739 -23.496 -0.818 -0.289 -0.676 "C1'" 5MD 5 5MD C1 C1 C 0 1 N N N 58.796 -5.719 -24.526 -0.355 -0.117 0.747 C1 5MD 6 5MD C6 C6 C 0 1 N N N 58.800 -7.048 -24.247 -1.012 -0.725 1.758 C6 5MD 7 5MD C2 C2 C 0 1 N N N 59.300 -5.242 -25.832 0.772 0.685 1.042 C2 5MD 8 5MD O2 O2 O 0 1 N N N 59.488 -4.103 -26.233 1.380 1.244 0.147 O2 5MD 9 5MD N3 N3 N 0 1 N N N 59.726 -6.251 -26.648 1.167 0.825 2.324 N3 5MD 10 5MD C4 C4 C 0 1 N N N 59.727 -7.588 -26.380 0.491 0.211 3.313 C4 5MD 11 5MD O4 O4 O 0 1 N N N 59.980 -8.335 -27.287 0.859 0.347 4.464 O4 5MD 12 5MD N5 N5 N 0 1 N N N 59.254 -7.979 -25.148 -0.578 -0.557 3.045 N5 5MD 13 5MD C5 C5 C 0 1 N N N 59.254 -9.381 -24.752 -1.291 -1.217 4.142 C5 5MD 14 5MD "C3'" "C3'" C 0 1 N N S 55.818 -4.279 -23.144 -0.958 0.790 -2.825 "C3'" 5MD 15 5MD "O3'" "O3'" O 0 1 N N N 55.639 -3.141 -22.324 -2.221 0.531 -3.439 "O3'" 5MD 16 5MD "C2'" "C2'" C 0 1 N N N 57.016 -3.969 -23.998 -1.139 1.085 -1.316 "C2'" 5MD 17 5MD "H5'" H5* H 0 1 N N N 56.463 -8.702 -22.437 2.824 -1.124 -4.172 "H5'" 5MD 18 5MD "H5'1" "1H5'" H 0 0 N N N 56.097 -6.914 -23.952 0.957 0.111 -4.663 "H5'1" 5MD 19 5MD "H5'2" "2H5'" H 0 0 N N N 54.832 -7.029 -22.844 1.757 0.633 -3.161 "H5'2" 5MD 20 5MD "H4'" "H4'" H 0 1 N N N 55.756 -5.367 -21.327 -0.610 -1.290 -3.327 "H4'" 5MD 21 5MD "H1'" "H1'" H 0 1 N N N 59.128 -4.128 -23.308 -1.688 -0.945 -0.719 "H1'" 5MD 22 5MD H6 H6 H 0 1 N N N 58.425 -7.379 -23.264 -1.874 -1.341 1.552 H6 5MD 23 5MD HN3 HN3 H 0 1 N N N 60.084 -5.974 -27.562 1.939 1.373 2.534 HN3 5MD 24 5MD H51 1H5 H 0 1 N N N 59.622 -10.137 -25.483 -0.808 -0.972 5.088 H51 5MD 25 5MD H52 2H5 H 0 1 N N N 59.823 -9.489 -23.799 -2.325 -0.873 4.163 H52 5MD 26 5MD H53 3H5 H 0 1 N N N 58.227 -9.665 -24.421 -1.269 -2.296 3.993 H53 5MD 27 5MD "H3'" "H3'" H 0 1 N N N 54.875 -4.510 -23.693 -0.458 1.624 -3.319 "H3'" 5MD 28 5MD "H3'A" H3* H 0 0 N N N 55.347 -2.408 -22.853 -2.753 1.332 -3.335 "H3'A" 5MD 29 5MD "H2'1" "1H2'" H 0 0 N N N 57.216 -2.873 -24.057 -2.164 1.385 -1.098 "H2'1" 5MD 30 5MD "H2'2" "2H2'" H 0 0 N N N 56.819 -4.156 -25.079 -0.433 1.844 -0.980 "H2'2" 5MD 31 # # 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 5MD "O5'" "C5'" SING N N 1 5MD "O5'" "H5'" SING N N 2 5MD "C5'" "C4'" SING N N 3 5MD "C5'" "H5'1" SING N N 4 5MD "C5'" "H5'2" SING N N 5 5MD "C4'" "O4'" SING N N 6 5MD "C4'" "C3'" SING N N 7 5MD "C4'" "H4'" SING N N 8 5MD "O4'" "C1'" SING N N 9 5MD "C1'" C1 SING N N 10 5MD "C1'" "C2'" SING N N 11 5MD "C1'" "H1'" SING N N 12 5MD C1 C6 DOUB N N 13 5MD C1 C2 SING N N 14 5MD C6 N5 SING N N 15 5MD C6 H6 SING N N 16 5MD C2 O2 DOUB N N 17 5MD C2 N3 SING N N 18 5MD N3 C4 SING N N 19 5MD N3 HN3 SING N N 20 5MD C4 O4 DOUB N N 21 5MD C4 N5 SING N N 22 5MD N5 C5 SING N N 23 5MD C5 H51 SING N N 24 5MD C5 H52 SING N N 25 5MD C5 H53 SING N N 26 5MD "C3'" "O3'" SING N N 27 5MD "C3'" "C2'" SING N N 28 5MD "C3'" "H3'" SING N N 29 5MD "O3'" "H3'A" SING N N 30 5MD "C2'" "H2'1" SING N N 31 5MD "C2'" "H2'2" SING N N 32 # # 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 5MD SMILES ACDLabs 10.04 "O=C1N(C=C(C(=O)N1)C2OC(CO)C(O)C2)C" 5MD SMILES_CANONICAL CACTVS 3.341 "CN1C=C([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O" 5MD SMILES CACTVS 3.341 "CN1C=C([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O" 5MD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CN1C=C(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O" 5MD SMILES "OpenEye OEToolkits" 1.5.0 "CN1C=C(C(=O)NC1=O)C2CC(C(O2)CO)O" 5MD InChI InChI 1.03 "InChI=1S/C10H14N2O5/c1-12-3-5(9(15)11-10(12)16)7-2-6(14)8(4-13)17-7/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1" 5MD InChIKey InChI 1.03 AMDJRICBYOAHBZ-XLPZGREQSA-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 5MD "SYSTEMATIC NAME" ACDLabs 10.04 "(1R)-1,4-anhydro-2-deoxy-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-erythro-pentitol" 5MD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "5-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5MD "Create component" 2000-07-26 RCSB 5MD "Modify descriptor" 2011-06-04 RCSB 5MD "Modify name" 2018-01-16 RCSB 5MD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5MD _pdbx_chem_comp_synonyms.name "5-METHYL-2'-DEOXYPSEUDOURIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##