data_Y19 # _chem_comp.id Y19 _chem_comp.name "1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol" _chem_comp.type non-polymer _chem_comp.pdbx_type ? _chem_comp.formula "C12 H20 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-11-27 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 332.310 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y19 _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 2VI5 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 Y19 O2 O2 O 0 1 N N N 10.113 10.066 -15.178 2.118 -4.055 -0.377 O2 Y19 1 Y19 C2 C2 C 0 1 N N N 10.001 8.959 -15.748 2.246 -2.871 -0.126 C2 Y19 2 Y19 N3 N3 N 0 1 N N N 8.990 8.748 -16.624 3.486 -2.410 0.075 N3 Y19 3 Y19 C4 C4 C 0 1 N N N 8.832 7.573 -17.271 3.718 -1.109 0.359 C4 Y19 4 Y19 O4 O4 O 0 1 N N N 7.877 7.421 -18.065 4.841 -0.691 0.540 O4 Y19 5 Y19 N1 N1 N 0 1 N N N 10.903 7.991 -15.482 1.139 -2.127 -0.076 N1 Y19 6 Y19 C6 C6 C 0 1 N N N 10.850 6.768 -16.067 1.162 -0.841 0.185 C6 Y19 7 Y19 C5 C5 C 0 1 N N S 9.749 6.435 -17.013 2.510 -0.194 0.439 C5 Y19 8 Y19 N13 N13 N 0 1 N N N 10.199 5.775 -18.234 2.686 0.881 -0.540 N13 Y19 9 Y19 C14 C14 C 0 1 N N N 9.783 4.547 -18.571 3.397 1.979 -0.215 C14 Y19 10 Y19 C15 C15 C 0 1 N N N 8.824 3.831 -17.640 3.579 3.085 -1.222 C15 Y19 11 Y19 C16 C16 C 0 1 N N N 7.443 3.695 -18.248 4.419 4.205 -0.604 C16 Y19 12 Y19 O23 O23 O 0 1 N N N 10.162 3.992 -19.588 3.891 2.076 0.888 O23 Y19 13 Y19 N7 N7 N 0 1 N N N 11.779 5.832 -15.737 0.022 -0.118 0.228 N7 Y19 14 Y19 C8 C8 C 0 1 N N N 12.864 6.134 -14.812 -1.267 -0.767 -0.021 C8 Y19 15 Y19 C9 C9 C 0 1 N N S 12.445 5.912 -13.362 -2.389 0.268 0.086 C9 Y19 16 Y19 O9 O9 O 0 1 N N N 11.623 6.995 -12.916 -2.387 0.838 1.397 O9 Y19 17 Y19 C10 C10 C 0 1 N N S 13.687 5.849 -12.476 -3.735 -0.410 -0.174 C10 Y19 18 Y19 O10 O10 O 0 1 N N N 14.591 6.906 -12.828 -3.737 -0.980 -1.484 O10 Y19 19 Y19 C11 C11 C 0 1 N N R 14.388 4.493 -12.590 -4.857 0.626 -0.066 C11 Y19 20 Y19 O11 O11 O 0 1 N N N 13.520 3.455 -12.114 -4.855 1.195 1.244 O11 Y19 21 Y19 C12 C12 C 0 1 N N N 15.707 4.459 -11.822 -6.203 -0.053 -0.326 C12 Y19 22 Y19 O12 O12 O 0 1 N N N 15.477 4.608 -10.417 -7.238 0.933 -0.342 O12 Y19 23 Y19 H3 H3 H 0 1 N N N 8.339 9.487 -16.798 4.236 -3.023 0.016 H3 Y19 24 Y19 H5 H5 H 0 1 N N N 9.146 5.680 -16.486 2.492 0.257 1.431 H5 Y19 25 Y19 H7 H7 H 0 1 N N N 11.717 4.918 -16.137 0.058 0.832 0.423 H7 Y19 26 Y19 H13 H13 H 0 1 N N N 10.837 6.254 -18.837 2.291 0.803 -1.423 H13 Y19 27 Y19 H151 1H15 H 0 0 N N N 9.219 2.825 -17.433 4.086 2.694 -2.104 H151 Y19 28 Y19 H152 2H15 H 0 0 N N N 8.735 4.424 -16.718 2.603 3.478 -1.509 H152 Y19 29 Y19 H161 1H16 H 0 0 N N N 6.690 3.662 -17.446 4.550 5.005 -1.333 H161 Y19 30 Y19 H162 2H16 H 0 0 N N N 7.244 4.557 -18.902 3.911 4.596 0.277 H162 Y19 31 Y19 H163 3H16 H 0 0 N N N 7.392 2.767 -18.837 5.394 3.811 -0.317 H163 Y19 32 Y19 H8C1 1H8C H 0 0 N N N 13.716 5.476 -15.039 -1.268 -1.202 -1.020 H8C1 Y19 33 Y19 H8C2 2H8C H 0 0 N N N 13.137 7.193 -14.934 -1.427 -1.553 0.717 H8C2 Y19 34 Y19 H9 H9 H 0 1 N N N 11.883 4.969 -13.298 -2.229 1.054 -0.652 H9 Y19 35 Y19 HA HA H 0 1 N N N 11.441 6.894 -11.989 -2.524 0.195 2.105 HA Y19 36 Y19 H10 H10 H 0 1 N N N 13.368 5.974 -11.431 -3.895 -1.196 0.565 H10 Y19 37 Y19 HB HB H 0 1 N N N 14.791 7.423 -12.056 -3.600 -0.336 -2.193 HB Y19 38 Y19 H11 H11 H 0 1 N N N 14.621 4.330 -13.653 -4.697 1.411 -0.805 H11 Y19 39 Y19 HC HC H 0 1 N N N 13.328 2.852 -12.823 -4.992 0.552 1.953 HC Y19 40 Y19 H121 1H12 H 0 0 N N N 16.205 3.495 -12.005 -6.174 -0.563 -1.289 H121 Y19 41 Y19 H122 2H12 H 0 0 N N N 16.340 5.289 -12.168 -6.404 -0.777 0.463 H122 Y19 42 Y19 H12 H12 H 0 1 N N N 16.310 4.641 -9.961 -8.121 0.574 -0.502 H12 Y19 43 # 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 Y19 O2 C2 DOUB N N 1 Y19 C2 N3 SING N N 2 Y19 C2 N1 SING N N 3 Y19 N3 C4 SING N N 4 Y19 C4 O4 DOUB N N 5 Y19 C4 C5 SING N N 6 Y19 N1 C6 DOUB N N 7 Y19 C6 C5 SING N N 8 Y19 C6 N7 SING N N 9 Y19 C5 N13 SING N N 10 Y19 N13 C14 SING N N 11 Y19 C14 C15 SING N N 12 Y19 C14 O23 DOUB N N 13 Y19 C15 C16 SING N N 14 Y19 N7 C8 SING N N 15 Y19 C8 C9 SING N N 16 Y19 C9 O9 SING N N 17 Y19 C9 C10 SING N N 18 Y19 C10 O10 SING N N 19 Y19 C10 C11 SING N N 20 Y19 C11 O11 SING N N 21 Y19 C11 C12 SING N N 22 Y19 C12 O12 SING N N 23 Y19 N3 H3 SING N N 24 Y19 C5 H5 SING N N 25 Y19 N7 H7 SING N N 26 Y19 N13 H13 SING N N 27 Y19 C15 H151 SING N N 28 Y19 C15 H152 SING N N 29 Y19 C16 H161 SING N N 30 Y19 C16 H162 SING N N 31 Y19 C16 H163 SING N N 32 Y19 C8 H8C1 SING N N 33 Y19 C8 H8C2 SING N N 34 Y19 C9 H9 SING N N 35 Y19 O9 HA SING N N 36 Y19 C10 H10 SING N N 37 Y19 O10 HB SING N N 38 Y19 C11 H11 SING N N 39 Y19 O11 HC SING N N 40 Y19 C12 H121 SING N N 41 Y19 C12 H122 SING N N 42 Y19 O12 H12 SING N N 43 # 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 Y19 SMILES ACDLabs 10.04 "O=C1NC(=O)N=C(NCC(O)C(O)C(O)CO)C1NC(=O)CC" Y19 SMILES_CANONICAL CACTVS 3.341 "CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@H](O)[C@H](O)[C@H](O)CO" Y19 SMILES CACTVS 3.341 "CCC(=O)N[CH]1C(=O)NC(=O)N=C1NC[CH](O)[CH](O)[CH](O)CO" Y19 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@@H]([C@@H]([C@@H](CO)O)O)O" Y19 SMILES "OpenEye OEToolkits" 1.5.0 "CCC(=O)NC1C(=O)NC(=O)N=C1NCC(C(C(CO)O)O)O" Y19 InChI InChI 1.03 "InChI=1S/C12H20N4O7/c1-2-7(20)14-8-10(15-12(23)16-11(8)22)13-3-5(18)9(21)6(19)4-17/h5-6,8-9,17-19,21H,2-4H2,1H3,(H,14,20)(H2,13,15,16,22,23)/t5-,6+,8-,9-/m0/s1" Y19 InChIKey InChI 1.03 NPNFNBTUUJYCDD-FAYXRDSDSA-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 Y19 "SYSTEMATIC NAME" ACDLabs 10.04 "1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol" Y19 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(5S)-2,4-dioxo-6-[[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino]-5H-pyrimidin-5-yl]propanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y19 "Create component" 2007-11-27 EBI Y19 "Modify descriptor" 2011-06-04 RCSB #