data_UM3 # _chem_comp.id UM3 _chem_comp.name ;2'-DEOXYURIDINE 3'-MONOPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 308.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UM3 _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 2RNF _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 UM3 N1 N1 N 0 1 Y N N -2.978 25.955 12.116 0.194 0.664 -2.247 N1 UM3 1 UM3 C2 C2 C 0 1 Y N N -3.579 24.903 11.427 -0.328 -0.575 -2.262 C2 UM3 2 UM3 N3 N3 N 0 1 Y N N -2.707 24.069 10.777 -0.821 -1.104 -3.398 N3 UM3 3 UM3 C4 C4 C 0 1 Y N N -1.334 24.164 10.731 -0.787 -0.399 -4.547 C4 UM3 4 UM3 C5 C5 C 0 1 Y N N -0.785 25.256 11.478 -0.234 0.904 -4.546 C5 UM3 5 UM3 C6 C6 C 0 1 Y N N -1.602 26.096 12.119 0.247 1.412 -3.392 C6 UM3 6 UM3 O2 O2 O 0 1 N N N -4.788 24.707 11.407 -0.366 -1.222 -1.234 O2 UM3 7 UM3 O4 O4 O 0 1 N N N -0.701 23.378 10.024 -1.228 -0.878 -5.575 O4 UM3 8 UM3 "C1'" C1* C 0 1 N N R -3.843 26.919 12.825 0.718 1.215 -0.995 "C1'" UM3 9 UM3 "C2'" C2* C 0 1 N N N -4.014 26.539 14.291 -0.397 1.266 0.065 "C2'" UM3 10 UM3 "C3'" C3* C 0 1 N N S -3.805 27.827 15.069 0.146 0.408 1.235 "C3'" UM3 11 UM3 "C4'" C4* C 0 1 N N R -3.003 28.721 14.123 1.671 0.415 0.957 "C4'" UM3 12 UM3 "O3'" O3* O 0 1 N N N -5.048 28.417 15.463 -0.151 1.013 2.494 "O3'" UM3 13 UM3 "O4'" O4* O 0 1 N N N -3.207 28.198 12.786 1.756 0.362 -0.482 "O4'" UM3 14 UM3 "C5'" C5* C 0 1 N N N -1.523 28.763 14.435 2.339 -0.811 1.582 "C5'" UM3 15 UM3 "O5'" O5* O 0 1 N N N -1.007 27.438 14.583 3.733 -0.805 1.269 "O5'" UM3 16 UM3 P P P 0 1 N N N -5.707 28.008 16.874 -1.019 -0.054 3.330 P UM3 17 UM3 O1P O1P O 0 1 N N N -6.547 26.813 16.620 -0.230 -1.293 3.516 O1P UM3 18 UM3 O2P O2P O 0 1 N N N -6.314 29.212 17.500 -1.392 0.565 4.768 O2P UM3 19 UM3 O3P O3P O 0 1 N N N -4.473 27.555 17.776 -2.371 -0.394 2.525 O3P UM3 20 UM3 HN3 HN3 H 0 1 N N N -3.127 23.289 10.270 -1.199 -1.997 -3.390 HN3 UM3 21 UM3 H5 H5 H 0 1 N N N 0.296 25.455 11.561 -0.199 1.484 -5.456 H5 UM3 22 UM3 H6 H6 H 0 1 N N N -1.127 26.928 12.665 0.673 2.404 -3.372 H6 UM3 23 UM3 "H1'" H1* H 0 1 N N N -4.842 26.926 12.330 1.112 2.216 -1.167 "H1'" UM3 24 UM3 "H2'1" 1H2* H 0 0 N N N -4.982 26.032 14.513 -0.564 2.292 0.394 "H2'1" UM3 25 UM3 "H2'2" 2H2* H 0 0 N N N -3.351 25.704 14.618 -1.318 0.837 -0.328 "H2'2" UM3 26 UM3 "H3'" H3* H 0 1 N N N -3.264 27.659 16.029 -0.248 -0.606 1.189 "H3'" UM3 27 UM3 "H4'" H4* H 0 1 N N N -3.361 29.771 14.234 2.125 1.332 1.335 "H4'" UM3 28 UM3 "H5'1" 1H5* H 0 0 N N N -0.954 29.347 13.674 1.880 -1.716 1.183 "H5'1" UM3 29 UM3 "H5'2" 2H5* H 0 0 N N N -1.304 29.395 15.326 2.209 -0.784 2.664 "H5'2" UM3 30 UM3 "HO5'" *HO5 H 0 0 N N N -0.077 27.464 14.778 4.115 -1.593 1.680 "HO5'" UM3 31 UM3 HOP2 2HOP H 0 0 N N N -6.702 28.970 18.332 -1.910 -0.104 5.235 HOP2 UM3 32 UM3 HOP3 3HOP H 0 0 N N N -4.861 27.313 18.608 -2.854 0.437 2.425 HOP3 UM3 33 # 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 UM3 N1 C2 SING Y N 1 UM3 N1 C6 SING Y N 2 UM3 N1 "C1'" SING N N 3 UM3 C2 N3 SING Y N 4 UM3 C2 O2 DOUB N N 5 UM3 N3 C4 SING Y N 6 UM3 N3 HN3 SING N N 7 UM3 C4 C5 SING Y N 8 UM3 C4 O4 DOUB N N 9 UM3 C5 C6 DOUB Y N 10 UM3 C5 H5 SING N N 11 UM3 C6 H6 SING N N 12 UM3 "C1'" "C2'" SING N N 13 UM3 "C1'" "O4'" SING N N 14 UM3 "C1'" "H1'" SING N N 15 UM3 "C2'" "C3'" SING N N 16 UM3 "C2'" "H2'1" SING N N 17 UM3 "C2'" "H2'2" SING N N 18 UM3 "C3'" "C4'" SING N N 19 UM3 "C3'" "O3'" SING N N 20 UM3 "C3'" "H3'" SING N N 21 UM3 "C4'" "O4'" SING N N 22 UM3 "C4'" "C5'" SING N N 23 UM3 "C4'" "H4'" SING N N 24 UM3 "O3'" P SING N N 25 UM3 "C5'" "O5'" SING N N 26 UM3 "C5'" "H5'1" SING N N 27 UM3 "C5'" "H5'2" SING N N 28 UM3 "O5'" "HO5'" SING N N 29 UM3 P O1P DOUB N N 30 UM3 P O2P SING N N 31 UM3 P O3P SING N N 32 UM3 O2P HOP2 SING N N 33 UM3 O3P HOP3 SING N N 34 # 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 UM3 SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2)CO" UM3 SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H](C[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" UM3 SMILES CACTVS 3.341 "OC[CH]1O[CH](C[CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" UM3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)OP(=O)(O)O" UM3 SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)CO)OP(=O)(O)O" UM3 InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-4-6-5(19-20(15,16)17)3-8(18-6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" UM3 InChIKey InChI 1.03 LXKGKXYIAAKOCT-SHYZEUOFSA-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 UM3 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-3'-uridylic acid ; UM3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl] 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 UM3 "Create component" 1999-07-08 RCSB UM3 "Modify descriptor" 2011-06-04 RCSB #