data_UMS # _chem_comp.id UMS _chem_comp.name "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-08-15 _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 401.168 _chem_comp.one_letter_code U _chem_comp.three_letter_code UMS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1MA8 _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 UMS OP3 O3P O 0 1 N Y N ? ? ? -4.762 1.995 0.821 OP3 UMS 1 UMS P P P 0 1 N N N -5.121 8.015 11.452 -4.794 0.725 -0.168 P UMS 2 UMS OP1 O1P O 0 1 N N N -6.464 8.650 11.533 -5.577 -0.366 0.454 OP1 UMS 3 UMS OP2 O2P O 0 1 N N N -5.037 6.600 11.736 -5.478 1.148 -1.563 OP2 UMS 4 UMS "O5'" "O5'" O 0 1 N N N -4.431 8.316 10.040 -3.290 0.217 -0.440 "O5'" UMS 5 UMS "C5'" "C5'" C 0 1 N N N -4.377 9.762 9.517 -2.455 -0.325 0.585 "C5'" UMS 6 UMS "C4'" "C4'" C 0 1 N N R -3.589 9.697 8.319 -1.098 -0.705 -0.011 "C4'" UMS 7 UMS "O4'" "O4'" O 0 1 N N N -2.172 9.324 8.685 -0.384 0.474 -0.442 "O4'" UMS 8 UMS "C3'" "C3'" C 0 1 N N R -3.810 8.595 7.276 -0.174 -1.309 1.077 "C3'" UMS 9 UMS "O3'" "O3'" O 0 1 N N N -4.942 8.908 6.483 -0.397 -2.714 1.212 "O3'" UMS 10 UMS "C2'" "C2'" C 0 1 N N R -2.554 8.507 6.442 1.235 -1.026 0.500 "C2'" UMS 11 UMS "SE2'" "SE2'" SE 0 0 N N N -2.422 10.183 5.350 1.930 -2.611 -0.420 "SE2'" UMS 12 UMS "C1'" "C1'" C 0 1 N N R -1.580 8.655 7.579 1.008 0.123 -0.502 "C1'" UMS 13 UMS "CA'" "CA'" C 0 1 N N N -0.856 9.505 4.255 1.990 -3.902 1.053 "CA'" UMS 14 UMS N1 N1 N 0 1 N N N -1.102 7.325 8.109 1.829 1.278 -0.128 N1 UMS 15 UMS C2 C2 C 0 1 N N N -0.034 6.764 7.490 2.807 1.694 -0.953 C2 UMS 16 UMS O2 O2 O 0 1 N N N 0.541 7.254 6.544 2.998 1.107 -2.001 O2 UMS 17 UMS N3 N3 N 0 1 N N N 0.345 5.584 8.091 3.576 2.752 -0.636 N3 UMS 18 UMS C4 C4 C 0 1 N N N -0.178 4.898 9.125 3.377 3.414 0.522 C4 UMS 19 UMS O4 O4 O 0 1 N N N 0.289 3.809 9.494 4.072 4.372 0.810 O4 UMS 20 UMS C5 C5 C 0 1 N N N -1.316 5.561 9.712 2.351 2.986 1.399 C5 UMS 21 UMS C6 C6 C 0 1 N N N -1.738 6.759 9.197 1.591 1.925 1.053 C6 UMS 22 UMS HOP3 HOP3 H 0 0 N N N 0.857 -0.405 -0.051 -4.264 2.749 0.476 HOP3 UMS 23 UMS HOP2 HOP2 H 0 0 N N N -5.019 6.113 10.920 -6.387 1.464 -1.475 HOP2 UMS 24 UMS "H5'" "H5'" H 0 1 N N N -5.387 10.141 9.303 -2.312 0.419 1.369 "H5'" UMS 25 UMS "H5'2" "H5'2" H 0 0 N N N -3.942 10.450 10.257 -2.927 -1.212 1.007 "H5'2" UMS 26 UMS "H4'" "H4'" H 0 1 N N N -3.850 10.678 7.896 -1.225 -1.401 -0.840 "H4'" UMS 27 UMS "H3'" "H3'" H 0 1 N N N -4.005 7.623 7.752 -0.313 -0.802 2.031 "H3'" UMS 28 UMS "HO3'" H3T H 0 0 N Y N -5.709 8.978 7.039 -1.295 -2.946 1.485 "HO3'" UMS 29 UMS "H2'" "H2'" H 0 1 N N N -2.450 7.639 5.774 1.916 -0.716 1.292 "H2'" UMS 30 UMS "H1'" "H1'" H 0 1 N N N -0.740 9.227 7.159 1.265 -0.207 -1.508 "H1'" UMS 31 UMS "HA'" "HA'" H 0 1 N N N -1.167 9.382 3.207 2.650 -3.529 1.837 "HA'" UMS 32 UMS "HA'2" "HA'2" H 0 0 N N N -0.030 10.229 4.310 0.988 -4.039 1.458 "HA'2" UMS 33 UMS "HA'3" "HA'3" H 0 0 N N N -0.522 8.536 4.654 2.367 -4.856 0.685 "HA'3" UMS 34 UMS H3 H3 H 0 1 N N N 1.155 5.160 7.686 4.277 3.039 -1.242 H3 UMS 35 UMS H5 H5 H 0 1 N N N -1.832 5.117 10.551 2.177 3.504 2.331 H5 UMS 36 UMS H6 H6 H 0 1 N N N -2.578 7.267 9.647 0.801 1.587 1.707 H6 UMS 37 # 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 UMS OP3 P SING N N 1 UMS OP3 HOP3 SING N N 2 UMS P OP1 DOUB N N 3 UMS P OP2 SING N N 4 UMS P "O5'" SING N N 5 UMS OP2 HOP2 SING N N 6 UMS "O5'" "C5'" SING N N 7 UMS "C5'" "C4'" SING N N 8 UMS "C5'" "H5'" SING N N 9 UMS "C5'" "H5'2" SING N N 10 UMS "C4'" "O4'" SING N N 11 UMS "C4'" "C3'" SING N N 12 UMS "C4'" "H4'" SING N N 13 UMS "O4'" "C1'" SING N N 14 UMS "C3'" "O3'" SING N N 15 UMS "C3'" "C2'" SING N N 16 UMS "C3'" "H3'" SING N N 17 UMS "O3'" "HO3'" SING N N 18 UMS "C2'" "SE2'" SING N N 19 UMS "C2'" "C1'" SING N N 20 UMS "C2'" "H2'" SING N N 21 UMS "SE2'" "CA'" SING N N 22 UMS "C1'" N1 SING N N 23 UMS "C1'" "H1'" SING N N 24 UMS "CA'" "HA'" SING N N 25 UMS "CA'" "HA'2" SING N N 26 UMS "CA'" "HA'3" SING N N 27 UMS N1 C2 SING N N 28 UMS N1 C6 SING N N 29 UMS C2 O2 DOUB N N 30 UMS C2 N3 SING N N 31 UMS N3 C4 SING N N 32 UMS N3 H3 SING N N 33 UMS C4 O4 DOUB N N 34 UMS C4 C5 SING N N 35 UMS C5 C6 DOUB N N 36 UMS C5 H5 SING N N 37 UMS C6 H6 SING N N 38 # 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 UMS SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2[Se]C)COP(=O)(O)O" UMS SMILES_CANONICAL CACTVS 3.341 "C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" UMS SMILES CACTVS 3.341 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" UMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[Se][C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" UMS SMILES "OpenEye OEToolkits" 1.5.0 "C[Se]C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" UMS InChI InChI 1.03 "InChI=1S/C10H15N2O8PSe/c1-22-8-7(14)5(4-19-21(16,17)18)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" UMS InChIKey InChI 1.03 PADIGPKUSVFCBC-ZOQUXTDFSA-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 UMS "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate) ; UMS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methylselanyl-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 UMS "Create component" 2002-08-15 RCSB UMS "Modify descriptor" 2011-06-04 RCSB #