data_UMX # _chem_comp.id UMX _chem_comp.name "[(1R,3R,4R,5S,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-10-11 _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 348.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UMX _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 3OZ5 _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 UMX P P P 0 1 N N N -10.442 4.754 -4.353 -4.251 -1.110 0.155 P UMX 1 UMX N1 N1 N 0 1 N N N -6.082 6.279 -7.141 2.461 -0.280 0.395 N1 UMX 2 UMX C2 C2 C 0 1 N N N -5.092 6.366 -8.070 3.730 -0.042 0.773 C2 UMX 3 UMX O2 O2 O 0 1 N N N -4.266 7.334 -7.997 3.976 0.920 1.475 O2 UMX 4 UMX N3 N3 N 0 1 N N N -4.960 5.447 -9.060 4.732 -0.853 0.386 N3 UMX 5 UMX C4 C4 C 0 1 N N N -5.810 4.437 -9.168 4.476 -1.924 -0.393 C4 UMX 6 UMX O4 O4 O 0 1 N N N -5.705 3.625 -10.087 5.381 -2.659 -0.744 O4 UMX 7 UMX C5 C5 C 0 1 N N N -6.882 4.334 -8.218 3.145 -2.187 -0.797 C5 UMX 8 UMX C6 C6 C 0 1 N N N -6.967 5.259 -7.220 2.159 -1.360 -0.389 C6 UMX 9 UMX "C1'" "C1'" C 0 1 N N R -6.120 7.275 -6.062 1.392 0.621 0.833 "C1'" UMX 10 UMX "C2'" "C2'" C 0 1 N N R -6.790 8.592 -6.402 1.276 1.835 -0.142 "C2'" UMX 11 UMX "C3'" "C3'" C 0 1 N N S -8.184 8.142 -6.172 0.305 1.199 -1.202 "C3'" UMX 12 UMX "O3'" "O3'" O 0 1 N N N -9.191 9.212 -6.190 -0.249 2.177 -2.085 "O3'" UMX 13 UMX "C4'" "C4'" C 0 1 N N R -7.934 7.684 -4.755 -0.735 0.700 -0.139 "C4'" UMX 14 UMX "O4'" "O4'" O 0 1 N N N -6.862 6.747 -4.963 0.119 -0.049 0.769 "O4'" UMX 15 UMX "C5'" "C5'" C 0 1 N N N -9.114 7.001 -4.088 -1.951 -0.045 -0.691 "C5'" UMX 16 UMX "O5'" "O5'" O 0 1 N N N -9.550 5.917 -4.942 -2.859 -0.332 0.375 "O5'" UMX 17 UMX "C6'" "C6'" C 0 1 N N S -6.422 9.446 -5.206 0.297 2.804 0.593 "C6'" UMX 18 UMX "C7'" "C7'" C 0 1 N N N -6.567 10.920 -5.410 0.149 4.112 -0.188 "C7'" UMX 19 UMX "C8'" "C8'" C 0 1 N N N -7.345 8.932 -4.088 -1.043 2.030 0.614 "C8'" UMX 20 UMX OP1 OP1 O 0 1 N N N -11.572 5.359 -3.452 -5.226 -0.217 -0.764 OP1 UMX 21 UMX OP2 OP2 O 0 1 N N N -10.873 3.958 -5.618 -3.993 -2.405 -0.513 OP2 UMX 22 UMX OP3 OP3 O 0 1 N Y N -9.420 3.932 -3.418 -4.950 -1.372 1.582 OP3 UMX 23 UMX H5 H5 H 0 1 N N N -7.608 3.538 -8.293 2.921 -3.040 -1.421 H5 UMX 24 UMX H6 H6 H 0 1 N N N -7.752 5.176 -6.482 1.138 -1.544 -0.688 H6 UMX 25 UMX "H1'" "H1'" H 0 1 N N N -5.060 7.478 -5.848 1.585 0.968 1.848 "H1'" UMX 26 UMX "H2'" "H2'" H 0 1 N N N -6.581 9.091 -7.360 2.210 2.255 -0.515 "H2'" UMX 27 UMX "H3'" "H3'" H 0 1 N N N -8.589 7.440 -6.915 0.768 0.375 -1.745 "H3'" UMX 28 UMX "HO3'" "HO3'" H 0 0 N Y N -10.052 8.840 -6.036 0.410 2.648 -2.613 "HO3'" UMX 29 UMX "H5'" "H5'" H 0 1 N N N -8.813 6.606 -3.106 -2.450 0.575 -1.436 "H5'" UMX 30 UMX "H5'A" "H5'A" H 0 0 N N N -9.934 7.721 -3.949 -1.627 -0.978 -1.153 "H5'A" UMX 31 UMX "H6'" "H6'" H 0 1 N N N -5.350 9.346 -4.979 0.642 3.000 1.608 "H6'" UMX 32 UMX "H7'" "H7'" H 0 1 N N N -6.277 11.448 -4.490 -0.243 3.899 -1.182 "H7'" UMX 33 UMX "H7'A" "H7'A" H 0 0 N N N -5.917 11.241 -6.237 -0.537 4.774 0.340 "H7'A" UMX 34 UMX "H7'B" "H7'B" H 0 0 N N N -7.614 11.155 -5.654 1.123 4.594 -0.276 "H7'B" UMX 35 UMX "H8'" "H8'" H 0 1 N N N -8.117 9.664 -3.810 -1.816 2.593 0.092 "H8'" UMX 36 UMX "H8'A" "H8'A" H 0 0 N N N -6.796 8.696 -3.164 -1.348 1.825 1.640 "H8'A" UMX 37 UMX HOP1 HOP1 H 0 0 N N N -12.421 5.146 -3.822 -5.439 0.648 -0.387 HOP1 UMX 38 UMX HOP3 HOP3 H 0 0 N Y N -9.250 3.082 -3.806 -5.796 -1.838 1.526 HOP3 UMX 39 UMX HN3 HN3 H 0 1 N N N -4.211 5.534 -9.717 5.641 -0.667 0.667 HN3 UMX 40 # 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 UMX OP2 P DOUB N N 1 UMX "O5'" P SING N N 2 UMX P OP1 SING N N 3 UMX P OP3 SING N N 4 UMX C2 N1 SING N N 5 UMX C6 N1 SING N N 6 UMX N1 "C1'" SING N N 7 UMX N3 C2 SING N N 8 UMX C2 O2 DOUB N N 9 UMX C4 N3 SING N N 10 UMX O4 C4 DOUB N N 11 UMX C4 C5 SING N N 12 UMX C5 C6 DOUB N N 13 UMX C5 H5 SING N N 14 UMX C6 H6 SING N N 15 UMX "C2'" "C1'" SING N N 16 UMX "C1'" "O4'" SING N N 17 UMX "C1'" "H1'" SING N N 18 UMX "C2'" "C3'" SING N N 19 UMX "C2'" "C6'" SING N N 20 UMX "C2'" "H2'" SING N N 21 UMX "O3'" "C3'" SING N N 22 UMX "C3'" "C4'" SING N N 23 UMX "C3'" "H3'" SING N N 24 UMX "O3'" "HO3'" SING N N 25 UMX "O4'" "C4'" SING N N 26 UMX "C4'" "C5'" SING N N 27 UMX "C4'" "C8'" SING N N 28 UMX "O5'" "C5'" SING N N 29 UMX "C5'" "H5'" SING N N 30 UMX "C5'" "H5'A" SING N N 31 UMX "C7'" "C6'" SING N N 32 UMX "C6'" "C8'" SING N N 33 UMX "C6'" "H6'" SING N N 34 UMX "C7'" "H7'" SING N N 35 UMX "C7'" "H7'A" SING N N 36 UMX "C7'" "H7'B" SING N N 37 UMX "C8'" "H8'" SING N N 38 UMX "C8'" "H8'A" SING N N 39 UMX OP1 HOP1 SING N N 40 UMX OP3 HOP3 SING N N 41 UMX N3 HN3 SING N N 42 # 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 UMX SMILES ACDLabs 12.01 "O=P(O)(O)OCC23OC(N1C(=O)NC(=O)C=C1)C(C(C2)C)C3O" UMX SMILES_CANONICAL CACTVS 3.370 "C[C@H]1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=CC(=O)NC3=O" UMX SMILES CACTVS 3.370 "C[CH]1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=CC(=O)NC3=O" UMX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@H]1C[C@]2([C@H]([C@@H]1[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" UMX SMILES "OpenEye OEToolkits" 1.7.0 "CC1CC2(C(C1C(O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" UMX InChI InChI 1.03 "InChI=1S/C12H17N2O8P/c1-6-4-12(5-21-23(18,19)20)9(16)8(6)10(22-12)14-3-2-7(15)13-11(14)17/h2-3,6,8-10,16H,4-5H2,1H3,(H,13,15,17)(H2,18,19,20)/t6-,8+,9-,10+,12+/m0/s1" UMX InChIKey InChI 1.03 BIKPERMTZJFCSY-UNUCDPEXSA-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 UMX "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,3R,4R,5S,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" UMX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(1R,2S,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-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 UMX "Create component" 2010-10-11 RCSB UMX "Modify descriptor" 2011-06-04 RCSB #