data_MDU # _chem_comp.id MDU _chem_comp.name ;3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-23 _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 352.234 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDU _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 3O1T _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 MDU P P P 0 1 N N N 0.890 0.704 -0.990 -4.666 1.167 -0.167 P MDU 1 MDU N1 N1 N 0 1 N N N 0.158 -1.740 3.435 1.814 -0.545 -0.128 N1 MDU 2 MDU C2 C2 C 0 1 N N N -0.447 -2.384 4.490 2.913 -0.380 -0.887 C2 MDU 3 MDU O2 O2 O 0 1 N N N 0.280 -2.846 5.405 2.937 -0.832 -2.015 O2 MDU 4 MDU N3 N3 N 0 1 N N N -1.814 -2.547 4.560 3.987 0.280 -0.414 N3 MDU 5 MDU C4 C4 C 0 1 N N N -2.599 -2.064 3.539 3.977 0.789 0.835 C4 MDU 6 MDU O4 O4 O 0 1 N N N -3.846 -2.216 3.564 4.948 1.386 1.263 O4 MDU 7 MDU C5 C5 C 0 1 N N N -2.030 -1.389 2.434 2.827 0.621 1.643 C5 MDU 8 MDU C6 C6 C 0 1 N N N -0.632 -1.230 2.443 1.764 -0.045 1.144 C6 MDU 9 MDU "C1'" "C1'" C 0 1 N N R 1.613 -1.660 3.338 0.659 -1.263 -0.672 "C1'" MDU 10 MDU O1P O1P O 0 1 N N N 1.480 1.694 -1.969 -5.936 0.235 0.169 O1P MDU 11 MDU "C2'" "C2'" C 0 1 N N N 2.215 -3.009 2.880 0.432 -2.566 0.118 "C2'" MDU 12 MDU C21 C21 C 0 1 N N N -2.445 -3.241 5.675 5.171 0.447 -1.260 C21 MDU 13 MDU O22 O22 O 0 1 N N N -3.327 -2.383 6.395 5.231 1.793 -1.737 O22 MDU 14 MDU O2P O2P O 0 1 N N N -0.053 1.406 -0.095 -4.337 1.996 1.014 O2P MDU 15 MDU "C3'" "C3'" C 0 1 N N S 3.394 -2.621 1.979 -1.009 -2.430 0.669 "C3'" MDU 16 MDU "O3'" "O3'" O 0 1 N N N 4.616 -2.590 2.716 -1.711 -3.671 0.571 "O3'" MDU 17 MDU "C4'" "C4'" C 0 1 N N R 3.016 -1.204 1.494 -1.622 -1.372 -0.284 "C4'" MDU 18 MDU "O4'" "O4'" O 0 1 N N N 2.125 -0.636 2.467 -0.526 -0.463 -0.526 "O4'" MDU 19 MDU "C5'" "C5'" C 0 1 N N N 2.337 -1.159 0.100 -2.785 -0.646 0.395 "C5'" MDU 20 MDU "O5'" "O5'" O 0 1 N N N 2.023 0.117 -0.163 -3.404 0.239 -0.541 "O5'" MDU 21 MDU C5M C5M C 0 1 N N N -2.810 -0.868 1.278 2.790 1.179 3.043 C5M MDU 22 MDU H6 H6 H 0 1 N N N -0.166 -0.685 1.636 0.878 -0.182 1.747 H6 MDU 23 MDU "H1'" "H1'" H 0 1 N N N 1.921 -1.397 4.361 0.827 -1.492 -1.724 "H1'" MDU 24 MDU "H2'" "H2'" H 0 1 N N N 2.553 -3.605 3.741 0.508 -3.431 -0.541 "H2'" MDU 25 MDU "H2'A" "H2'A" H 0 0 N N N 1.474 -3.607 2.328 1.147 -2.645 0.937 "H2'A" MDU 26 MDU H21 H21 H 0 1 N N N -3.021 -4.092 5.282 6.067 0.228 -0.678 H21 MDU 27 MDU "H3'" "H3'" H 0 1 N N N 3.558 -3.334 1.158 -1.000 -2.070 1.697 "H3'" MDU 28 MDU "HO3'" "HO3'" H 0 0 N N N 5.329 -2.348 2.137 -1.312 -4.390 1.080 "HO3'" MDU 29 MDU "H4'" "H4'" H 0 1 N N N 3.952 -0.637 1.387 -1.948 -1.836 -1.214 "H4'" MDU 30 MDU "H5'" "H5'" H 0 1 N N N 3.026 -1.543 -0.667 -3.515 -1.375 0.743 "H5'" MDU 31 MDU "H5'A" "H5'A" H 0 0 N N N 1.427 -1.777 0.104 -2.410 -0.073 1.243 "H5'A" MDU 32 MDU H5M H5M H 0 1 N N N -2.128 -0.388 0.561 3.734 1.678 3.260 H5M MDU 33 MDU H5MA H5MA H 0 0 N N N -3.334 -1.700 0.785 1.973 1.896 3.127 H5MA MDU 34 MDU H5MB H5MB H 0 0 N N N -3.545 -0.131 1.634 2.636 0.367 3.754 H5MB MDU 35 MDU O9 O9 O 0 1 N N N 0.156 -0.368 -1.759 -5.017 2.124 -1.413 O9 MDU 36 MDU H14 H14 H 0 1 N N N 1.120 2.557 -1.802 -6.208 -0.336 -0.562 H14 MDU 37 MDU H15 H15 H 0 1 N N N -0.760 -0.368 -1.507 -5.769 2.711 -1.259 H15 MDU 38 MDU H16 H16 H 0 1 N N N -1.661 -3.598 6.359 5.112 -0.237 -2.107 H16 MDU 39 MDU H17 H17 H 0 1 N N N -3.902 -1.936 5.785 5.991 1.975 -2.305 H17 MDU 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 MDU P O1P SING N N 1 MDU P O2P DOUB N N 2 MDU P "O5'" SING N N 3 MDU N1 C2 SING N N 4 MDU N1 C6 SING N N 5 MDU N1 "C1'" SING N N 6 MDU C2 O2 DOUB N N 7 MDU C2 N3 SING N N 8 MDU N3 C4 SING N N 9 MDU N3 C21 SING N N 10 MDU C4 O4 DOUB N N 11 MDU C4 C5 SING N N 12 MDU C5 C6 DOUB N N 13 MDU C5 C5M SING N N 14 MDU C6 H6 SING N N 15 MDU "C1'" "C2'" SING N N 16 MDU "C1'" "O4'" SING N N 17 MDU "C1'" "H1'" SING N N 18 MDU O1P H14 SING N N 19 MDU "C2'" "C3'" SING N N 20 MDU "C2'" "H2'" SING N N 21 MDU "C2'" "H2'A" SING N N 22 MDU C21 O22 SING N N 23 MDU C21 H21 SING N N 24 MDU "C3'" "O3'" SING N N 25 MDU "C3'" "C4'" SING N N 26 MDU "C3'" "H3'" SING N N 27 MDU "O3'" "HO3'" SING N N 28 MDU "C4'" "O4'" SING N N 29 MDU "C4'" "C5'" SING N N 30 MDU "C4'" "H4'" SING N N 31 MDU "C5'" "O5'" SING N N 32 MDU "C5'" "H5'" SING N N 33 MDU "C5'" "H5'A" SING N N 34 MDU C5M H5M SING N N 35 MDU C5M H5MA SING N N 36 MDU C5M H5MB SING N N 37 MDU O9 P SING N N 38 MDU O9 H15 SING N N 39 MDU C21 H16 SING N N 40 MDU O22 H17 SING N N 41 # 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 MDU SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N(C(=O)C(=C1)C)CO)CC2O" MDU SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N(CO)C1=O" MDU SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N(CO)C1=O" MDU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)CO)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" MDU SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)CO)C2CC(C(O2)COP(=O)(O)O)O" MDU InChI InChI 1.03 "InChI=1S/C11H17N2O9P/c1-6-3-12(11(17)13(5-14)10(6)16)9-2-7(15)8(22-9)4-21-23(18,19)20/h3,7-9,14-15H,2,4-5H2,1H3,(H2,18,19,20)/t7-,8+,9+/m0/s1" MDU InChIKey InChI 1.03 UGQLUWYICJLJKZ-DJLDLDEBSA-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 MDU "SYSTEMATIC NAME" ACDLabs 12.01 ;3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate) ; MDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-3-hydroxy-5-[3-(hydroxymethyl)-5-methyl-2,4-dioxo-pyrimidin-1-yl]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 MDU "Create component" 2010-07-23 RCSB MDU "Modify descriptor" 2011-06-04 RCSB #