data_UDM # _chem_comp.id UDM _chem_comp.name URIDINE-DIPHOSPHATE-METHYLENE-N-ACETYL-GLUCOSAMINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H29 N3 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;((2S,3R,4R,5S,6R)-3-ACETAMIDO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)METHYLPHOSPHONIC (((2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC) ANHYDRIDE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-09-21 _chem_comp.pdbx_modified_date 2020-06-17 _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 605.381 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UDM _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 2APC _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 UDM "C1'" "C1'" C 0 1 N N S 2.860 20.118 15.010 4.962 0.463 0.495 "C1'" UDM 1 UDM "C2'" "C2'" C 0 1 N N R 2.519 18.753 15.657 6.201 0.286 -0.384 "C2'" UDM 2 UDM "C3'" "C3'" C 0 1 N N R 1.347 18.200 14.847 6.163 -1.104 -1.031 "C3'" UDM 3 UDM "C4'" "C4'" C 0 1 N N S 0.132 19.158 14.952 5.991 -2.153 0.073 "C4'" UDM 4 UDM "C5'" "C5'" C 0 1 N N R 0.509 20.595 14.559 4.766 -1.793 0.916 "C5'" UDM 5 UDM "C6'" "C6'" C 0 1 N N N -0.572 21.555 15.101 4.566 -2.853 2.001 "C6'" UDM 6 UDM "C7'" "C7'" C 0 1 N N N 4.279 17.382 16.665 7.377 1.690 -1.992 "C7'" UDM 7 UDM "C8'" "C8'" C 0 1 N N N 5.444 16.452 16.501 7.387 2.746 -3.067 "C8'" UDM 8 UDM "N2'" "N2'" N 0 1 N N N 3.669 17.829 15.550 6.212 1.313 -1.429 "N2'" UDM 9 UDM CB CB C 0 1 N N N 3.150 20.190 13.511 3.706 0.301 -0.364 CB UDM 10 UDM "O3'" "O3'" O 0 1 N N N 0.944 16.911 15.344 7.385 -1.339 -1.734 "O3'" UDM 11 UDM "O4'" "O4'" O 0 1 N N N -0.996 18.780 14.145 5.805 -3.442 -0.518 "O4'" UDM 12 UDM "O5'" "O5'" O 0 1 N N N 1.712 20.982 15.271 4.958 -0.520 1.529 "O5'" UDM 13 UDM "O6'" "O6'" O 0 1 N N N -0.239 22.934 14.811 3.358 -2.583 2.715 "O6'" UDM 14 UDM "O7'" "O7'" O 0 1 N N N 3.920 17.698 17.803 8.417 1.179 -1.634 "O7'" UDM 15 UDM N1 N1 N 0 1 N N N -0.678 19.650 6.941 -6.504 -0.440 -0.972 N1 UDM 16 UDM C2 C2 C 0 1 N N N -1.928 20.010 6.396 -6.172 -1.455 -0.154 C2 UDM 17 UDM N3 N3 N 0 1 N N N -1.895 21.164 5.659 -6.729 -2.672 -0.300 N3 UDM 18 UDM C4 C4 C 0 1 N N N -0.750 21.969 5.431 -7.626 -2.896 -1.281 C4 UDM 19 UDM C5 C5 C 0 1 N N N 0.475 21.509 6.044 -7.980 -1.838 -2.153 C5 UDM 20 UDM C6 C6 C 0 1 N N N 0.479 20.406 6.752 -7.410 -0.626 -1.981 C6 UDM 21 UDM O2 O2 O 0 1 N N N -2.954 19.364 6.556 -5.365 -1.269 0.736 O2 UDM 22 UDM O4 O4 O 0 1 N N N -0.878 22.973 4.748 -8.127 -3.997 -1.417 O4 UDM 23 UDM C1D C1* C 0 1 N N R -0.615 18.409 7.742 -5.885 0.874 -0.785 C1D UDM 24 UDM C2D C2* C 0 1 N N R 0.496 17.434 7.442 -6.218 1.444 0.617 C2D UDM 25 UDM "O2'" O2* O 0 1 N N N 0.155 16.617 6.318 -7.465 2.142 0.600 "O2'" UDM 26 UDM C3D C3* C 0 1 N N S 0.600 16.638 8.758 -5.040 2.424 0.858 C3D UDM 27 UDM C4D C4* C 0 1 N N R 0.190 17.649 9.829 -3.940 1.928 -0.101 C4D UDM 28 UDM O4D O4* O 0 1 N N N -0.504 18.727 9.124 -4.446 0.761 -0.769 O4D UDM 29 UDM O3D O3* O 0 1 N N N -0.299 15.503 8.778 -5.427 3.761 0.538 O3D UDM 30 UDM C5D C5* C 0 1 N N N 1.286 18.265 10.697 -2.681 1.570 0.691 C5D UDM 31 UDM O5D O5* O 0 1 N N N 2.221 18.933 9.852 -1.633 1.217 -0.214 O5D UDM 32 UDM PA PA P 0 1 N N R 3.781 18.666 9.920 -0.346 0.854 0.683 PA UDM 33 UDM O1A O1A O 0 1 N N N 4.053 17.228 10.186 -0.037 1.987 1.584 O1A UDM 34 UDM O2A O2A O 0 1 N N N 4.326 19.222 8.669 -0.657 -0.459 1.561 O2A UDM 35 UDM O3A O3A O 0 1 N N N 4.460 19.530 11.141 0.915 0.572 -0.277 O3A UDM 36 UDM PB PB P 0 1 N N S 4.544 19.425 12.713 2.227 0.613 0.655 PB UDM 37 UDM O1B O1B O 0 1 N N N 4.668 17.953 12.953 2.339 1.945 1.292 O1B UDM 38 UDM O2B O2B O 0 1 N N N 5.805 20.155 13.084 2.112 -0.519 1.794 O2B UDM 39 UDM "H1'" "H1'" H 0 1 N N N 3.821 20.404 15.462 4.970 1.457 0.941 "H1'" UDM 40 UDM "H2'" "H2'" H 0 1 N N N 2.277 18.863 16.725 7.099 0.379 0.227 "H2'" UDM 41 UDM "H3'" "H3'" H 0 1 N N N 1.676 18.107 13.801 5.325 -1.161 -1.725 "H3'" UDM 42 UDM "H4'" "H4'" H 0 1 N N N -0.160 19.093 16.011 6.878 -2.167 0.705 "H4'" UDM 43 UDM "H5'" "H5'" H 0 1 N N N 0.625 20.641 13.466 3.883 -1.758 0.277 "H5'" UDM 44 UDM "H6'1" "1H6'" H 0 0 N N N -0.633 21.432 16.192 4.502 -3.839 1.539 "H6'1" UDM 45 UDM "H6'2" "2H6'" H 0 0 N N N -1.534 21.313 14.626 5.409 -2.830 2.692 "H6'2" UDM 46 UDM "H8'1" "1H8'" H 0 0 N N N 5.249 15.520 17.052 8.412 2.916 -3.399 "H8'1" UDM 47 UDM "H8'2" "2H8'" H 0 0 N N N 6.353 16.929 16.897 6.783 2.412 -3.911 "H8'2" UDM 48 UDM "H8'3" "3H8'" H 0 0 N N N 5.585 16.224 15.434 6.975 3.673 -2.669 "H8'3" UDM 49 UDM H3 H3 H 0 1 N N N 3.994 17.536 14.651 5.380 1.721 -1.716 H3 UDM 50 UDM HB1 1HB H 0 1 N N N 3.396 21.256 13.393 3.736 1.013 -1.189 HB1 UDM 51 UDM HB2 2HB H 0 1 N N N 2.270 19.733 13.034 3.666 -0.713 -0.762 HB2 UDM 52 UDM H4 H4 H 0 1 N N N 0.855 16.305 14.618 7.318 -2.221 -2.124 H4 UDM 53 UDM H7 H7 H 0 1 N N N -1.766 18.697 14.695 5.701 -4.070 0.210 H7 UDM 54 UDM "H6'" "H6'" H 0 1 N N N -0.166 23.420 15.624 3.270 -3.272 3.388 "H6'" UDM 55 UDM HN3 HN3 H 0 1 N N N -2.754 21.465 5.245 -6.482 -3.392 0.302 HN3 UDM 56 UDM H5 H5 H 0 1 N N N 1.387 22.074 5.919 -8.697 -1.997 -2.945 H5 UDM 57 UDM H6 H6 H 0 1 N N N 1.403 20.073 7.201 -7.668 0.193 -2.636 H6 UDM 58 UDM H1D H1* H 0 1 N N N -1.551 17.904 7.462 -6.207 1.563 -1.566 H1D UDM 59 UDM H2D H2* H 0 1 N N N 1.452 17.899 7.161 -6.228 0.653 1.366 H2D UDM 60 UDM H1 H1 H 0 1 N N N 0.079 17.160 5.542 -7.613 2.470 1.498 H1 UDM 61 UDM H3D H3* H 0 1 N N N 1.608 16.223 8.905 -4.699 2.363 1.892 H3D UDM 62 UDM H4D H4* H 0 1 N N N -0.414 17.084 10.554 -3.710 2.703 -0.832 H4D UDM 63 UDM H2 H2 H 0 1 N N N -0.496 15.239 7.887 -6.156 3.991 1.131 H2 UDM 64 UDM "H5'1" 1H5* H 0 0 N N N 1.797 17.476 11.269 -2.893 0.727 1.349 "H5'1" UDM 65 UDM "H5'2" 2H5* H 0 0 N N N 0.841 18.985 11.400 -2.372 2.428 1.289 "H5'2" UDM 66 UDM H2A H2A H 0 1 N N N 4.443 20.160 8.763 -0.853 -1.172 0.937 H2A UDM 67 UDM H2B H2B H 0 1 N N N 6.324 20.309 12.303 2.042 -1.368 1.338 H2B UDM 68 # # 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 UDM "C1'" "C2'" SING N N 1 UDM "C1'" CB SING N N 2 UDM "C1'" "O5'" SING N N 3 UDM "C1'" "H1'" SING N N 4 UDM "C2'" "C3'" SING N N 5 UDM "C2'" "N2'" SING N N 6 UDM "C2'" "H2'" SING N N 7 UDM "C3'" "C4'" SING N N 8 UDM "C3'" "O3'" SING N N 9 UDM "C3'" "H3'" SING N N 10 UDM "C4'" "C5'" SING N N 11 UDM "C4'" "O4'" SING N N 12 UDM "C4'" "H4'" SING N N 13 UDM "C5'" "C6'" SING N N 14 UDM "C5'" "O5'" SING N N 15 UDM "C5'" "H5'" SING N N 16 UDM "C6'" "O6'" SING N N 17 UDM "C6'" "H6'1" SING N N 18 UDM "C6'" "H6'2" SING N N 19 UDM "C7'" "C8'" SING N N 20 UDM "C7'" "N2'" SING N N 21 UDM "C7'" "O7'" DOUB N N 22 UDM "C8'" "H8'1" SING N N 23 UDM "C8'" "H8'2" SING N N 24 UDM "C8'" "H8'3" SING N N 25 UDM "N2'" H3 SING N N 26 UDM CB PB SING N N 27 UDM CB HB1 SING N N 28 UDM CB HB2 SING N N 29 UDM "O3'" H4 SING N N 30 UDM "O4'" H7 SING N N 31 UDM "O6'" "H6'" SING N N 32 UDM N1 C2 SING N N 33 UDM N1 C6 SING N N 34 UDM N1 C1D SING N N 35 UDM C2 N3 SING N N 36 UDM C2 O2 DOUB N N 37 UDM N3 C4 SING N N 38 UDM N3 HN3 SING N N 39 UDM C4 C5 SING N N 40 UDM C4 O4 DOUB N N 41 UDM C5 C6 DOUB N N 42 UDM C5 H5 SING N N 43 UDM C6 H6 SING N N 44 UDM C1D C2D SING N N 45 UDM C1D O4D SING N N 46 UDM C1D H1D SING N N 47 UDM C2D "O2'" SING N N 48 UDM C2D C3D SING N N 49 UDM C2D H2D SING N N 50 UDM "O2'" H1 SING N N 51 UDM C3D C4D SING N N 52 UDM C3D O3D SING N N 53 UDM C3D H3D SING N N 54 UDM C4D O4D SING N N 55 UDM C4D C5D SING N N 56 UDM C4D H4D SING N N 57 UDM O3D H2 SING N N 58 UDM C5D O5D SING N N 59 UDM C5D "H5'1" SING N N 60 UDM C5D "H5'2" SING N N 61 UDM O5D PA SING N N 62 UDM PA O1A DOUB N N 63 UDM PA O2A SING N N 64 UDM PA O3A SING N N 65 UDM O2A H2A SING N N 66 UDM O3A PB SING N N 67 UDM PB O1B DOUB N N 68 UDM PB O2B SING N N 69 UDM O2B H2B SING N N 70 # # 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 UDM SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1C[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" UDM SMILES CACTVS 3.341 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1C[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" UDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@H]1[C@H](O[C@@H]([C@H]([C@@H]1O)O)CO)C[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O" UDM SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(OC(C(C1O)O)CO)CP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O" UDM InChI InChI 1.03 "InChI=1S/C18H29N3O16P2/c1-7(23)19-12-10(35-8(4-22)13(25)15(12)27)6-38(30,31)37-39(32,33)34-5-9-14(26)16(28)17(36-9)21-3-2-11(24)20-18(21)29/h2-3,8-10,12-17,22,25-28H,4-6H2,1H3,(H,19,23)(H,30,31)(H,32,33)(H,20,24,29)/t8-,9-,10-,12+,13-,14-,15-,16-,17-/m1/s1" UDM InChIKey InChI 1.03 KUFKOJZYUNOEES-DLLWPQOWSA-N # _pdbx_chem_comp_identifier.comp_id UDM _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.5.0 _pdbx_chem_comp_identifier.identifier "[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]methyl-[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UDM "Create component" 2005-09-21 RCSB UDM "Modify descriptor" 2011-06-04 RCSB UDM "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UDM _pdbx_chem_comp_synonyms.name "((2S,3R,4R,5S,6R)-3-ACETAMIDO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)METHYLPHOSPHONIC (((2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC) ANHYDRIDE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##