data_UBB # _chem_comp.id UBB _chem_comp.name "2',3'-DIDEOXY-URIDINE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-02-13 _chem_comp.pdbx_modified_date 2024-09-27 _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 292.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UBB _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NH3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 UBB O1P O1P O 0 1 N N N N N N 122.486 -66.842 -8.186 1.132 -0.005 6.219 O1P UBB 1 UBB P P P 0 1 N N N N N N 121.262 -66.590 -8.991 1.672 1.380 5.584 P UBB 2 UBB O2P O2P O 0 1 N N N N N N 120.863 -67.561 -10.038 2.913 1.936 6.219 O2P UBB 3 UBB O3P O3P O 0 1 N N N N N N ? ? ? 0.379 2.348 5.648 O3P UBB 4 UBB "O5'" O5* O 0 1 N N N N N N 120.074 -66.390 -7.949 1.800 1.054 4.004 "O5'" UBB 5 UBB "C5'" C5* C 0 1 N N N N N N 120.267 -65.569 -6.792 0.670 0.525 3.329 "C5'" UBB 6 UBB "C4'" C4* C 0 1 N N S N N N 119.173 -65.814 -5.781 1.027 0.302 1.866 "C4'" UBB 7 UBB "O4'" O4* O 0 1 N N N N N N 117.955 -65.156 -6.202 2.097 -0.657 1.801 "O4'" UBB 8 UBB "C1'" C1* C 0 1 N N R N N N 116.900 -66.099 -6.260 1.600 -1.869 1.217 "C1'" UBB 9 UBB N1 N1 N 0 1 N N N N N N 115.977 -65.667 -7.322 2.073 -2.991 1.972 N1 UBB 10 UBB C6 C6 C 0 1 N N N N N N 116.231 -65.885 -8.657 2.255 -2.839 3.341 C6 UBB 11 UBB C5 C5 C 0 1 N N N N N N 115.440 -65.422 -9.633 2.689 -3.810 4.147 C5 UBB 12 UBB C4 C4 C 0 1 N N N N N N 114.283 -64.672 -9.302 3.002 -5.136 3.577 C4 UBB 13 UBB O4 O4 O 0 1 N N N N N N 113.596 -64.029 -10.089 3.404 -6.049 4.292 O4 UBB 14 UBB N3 N3 N 0 1 N N N N N N 114.061 -64.533 -7.953 2.805 -5.238 2.209 N3 UBB 15 UBB C2 C2 C 0 1 N N N N N N 114.845 -65.000 -6.928 2.350 -4.229 1.349 C2 UBB 16 UBB O2 O2 O 0 1 N N N N N N 114.550 -64.833 -5.756 2.212 -4.436 0.142 O2 UBB 17 UBB "C2'" C2* C 0 1 N N N N N N 117.566 -67.455 -6.424 0.087 -1.764 1.201 "C2'" UBB 18 UBB "C3'" C3* C 0 1 N N N N N N 118.818 -67.289 -5.581 -0.121 -0.277 1.054 "C3'" UBB 19 UBB H1P H1P H 0 1 N N N N N N 122.741 -66.219 -7.515 1.038 -0.076 7.193 H1P UBB 20 UBB H3P H3P H 0 1 N N N N N N -0.782 0.161 -0.514 0.141 2.766 6.503 H3P UBB 21 UBB "H5'1" 1H5* H 0 0 N N N N N N 121.280 -65.709 -6.348 0.386 -0.420 3.801 "H5'1" UBB 22 UBB "H5'2" 2H5* H 0 0 N N N N N N 120.350 -64.489 -7.058 -0.158 1.234 3.416 "H5'2" UBB 23 UBB "H4'" H4* H 0 1 N N N N N N 119.576 -65.413 -4.821 1.377 1.247 1.439 "H4'" UBB 24 UBB "H1'" H1* H 0 1 N N N N N N 116.258 -66.176 -5.351 2.006 -1.949 0.203 "H1'" UBB 25 UBB H6 H6 H 0 1 N N N N N N 117.119 -66.463 -8.962 2.019 -1.858 3.738 H6 UBB 26 UBB H5 H5 H 0 1 N N N N N N 115.731 -65.650 -10.672 2.819 -3.655 5.211 H5 UBB 27 UBB HN3 HN3 H 0 1 N N N N N N 113.218 -64.025 -7.681 3.012 -6.138 1.785 HN3 UBB 28 UBB "H2'1" 1H2* H 0 0 N N N N N N 116.929 -68.330 -6.159 -0.342 -2.106 2.152 "H2'1" UBB 29 UBB "H2'2" 2H2* H 0 0 N N N N N N 117.743 -67.771 -7.478 -0.371 -2.351 0.399 "H2'2" UBB 30 UBB "H3'1" 1H3* H 0 0 N N N N N N 119.640 -68.002 -5.822 -0.001 0.001 0.000 "H3'1" UBB 31 UBB "H3'2" 2H3* H 0 0 N N N N N N 118.707 -67.601 -4.516 -1.108 0.062 1.383 "H3'2" UBB 32 # 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 UBB O1P P SING N N 1 UBB O1P H1P SING N N 2 UBB P O2P DOUB N N 3 UBB P O3P SING N N 4 UBB P "O5'" SING N N 5 UBB O3P H3P SING N N 6 UBB "O5'" "C5'" SING N N 7 UBB "C5'" "C4'" SING N N 8 UBB "C5'" "H5'1" SING N N 9 UBB "C5'" "H5'2" SING N N 10 UBB "C4'" "O4'" SING N N 11 UBB "C4'" "C3'" SING N N 12 UBB "C4'" "H4'" SING N N 13 UBB "O4'" "C1'" SING N N 14 UBB "C1'" N1 SING N N 15 UBB "C1'" "C2'" SING N N 16 UBB "C1'" "H1'" SING N N 17 UBB N1 C6 SING N N 18 UBB N1 C2 SING N N 19 UBB C6 C5 DOUB N N 20 UBB C6 H6 SING N N 21 UBB C5 C4 SING N N 22 UBB C5 H5 SING N N 23 UBB C4 O4 DOUB N N 24 UBB C4 N3 SING N N 25 UBB N3 C2 SING N N 26 UBB N3 HN3 SING N N 27 UBB C2 O2 DOUB N N 28 UBB "C2'" "C3'" SING N N 29 UBB "C2'" "H2'1" SING N N 30 UBB "C2'" "H2'2" SING N N 31 UBB "C3'" "H3'1" SING N N 32 UBB "C3'" "H3'2" SING N N 33 # 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 UBB SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(CC2)COP(=O)(O)O" UBB SMILES_CANONICAL CACTVS 3.341 "O[P](O)(=O)OC[C@@H]1CC[C@@H](O1)N2C=CC(=O)NC2=O" UBB SMILES CACTVS 3.341 "O[P](O)(=O)OC[CH]1CC[CH](O1)N2C=CC(=O)NC2=O" UBB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=O)NC2=O" UBB SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(OC1COP(=O)(O)O)N2C=CC(=O)NC2=O" UBB InChI InChI 1.03 "InChI=1S/C9H13N2O7P/c12-7-3-4-11(9(13)10-7)8-2-1-6(18-8)5-17-19(14,15)16/h3-4,6,8H,1-2,5H2,(H,10,12,13)(H2,14,15,16)/t6-,8+/m0/s1" UBB InChIKey InChI 1.03 YHPMDBWWRCBXNU-POYBYMJQSA-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 UBB "SYSTEMATIC NAME" ACDLabs 10.04 "[(2S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate" UBB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(2,4-dioxopyrimidin-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 UBB "Create component" 2003-02-13 RCSB UBB "Modify descriptor" 2011-06-04 RCSB UBB "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id UBB _pdbx_chem_comp_pcm.modified_residue_id PTR _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "C3'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom O3P _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #