data_UDP # _chem_comp.id UDP _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N2 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 404.161 _chem_comp.one_letter_code N _chem_comp.three_letter_code UDP _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 1NAH _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 UDP N1 N1 N 0 1 N N N N N N 15.861 15.192 39.665 -3.586 0.410 0.193 N1 UDP 1 UDP C2 C2 C 0 1 N N N N N N 15.566 16.502 40.157 -4.585 0.798 1.007 C2 UDP 2 UDP N3 N3 N 0 1 N N N N N N 16.683 17.291 40.382 -5.335 1.877 0.717 N3 UDP 3 UDP C4 C4 C 0 1 N N N N N N 18.033 16.891 40.187 -5.094 2.591 -0.401 C4 UDP 4 UDP C5 C5 C 0 1 N N N N N N 18.234 15.529 39.704 -4.045 2.195 -1.266 C5 UDP 5 UDP C6 C6 C 0 1 N N N N N N 17.189 14.755 39.468 -3.309 1.107 -0.951 C6 UDP 6 UDP O2 O2 O 0 1 N N N N N N 14.442 16.927 40.336 -4.815 0.163 2.019 O2 UDP 7 UDP O4 O4 O 0 1 N N N N N N 18.907 17.729 40.403 -5.771 3.568 -0.665 O4 UDP 8 UDP "C1'" "C1'" C 0 1 N N R N N N 14.733 14.256 39.447 -2.784 -0.766 0.539 "C1'" UDP 9 UDP "C2'" "C2'" C 0 1 N N R N N N 14.571 13.772 38.009 -2.990 -1.893 -0.505 "C2'" UDP 10 UDP "O2'" "O2'" O 0 1 N N N N N N 13.698 14.717 37.300 -4.127 -2.694 -0.174 "O2'" UDP 11 UDP "C3'" "C3'" C 0 1 N N S N N N 13.871 12.378 38.197 -1.681 -2.708 -0.366 "C3'" UDP 12 UDP "C4'" "C4'" C 0 1 N N R N N N 14.520 11.865 39.442 -0.691 -1.722 0.283 "C4'" UDP 13 UDP "O4'" "O4'" O 0 1 N N N N N N 14.969 13.076 40.161 -1.375 -0.468 0.438 "O4'" UDP 14 UDP "O3'" "O3'" O 0 1 N N N N N N 12.489 12.489 38.456 -1.885 -3.842 0.479 "O3'" UDP 15 UDP "C5'" "C5'" C 0 1 N N N N N N 15.675 10.964 39.264 0.530 -1.540 -0.621 "C5'" UDP 16 UDP "O5'" "O5'" O 0 1 N N N N N N 16.615 11.736 38.492 1.494 -0.718 0.040 "O5'" UDP 17 UDP PA PA P 0 1 N N N N N N 18.056 11.086 38.175 2.907 -0.318 -0.621 PA UDP 18 UDP O1A O1A O 0 1 N N N N N N 18.751 11.990 37.180 3.630 -1.546 -1.019 O1A UDP 19 UDP O2A O2A O 0 1 N N N N N N 18.899 10.824 39.383 2.651 0.599 -1.920 O2A UDP 20 UDP O3A O3A O 0 1 N N N N N N 17.921 9.607 37.471 3.787 0.501 0.449 O3A UDP 21 UDP PB PB P 0 1 N N N N N N 16.971 9.089 36.332 5.343 0.907 0.541 PB UDP 22 UDP O1B O1B O 0 1 N N N N N N 17.723 7.785 35.830 6.176 -0.227 0.081 O1B UDP 23 UDP O2B O2B O 0 1 N Y N N N N 16.843 10.179 35.297 5.619 2.189 -0.393 O2B UDP 24 UDP O3B O3B O 0 1 N N N N N N 15.643 8.680 36.921 5.716 1.263 2.066 O3B UDP 25 UDP HN3 HN3 H 0 1 N N N N N N 16.526 18.222 40.710 -6.052 2.143 1.314 HN3 UDP 26 UDP H5 H5 H 0 1 N N N N N N 19.234 15.154 39.540 -3.837 2.754 -2.166 H5 UDP 27 UDP H6 H6 H 0 1 N N N N N N 17.357 13.750 39.111 -2.506 0.790 -1.599 H6 UDP 28 UDP "H1'" "H1'" H 0 1 N N N N N N 13.844 14.827 39.755 -3.034 -1.119 1.539 "H1'" UDP 29 UDP "H2'" "H2'" H 0 1 N N N N N N 15.504 13.699 37.430 -3.087 -1.480 -1.510 "H2'" UDP 30 UDP "HO2'" "HO2'" H 0 0 N N N N N N 13.585 14.431 36.401 -4.297 -3.412 -0.798 "HO2'" UDP 31 UDP "H3'" "H3'" H 0 1 N N N N N N 13.971 11.753 37.297 -1.321 -3.021 -1.346 "H3'" UDP 32 UDP "H4'" "H4'" H 0 1 N N N N N N 13.783 11.242 39.970 -0.380 -2.098 1.258 "H4'" UDP 33 UDP "HO3'" "HO3'" H 0 0 N N N N N N 12.115 11.622 38.561 -2.544 -4.467 0.146 "HO3'" UDP 34 UDP "H5'1" "H5'1" H 0 0 N N N N N N 16.103 10.670 40.234 0.970 -2.514 -0.837 "H5'1" UDP 35 UDP "H5'2" "H5'2" H 0 0 N N N N N N 15.385 10.045 38.734 0.225 -1.064 -1.553 "H5'2" UDP 36 UDP HOA2 HOA2 H 0 0 N N N N N N 19.727 11.282 39.297 2.179 1.422 -1.733 HOA2 UDP 37 UDP HOB2 HOB2 H 0 0 N N N N N N 17.248 9.895 34.486 5.105 2.971 -0.148 HOB2 UDP 38 UDP HOB3 HOB3 H 0 0 N N N N N N 15.547 7.737 36.863 6.640 1.517 2.196 HOB3 UDP 39 # 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 UDP N1 C2 SING N N 1 UDP N1 C6 SING N N 2 UDP N1 "C1'" SING N N 3 UDP C2 N3 SING N N 4 UDP C2 O2 DOUB N N 5 UDP N3 C4 SING N N 6 UDP N3 HN3 SING N N 7 UDP C4 C5 SING N N 8 UDP C4 O4 DOUB N N 9 UDP C5 C6 DOUB N N 10 UDP C5 H5 SING N N 11 UDP C6 H6 SING N N 12 UDP "C1'" "C2'" SING N N 13 UDP "C1'" "O4'" SING N N 14 UDP "C1'" "H1'" SING N N 15 UDP "C2'" "O2'" SING N N 16 UDP "C2'" "C3'" SING N N 17 UDP "C2'" "H2'" SING N N 18 UDP "O2'" "HO2'" SING N N 19 UDP "C3'" "C4'" SING N N 20 UDP "C3'" "O3'" SING N N 21 UDP "C3'" "H3'" SING N N 22 UDP "C4'" "O4'" SING N N 23 UDP "C4'" "C5'" SING N N 24 UDP "C4'" "H4'" SING N N 25 UDP "O3'" "HO3'" SING N N 26 UDP "C5'" "O5'" SING N N 27 UDP "C5'" "H5'1" SING N N 28 UDP "C5'" "H5'2" SING N N 29 UDP "O5'" PA SING N N 30 UDP PA O1A DOUB N N 31 UDP PA O2A SING N N 32 UDP PA O3A SING N N 33 UDP O2A HOA2 SING N N 34 UDP O3A PB SING N N 35 UDP PB O1B DOUB N N 36 UDP PB O2B SING N N 37 UDP PB O3B SING N N 38 UDP O2B HOB2 SING N N 39 UDP O3B HOB3 SING N N 40 # 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 UDP SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O" UDP SMILES_CANONICAL CACTVS 3.370 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" UDP SMILES CACTVS 3.370 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" UDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O" UDP SMILES "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O" UDP InChI InChI 1.03 "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" UDP InChIKey InChI 1.03 XCCTYIAWTASOJW-XVFCMESISA-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 UDP "SYSTEMATIC NAME" ACDLabs 12.01 ;uridine 5'-(trihydrogen diphosphate) ; UDP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen 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 UDP "Create component" 1999-07-08 RCSB UDP "Modify descriptor" 2011-06-04 RCSB UDP "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id UDP _pdbx_chem_comp_pcm.modified_residue_id SRZ _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 O3B _pdbx_chem_comp_pcm.modified_residue_id_linking_atom CZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #