data_UDH # _chem_comp.id UDH _chem_comp.name "6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H27 N3 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-07-07 _chem_comp.pdbx_modified_date 2012-01-05 _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 503.335 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UDH _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 2AH9 _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 UDH N1 N1 N 0 1 N N N 37.838 51.204 41.075 5.268 -1.322 0.021 N1 UDH 1 UDH C2 C2 C 0 1 N N N 38.961 51.744 40.390 5.833 -2.507 0.314 C2 UDH 2 UDH N3 N3 N 0 1 N N N 39.963 50.830 40.091 6.450 -3.233 -0.636 N3 UDH 3 UDH C4 C4 C 0 1 N N N 39.970 49.452 40.399 6.512 -2.780 -1.905 C4 UDH 4 UDH C5 C5 C 0 1 N N N 38.794 48.975 41.089 5.922 -1.534 -2.227 C5 UDH 5 UDH C6 C6 C 0 1 N N N 37.801 49.817 41.398 5.309 -0.826 -1.254 C6 UDH 6 UDH O2 O2 O 0 1 N N N 38.979 52.939 40.120 5.785 -2.928 1.454 O2 UDH 7 UDH O4 O4 O 0 1 N N N 40.925 48.765 40.084 7.070 -3.436 -2.765 O4 UDH 8 UDH C1B C1* C 0 1 N N R 36.738 52.184 41.430 4.599 -0.556 1.076 C1B UDH 9 UDH C2B C2* C 0 1 N N R 35.938 52.830 40.352 5.345 0.776 1.341 C2B UDH 10 UDH "O2'" O2* O 0 1 N N N 35.501 54.158 40.716 6.402 0.589 2.285 "O2'" UDH 11 UDH C3B C3* C 0 1 N N S 34.844 51.815 40.222 4.224 1.663 1.936 C3B UDH 12 UDH C4B C4* C 0 1 N N R 34.471 51.536 41.679 2.921 0.992 1.462 C4B UDH 13 UDH "O4'" O4* O 0 1 N N N 35.814 51.431 42.218 3.290 -0.128 0.641 "O4'" UDH 14 UDH "O3'" O3* O 0 1 N N N 33.727 52.253 39.464 4.294 1.667 3.363 "O3'" UDH 15 UDH C5B C5* C 0 1 N N N 33.666 50.271 41.770 2.092 1.985 0.645 C5B UDH 16 UDH "O5'" O5* O 0 1 N N N 34.375 49.091 41.424 0.835 1.393 0.309 "O5'" UDH 17 UDH PA PA P 0 1 N N R 33.968 48.196 40.177 -0.292 2.157 -0.550 PA UDH 18 UDH O1A O1A O 0 1 N N N 33.556 49.067 39.051 -0.616 3.448 0.098 O1A UDH 19 UDH O2A O2A O 0 1 N N N 34.977 47.186 39.793 0.258 2.427 -2.038 O2A UDH 20 UDH O3A O3A O 0 1 N N N 32.651 47.398 40.801 -1.619 1.247 -0.624 O3A UDH 21 UDH PB PB P 0 1 N N S 31.505 46.708 39.991 -3.148 1.531 -1.041 PB UDH 22 UDH O1B O1B O 0 1 N N N 30.653 46.106 41.194 -3.565 2.851 -0.516 O1B UDH 23 UDH O2B O2B O 0 1 N N N 32.185 45.603 39.239 -4.094 0.384 -0.424 O2B UDH 24 UDH O3B O3B O 0 1 N N N 31.005 47.621 38.937 -3.276 1.527 -2.646 O3B UDH 25 UDH "C1'" "C1'" C 0 1 N N N 32.806 44.448 39.873 -5.519 0.411 -0.528 "C1'" UDH 26 UDH "C2'" "C2'" C 0 1 N N N 33.599 43.777 38.730 -6.104 -0.822 0.163 "C2'" UDH 27 UDH "C3'" "C3'" C 0 1 N N N 32.598 42.780 38.129 -7.630 -0.794 0.051 "C3'" UDH 28 UDH "C4'" "C4'" C 0 1 N N N 32.847 42.876 36.621 -8.215 -2.027 0.742 "C4'" UDH 29 UDH "C5'" "C5'" C 0 1 N N N 32.320 41.540 36.084 -9.741 -1.998 0.630 "C5'" UDH 30 UDH "C6'" "C6'" C 0 1 N N N 32.117 41.805 34.592 -10.326 -3.232 1.320 "C6'" UDH 31 UDH "N6'" "N6'" N 0 1 N N N 31.319 40.729 34.176 -11.791 -3.204 1.213 "N6'" UDH 32 UDH HN3 HN3 H 0 1 N N N 40.763 51.185 39.607 6.853 -4.086 -0.408 HN3 UDH 33 UDH H5 H5 H 0 1 N N N 38.716 47.932 41.357 5.961 -1.155 -3.237 H5 UDH 34 UDH H6 H6 H 0 1 N N N 36.935 49.429 41.914 4.853 0.126 -1.481 H6 UDH 35 UDH "H1'" H1* H 0 1 N N N 37.262 53.032 41.895 4.528 -1.146 1.990 "H1'" UDH 36 UDH "H2'" H2* H 0 1 N N N 36.465 53.034 39.408 5.726 1.200 0.412 "H2'" UDH 37 UDH "HO2'" *HO2 H 0 0 N N N 35.405 54.213 41.660 6.899 1.394 2.484 "HO2'" UDH 38 UDH "H3'" H3* H 0 1 N N N 35.176 50.927 39.664 4.294 2.678 1.546 "H3'" UDH 39 UDH "H4'" H4* H 0 1 N N N 33.837 52.269 42.200 2.347 0.647 2.323 "H4'" UDH 40 UDH "HO3'" *HO3 H 0 0 N N N 32.975 52.351 40.036 5.121 2.026 3.715 "HO3'" UDH 41 UDH "H5'1" 1H5* H 0 0 N N N 33.324 50.165 42.810 1.923 2.887 1.233 "H5'1" UDH 42 UDH "H5'2" 2H5* H 0 0 N N N 32.845 50.368 41.044 2.628 2.241 -0.268 "H5'2" UDH 43 UDH HOA2 2HOA H 0 0 N N N 35.193 47.288 38.874 0.490 1.624 -2.523 HOA2 UDH 44 UDH HOB3 3HOB H 0 0 N N N 30.898 48.493 39.298 -3.019 0.692 -3.059 HOB3 UDH 45 UDH "H1'1" "1H1'" H 0 0 N N N 33.469 44.752 40.696 -5.901 1.312 -0.048 "H1'1" UDH 46 UDH "H1'2" "2H1'" H 0 0 N N N 32.069 43.771 40.329 -5.806 0.409 -1.579 "H1'2" UDH 47 UDH "H2'1" "1H2'" H 0 0 N N N 33.930 44.514 37.983 -5.721 -1.723 -0.317 "H2'1" UDH 48 UDH "H2'2" "2H2'" H 0 0 N N N 34.521 43.292 39.082 -5.817 -0.820 1.214 "H2'2" UDH 49 UDH "H3'1" "1H3'" H 0 0 N N N 32.775 41.760 38.501 -8.012 0.107 0.530 "H3'1" UDH 50 UDH "H3'2" "2H3'" H 0 0 N N N 31.557 43.010 38.401 -7.917 -0.795 -1.001 "H3'2" UDH 51 UDH "H4'1" "1H4'" H 0 0 N N N 32.311 43.728 36.177 -7.832 -2.928 0.262 "H4'1" UDH 52 UDH "H4'2" "2H4'" H 0 0 N N N 33.906 43.046 36.375 -7.928 -2.025 1.793 "H4'2" UDH 53 UDH H5B "1H5'" H 0 1 N N N 33.040 40.726 36.254 -10.123 -1.097 1.109 H5B UDH 54 UDH H5D "2H5'" H 0 1 N N N 31.397 41.215 36.587 -10.028 -2.000 -0.422 H5D UDH 55 UDH "H6'1" "1H6'" H 0 0 N N N 31.618 42.769 34.417 -9.943 -4.133 0.841 "H6'1" UDH 56 UDH "H6'2" "2H6'" H 0 0 N N N 33.065 41.873 34.038 -10.039 -3.230 2.372 "H6'2" UDH 57 UDH "HN'1" "1HN'" H 0 0 N N N 31.129 40.813 33.198 -12.082 -3.140 0.249 "HN'1" UDH 58 UDH "HN'2" "2HN'" H 0 0 N N N 31.801 39.870 34.349 -12.201 -4.009 1.662 "HN'2" UDH 59 # 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 UDH N1 C2 SING N N 1 UDH N1 C6 SING N N 2 UDH N1 C1B SING N N 3 UDH C2 N3 SING N N 4 UDH C2 O2 DOUB N N 5 UDH N3 C4 SING N N 6 UDH N3 HN3 SING N N 7 UDH C4 C5 SING N N 8 UDH C4 O4 DOUB N N 9 UDH C5 C6 DOUB N N 10 UDH C5 H5 SING N N 11 UDH C6 H6 SING N N 12 UDH C1B C2B SING N N 13 UDH C1B "O4'" SING N N 14 UDH C1B "H1'" SING N N 15 UDH C2B "O2'" SING N N 16 UDH C2B C3B SING N N 17 UDH C2B "H2'" SING N N 18 UDH "O2'" "HO2'" SING N N 19 UDH C3B C4B SING N N 20 UDH C3B "O3'" SING N N 21 UDH C3B "H3'" SING N N 22 UDH C4B "O4'" SING N N 23 UDH C4B C5B SING N N 24 UDH C4B "H4'" SING N N 25 UDH "O3'" "HO3'" SING N N 26 UDH C5B "O5'" SING N N 27 UDH C5B "H5'1" SING N N 28 UDH C5B "H5'2" SING N N 29 UDH "O5'" PA SING N N 30 UDH PA O1A DOUB N N 31 UDH PA O2A SING N N 32 UDH PA O3A SING N N 33 UDH O2A HOA2 SING N N 34 UDH O3A PB SING N N 35 UDH PB O1B DOUB N N 36 UDH PB O2B SING N N 37 UDH PB O3B SING N N 38 UDH O2B "C1'" SING N N 39 UDH O3B HOB3 SING N N 40 UDH "C1'" "C2'" SING N N 41 UDH "C1'" "H1'1" SING N N 42 UDH "C1'" "H1'2" SING N N 43 UDH "C2'" "C3'" SING N N 44 UDH "C2'" "H2'1" SING N N 45 UDH "C2'" "H2'2" SING N N 46 UDH "C3'" "C4'" SING N N 47 UDH "C3'" "H3'1" SING N N 48 UDH "C3'" "H3'2" SING N N 49 UDH "C4'" "C5'" SING N N 50 UDH "C4'" "H4'1" SING N N 51 UDH "C4'" "H4'2" SING N N 52 UDH "C5'" "C6'" SING N N 53 UDH "C5'" H5B SING N N 54 UDH "C5'" H5D SING N N 55 UDH "C6'" "N6'" SING N N 56 UDH "C6'" "H6'1" SING N N 57 UDH "C6'" "H6'2" SING N N 58 UDH "N6'" "HN'1" SING N N 59 UDH "N6'" "HN'2" SING N N 60 # 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 UDH SMILES ACDLabs 10.04 "O=P(O)(OCCCCCCN)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O" UDH InChI InChI 1.03 "InChI=1S/C15H27N3O12P2/c16-6-3-1-2-4-8-27-31(23,24)30-32(25,26)28-9-10-12(20)13(21)14(29-10)18-7-5-11(19)17-15(18)22/h5,7,10,12-14,20-21H,1-4,6,8-9,16H2,(H,23,24)(H,25,26)(H,17,19,22)/t10-,12-,13-,14-/m1/s1" UDH InChIKey InChI 1.03 MLWJBKPFDKRHBM-FMKGYKFTSA-N UDH SMILES_CANONICAL CACTVS 3.385 "NCCCCCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O" UDH SMILES CACTVS 3.385 "NCCCCCCO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O" UDH SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OCCCCCCN)O)O" UDH SMILES "OpenEye OEToolkits" 1.7.5 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCCCCCCN)O)O" # 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 UDH "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(S)-[(6-aminohexyl)oxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]uridine" UDH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(6-aminohexoxy-hydroxy-phosphoryl) [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 UDH "Create component" 2004-07-07 RCSB UDH "Modify descriptor" 2011-06-04 RCSB UDH "Modify descriptor" 2012-01-05 RCSB UDH "Modify coordinates" 2012-01-05 RCSB #