data_CXY # _chem_comp.id CXY _chem_comp.name "CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H23 N3 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-01-04 _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 535.291 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CXY _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 1WVG _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 CXY O1B O1B O 0 1 N N N 63.438 19.257 53.266 3.064 -1.471 -1.372 O1B CXY 1 CXY PB PB P 0 1 N N S 63.359 20.723 52.889 2.907 -0.267 -0.526 PB CXY 2 CXY O2B O2B O 0 1 N N N 62.352 21.510 53.686 2.491 0.986 -1.448 O2B CXY 3 CXY "O1'" "O1'" O 0 1 N N N 63.027 20.856 51.284 4.299 0.053 0.217 "O1'" CXY 4 CXY O3A O3A O 0 1 N N N 64.844 21.069 53.140 1.760 -0.528 0.573 O3A CXY 5 CXY PA PA P 0 1 N N S 65.577 21.990 54.290 0.582 -1.339 -0.167 PA CXY 6 CXY O1A O1A O 0 1 N N N 64.972 23.337 54.357 0.981 -2.896 -0.263 O1A CXY 7 CXY O2A O2A O 0 1 N N N 67.018 21.981 53.921 0.389 -0.794 -1.529 O2A CXY 8 CXY O5D O5* O 0 1 N N N 65.229 21.178 55.615 -0.784 -1.186 0.671 O5D CXY 9 CXY C5D C5* C 0 1 N N N 65.948 19.963 55.867 -1.810 -1.823 -0.092 C5D CXY 10 CXY C4D C4* C 0 1 N N R 65.745 19.577 57.312 -3.142 -1.713 0.653 C4D CXY 11 CXY O4D O4* O 0 1 N N N 66.741 20.277 58.098 -3.569 -0.334 0.718 O4D CXY 12 CXY C3D C3* C 0 1 N N S 64.380 19.859 57.939 -4.260 -2.436 -0.130 C3D CXY 13 CXY O3D O3* O 0 1 N N N 63.923 18.879 58.939 -4.481 -3.743 0.404 O3D CXY 14 CXY C2D C2* C 0 1 N N R 64.704 21.227 58.566 -5.507 -1.545 0.085 C2D CXY 15 CXY O2D O2* O 0 1 N N N 63.768 21.482 59.617 -6.535 -2.276 0.755 O2D CXY 16 CXY C1D C1* C 0 1 N N R 66.081 20.952 59.126 -4.991 -0.388 0.969 C1D CXY 17 CXY N1 N1 N 0 1 N N N 66.845 22.164 59.437 -5.625 0.874 0.579 N1 CXY 18 CXY C6 C6 C 0 1 N N N 67.159 23.068 58.435 -6.427 1.531 1.464 C6 CXY 19 CXY C5 C5 C 0 1 N N N 67.857 24.154 58.656 -7.003 2.699 1.095 C5 CXY 20 CXY C4 C4 C 0 1 N N N 68.320 24.482 59.960 -6.765 3.197 -0.203 C4 CXY 21 CXY N3 N3 N 0 1 N N N 67.987 23.525 60.933 -5.978 2.523 -1.030 N3 CXY 22 CXY C2 C2 C 0 1 N N N 67.254 22.366 60.741 -5.414 1.377 -0.650 C2 CXY 23 CXY N4 N4 N 0 1 N N N 68.949 25.488 60.269 -7.342 4.379 -0.606 N4 CXY 24 CXY O2 O2 O 0 1 N N N 66.977 21.579 61.653 -4.694 0.776 -1.429 O2 CXY 25 CXY "C1'" "C1'" C 0 1 N N R 64.180 20.800 50.462 5.296 0.157 -0.802 "C1'" CXY 26 CXY "C2'" "C2'" C 0 1 N N R 63.954 21.801 49.356 6.648 -0.285 -0.238 "C2'" CXY 27 CXY "C3'" "C3'" C 0 1 N N S 62.715 21.346 48.609 7.004 0.600 0.961 "C3'" CXY 28 CXY "C4'" "C4'" C 0 1 N N R 62.924 19.942 48.042 6.928 2.068 0.525 "C4'" CXY 29 CXY "C5'" "C5'" C 0 1 N N N 63.290 18.983 49.167 5.555 2.333 -0.096 "C5'" CXY 30 CXY "O2'" "O2'" O 0 1 N N N 63.714 23.127 49.874 6.569 -1.648 0.182 "O2'" CXY 31 CXY "O3'" "O3'" O 0 1 N N N 62.487 22.220 47.488 8.328 0.300 1.406 "O3'" CXY 32 CXY "O4'" "O4'" O 0 1 N N N 61.748 19.508 47.362 7.111 2.915 1.661 "O4'" CXY 33 CXY "O5'" "O5'" O 0 1 N N N 64.416 19.471 49.903 5.379 1.510 -1.247 "O5'" CXY 34 CXY H2B H2B H 0 1 N N N 62.303 22.429 53.450 2.399 1.748 -0.860 H2B CXY 35 CXY H1A H1A H 0 1 N N N 65.395 23.869 55.021 1.098 -3.211 0.643 H1A CXY 36 CXY "H5'1" 1H5* H 0 0 N N N 67.026 20.039 55.592 -1.559 -2.874 -0.233 "H5'1" CXY 37 CXY "H5'2" 2H5* H 0 0 N N N 65.667 19.146 55.162 -1.896 -1.336 -1.063 "H5'2" CXY 38 CXY H4D H4* H 0 1 N N N 65.831 18.465 57.318 -3.051 -2.129 1.656 H4D CXY 39 CXY H3D H3* H 0 1 N N N 63.532 19.818 57.216 -4.009 -2.494 -1.189 H3D CXY 40 CXY H4 H4 H 0 1 N N N 63.075 19.054 59.329 -5.186 -4.144 -0.122 H4 CXY 41 CXY H2D H2* H 0 1 N N N 64.659 22.105 57.880 -5.871 -1.162 -0.869 H2D CXY 42 CXY H7 H7 H 0 1 N N N 63.968 22.326 60.004 -6.771 -3.017 0.181 H7 CXY 43 CXY H1D H1* H 0 1 N N N 65.992 20.390 60.085 -5.183 -0.600 2.021 H1D CXY 44 CXY H6 H6 H 0 1 N N N 66.832 22.913 57.393 -6.597 1.126 2.451 H6 CXY 45 CXY H5 H5 H 0 1 N N N 68.050 24.777 57.766 -7.641 3.236 1.780 H5 CXY 46 CXY HN41 1HN4 H 0 0 N N N 68.395 26.283 59.952 -7.174 4.721 -1.498 HN41 CXY 47 CXY HN42 2HN4 H 0 0 N N N 69.281 25.723 61.204 -7.921 4.868 0.000 HN42 CXY 48 CXY "H1'" "H1'" H 0 1 N N N 65.087 21.034 51.068 5.026 -0.485 -1.641 "H1'" CXY 49 CXY "H2'" "H2'" H 0 1 N N N 64.858 21.850 48.706 7.415 -0.183 -1.006 "H2'" CXY 50 CXY "H3'" "H3'" H 0 1 N N N 61.856 21.358 49.319 6.296 0.422 1.770 "H3'" CXY 51 CXY "H4'" "H4'" H 0 1 N N N 63.762 19.960 47.307 7.707 2.271 -0.210 "H4'" CXY 52 CXY H5D "1H5'" H 0 1 N N N 63.461 17.948 48.788 5.485 3.382 -0.386 H5D CXY 53 CXY H5B "2H5'" H 0 1 N N N 62.420 18.776 49.833 4.777 2.108 0.633 H5B CXY 54 CXY H3 H3 H 0 1 N N N 63.572 23.757 49.178 6.343 -2.169 -0.602 H3 CXY 55 CXY H2 H2 H 0 1 N N N 61.711 21.935 47.020 8.512 0.888 2.152 H2 CXY 56 CXY H1 H1 H 0 1 N N N 61.878 18.635 47.010 7.049 3.827 1.343 H1 CXY 57 # 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 CXY O1B PB DOUB N N 1 CXY PB O2B SING N N 2 CXY PB "O1'" SING N N 3 CXY PB O3A SING N N 4 CXY O2B H2B SING N N 5 CXY "O1'" "C1'" SING N N 6 CXY O3A PA SING N N 7 CXY PA O1A SING N N 8 CXY PA O2A DOUB N N 9 CXY PA O5D SING N N 10 CXY O1A H1A SING N N 11 CXY O5D C5D SING N N 12 CXY C5D C4D SING N N 13 CXY C5D "H5'1" SING N N 14 CXY C5D "H5'2" SING N N 15 CXY C4D O4D SING N N 16 CXY C4D C3D SING N N 17 CXY C4D H4D SING N N 18 CXY O4D C1D SING N N 19 CXY C3D O3D SING N N 20 CXY C3D C2D SING N N 21 CXY C3D H3D SING N N 22 CXY O3D H4 SING N N 23 CXY C2D O2D SING N N 24 CXY C2D C1D SING N N 25 CXY C2D H2D SING N N 26 CXY O2D H7 SING N N 27 CXY C1D N1 SING N N 28 CXY C1D H1D SING N N 29 CXY N1 C6 SING N N 30 CXY N1 C2 SING N N 31 CXY C6 C5 DOUB N N 32 CXY C6 H6 SING N N 33 CXY C5 C4 SING N N 34 CXY C5 H5 SING N N 35 CXY C4 N3 DOUB N N 36 CXY C4 N4 SING N N 37 CXY N3 C2 SING N N 38 CXY C2 O2 DOUB N N 39 CXY N4 HN41 SING N N 40 CXY N4 HN42 SING N N 41 CXY "C1'" "C2'" SING N N 42 CXY "C1'" "O5'" SING N N 43 CXY "C1'" "H1'" SING N N 44 CXY "C2'" "C3'" SING N N 45 CXY "C2'" "O2'" SING N N 46 CXY "C2'" "H2'" SING N N 47 CXY "C3'" "C4'" SING N N 48 CXY "C3'" "O3'" SING N N 49 CXY "C3'" "H3'" SING N N 50 CXY "C4'" "C5'" SING N N 51 CXY "C4'" "O4'" SING N N 52 CXY "C4'" "H4'" SING N N 53 CXY "C5'" "O5'" SING N N 54 CXY "C5'" H5D SING N N 55 CXY "C5'" H5B SING N N 56 CXY "O2'" H3 SING N N 57 CXY "O3'" H2 SING N N 58 CXY "O4'" H1 SING N N 59 # 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 CXY SMILES ACDLabs 10.04 "O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=NC2=O)N)C(O)C3O" CXY SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O" CXY SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)[CH](O)[CH]2O" CXY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)O)O)O" CXY SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)O)O)O" CXY InChI InChI 1.03 "InChI=1S/C14H23N3O15P2/c15-7-1-2-17(14(23)16-7)12-10(21)9(20)6(30-12)4-29-33(24,25)32-34(26,27)31-13-11(22)8(19)5(18)3-28-13/h1-2,5-6,8-13,18-22H,3-4H2,(H,24,25)(H,26,27)(H2,15,16,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1" CXY InChIKey InChI 1.03 NWSKPSPTJOAICE-OCIMBMBZSA-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 CXY "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" CXY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl] 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 CXY "Create component" 2005-01-04 RCSB CXY "Modify descriptor" 2011-06-04 RCSB #