data_XC5 # _chem_comp.id XC5 _chem_comp.name "2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H18 N3 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-03-06 _chem_comp.pdbx_modified_date 2017-05-05 _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 465.184 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XC5 _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 5V1P _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 XC5 PA P1 P 0 1 N N N 55.950 6.099 14.952 1.177 -1.074 -0.507 PA XC5 1 XC5 O1A O1 O 0 1 N N N 54.700 6.177 15.952 1.014 -0.300 -1.910 O1A XC5 2 XC5 O2A O2 O 0 1 N N N 57.148 6.586 15.659 1.700 -2.437 -0.753 O2A XC5 3 XC5 C3A C1 C 0 1 N N N 56.322 4.397 14.450 2.340 -0.161 0.559 C3A XC5 4 XC5 PB P2 P 0 1 N N N 54.901 3.375 13.958 3.962 -0.049 -0.266 PB XC5 5 XC5 O1B O3 O 0 1 N N N 54.989 3.035 12.507 3.812 0.662 -1.555 O1B XC5 6 XC5 O2B O4 O 0 1 N N N 53.504 4.043 14.302 4.530 -1.532 -0.534 O2B XC5 7 XC5 O3B O5 O 0 1 N N N 55.029 2.019 14.781 4.989 0.757 0.676 O3B XC5 8 XC5 PG P3 P 0 1 N N N 54.950 1.881 16.365 6.534 1.187 0.534 PG XC5 9 XC5 O1G O6 O 0 1 N N N 54.499 3.210 16.844 7.137 1.510 1.992 O1G XC5 10 XC5 O2G O7 O 0 1 N N N 53.936 0.702 16.732 7.300 0.080 -0.082 O2G XC5 11 XC5 O3G O8 O 0 1 N N N 56.397 1.555 16.951 6.644 2.498 -0.395 O3G XC5 12 XC5 N1 N1 N 0 1 N N N 57.598 8.283 10.392 -5.242 0.574 0.647 N1 XC5 13 XC5 C2 C2 C 0 1 N N N 58.444 8.679 9.417 -5.299 0.898 -0.658 C2 XC5 14 XC5 N3 N2 N 0 1 N N N 59.780 8.715 9.614 -6.021 1.935 -1.077 N3 XC5 15 XC5 C4 C3 C 0 1 N N N 60.298 8.359 10.787 -6.705 2.677 -0.216 C4 XC5 16 XC5 C5 C4 C 0 1 N N N 59.441 7.955 11.824 -6.667 2.363 1.158 C5 XC5 17 XC5 C6 C5 C 0 1 N N N 58.094 7.919 11.602 -5.927 1.306 1.569 C6 XC5 18 XC5 O2 O9 O 0 1 N N N 57.962 8.988 8.338 -4.679 0.231 -1.469 O2 XC5 19 XC5 N4 N3 N 0 1 N N N 61.654 8.386 10.994 -7.448 3.746 -0.661 N4 XC5 20 XC5 "C1'" C6 C 0 1 N N R 56.145 8.256 10.118 -4.443 -0.576 1.078 "C1'" XC5 21 XC5 "C2'" C7 C 0 1 N N N 55.751 6.852 9.649 -4.981 -1.875 0.438 "C2'" XC5 22 XC5 "C3'" C8 C 0 1 N N S 55.299 6.185 10.970 -3.710 -2.698 0.133 "C3'" XC5 23 XC5 "C4'" C9 C 0 1 N N R 54.526 7.379 11.597 -2.554 -1.800 0.625 "C4'" XC5 24 XC5 "O4'" O10 O 0 1 N N N 55.415 8.490 11.322 -3.089 -0.459 0.591 "O4'" XC5 25 XC5 "O5'" O11 O 0 1 N N N 55.658 6.929 13.666 -0.255 -1.172 0.221 "O5'" XC5 26 XC5 "C5'" C10 C 0 1 N N N 54.369 7.197 13.112 -1.351 -1.918 -0.313 "C5'" XC5 27 XC5 "O3'" O12 O 0 1 N N N 54.474 5.035 10.690 -3.727 -3.932 0.854 "O3'" XC5 28 XC5 H1 H1 H 0 1 N N N 54.986 6.519 16.791 0.675 0.601 -1.824 H1 XC5 29 XC5 H2 H2 H 0 1 N N N 56.817 3.898 15.296 1.955 0.843 0.740 H2 XC5 30 XC5 H3 H3 H 0 1 N N N 57.014 4.443 13.596 2.451 -0.684 1.508 H3 XC5 31 XC5 H4 H4 H 0 1 N N N 52.978 4.103 13.513 4.654 -2.057 0.269 H4 XC5 32 XC5 H5 H5 H 0 1 N N N 53.667 3.119 17.294 8.066 1.777 1.983 H5 XC5 33 XC5 H6 H6 H 0 1 N N N 56.375 0.721 17.405 6.164 3.264 -0.051 H6 XC5 34 XC5 H7 H7 H 0 1 N N N 59.843 7.676 12.787 -7.219 2.957 1.872 H7 XC5 35 XC5 H8 H8 H 0 1 N N N 57.425 7.601 12.388 -5.882 1.046 2.616 H8 XC5 36 XC5 H9 H9 H 0 1 N N N 62.266 8.676 10.258 -7.472 3.960 -1.607 H9 XC5 37 XC5 H10 H10 H 0 1 N N N 62.030 8.116 11.880 -7.947 4.287 -0.029 H10 XC5 38 XC5 H11 H11 H 0 1 N N N 55.885 8.993 9.344 -4.450 -0.656 2.165 H11 XC5 39 XC5 H12 H12 H 0 1 N N N 54.929 6.891 8.919 -5.623 -2.409 1.138 H12 XC5 40 XC5 H13 H13 H 0 1 N N N 56.608 6.323 9.207 -5.521 -1.652 -0.483 H13 XC5 41 XC5 H14 H14 H 0 1 N N N 56.171 5.926 11.588 -3.621 -2.882 -0.938 H14 XC5 42 XC5 H15 H15 H 0 1 N N N 53.546 7.502 11.113 -2.269 -2.070 1.642 H15 XC5 43 XC5 H16 H16 H 0 1 N N N 53.956 8.115 13.556 -1.065 -2.965 -0.408 H16 XC5 44 XC5 H17 H17 H 0 1 N N N 53.693 6.354 13.318 -1.615 -1.523 -1.294 H17 XC5 45 XC5 H18 H18 H 0 1 N N N 54.659 4.350 11.322 -4.469 -4.510 0.627 H18 XC5 46 # 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 XC5 O2 C2 DOUB N N 1 XC5 C2 N3 SING N N 2 XC5 C2 N1 SING N N 3 XC5 N3 C4 DOUB N N 4 XC5 "C2'" "C1'" SING N N 5 XC5 "C2'" "C3'" SING N N 6 XC5 "C1'" N1 SING N N 7 XC5 "C1'" "O4'" SING N N 8 XC5 N1 C6 SING N N 9 XC5 "O3'" "C3'" SING N N 10 XC5 C4 N4 SING N N 11 XC5 C4 C5 SING N N 12 XC5 "C3'" "C4'" SING N N 13 XC5 "O4'" "C4'" SING N N 14 XC5 "C4'" "C5'" SING N N 15 XC5 C6 C5 DOUB N N 16 XC5 O1B PB DOUB N N 17 XC5 "C5'" "O5'" SING N N 18 XC5 "O5'" PA SING N N 19 XC5 PB O2B SING N N 20 XC5 PB C3A SING N N 21 XC5 PB O3B SING N N 22 XC5 C3A PA SING N N 23 XC5 O3B PG SING N N 24 XC5 PA O2A DOUB N N 25 XC5 PA O1A SING N N 26 XC5 PG O2G DOUB N N 27 XC5 PG O1G SING N N 28 XC5 PG O3G SING N N 29 XC5 O1A H1 SING N N 30 XC5 C3A H2 SING N N 31 XC5 C3A H3 SING N N 32 XC5 O2B H4 SING N N 33 XC5 O1G H5 SING N N 34 XC5 O3G H6 SING N N 35 XC5 C5 H7 SING N N 36 XC5 C6 H8 SING N N 37 XC5 N4 H9 SING N N 38 XC5 N4 H10 SING N N 39 XC5 "C1'" H11 SING N N 40 XC5 "C2'" H12 SING N N 41 XC5 "C2'" H13 SING N N 42 XC5 "C3'" H14 SING N N 43 XC5 "C4'" H15 SING N N 44 XC5 "C5'" H16 SING N N 45 XC5 "C5'" H17 SING N N 46 XC5 "O3'" H18 SING N N 47 # 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 XC5 SMILES ACDLabs 12.01 "P(=O)(O)(CP(O)(OP(=O)(O)O)=O)OCC2C(CC(N1C=CC(=NC1=O)N)O2)O" XC5 InChI InChI 1.03 "InChI=1S/C10H18N3O12P3/c11-8-1-2-13(10(15)12-8)9-3-6(14)7(24-9)4-23-26(16,17)5-27(18,19)25-28(20,21)22/h1-2,6-7,9,14H,3-5H2,(H,16,17)(H,18,19)(H2,11,12,15)(H2,20,21,22)/t6-,7+,9+/m0/s1" XC5 InChIKey InChI 1.03 YSCOIIOUWFAHFY-LKEWCRSYSA-N XC5 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2" XC5 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2" XC5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O" XC5 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)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 XC5 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" XC5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]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 XC5 "Create component" 2017-03-06 RCSB XC5 "Initial release" 2017-05-10 RCSB #