data_YYY # _chem_comp.id YYY _chem_comp.name "DEOXYCYTIDINE DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N3 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-08-31 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 387.177 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YYY _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 YYY O3B O3B O 0 1 N N N 11.481 -10.070 20.745 -5.458 -4.404 1.723 O3B YYY 1 YYY PB PB P 0 1 N N N 11.937 -9.818 22.248 -5.113 -3.093 0.842 PB YYY 2 YYY O1B O1B O 0 1 N N N 11.230 -10.919 23.134 -6.284 -2.211 0.523 O1B YYY 3 YYY O2B O2B O 0 1 N N N 13.541 -9.886 22.367 -4.331 -3.694 -0.439 O2B YYY 4 YYY O3A O3A O 0 1 N N N 11.583 -8.275 22.662 -3.941 -2.377 1.693 O3A YYY 5 YYY PA PA P 0 1 N N R 10.610 -7.760 23.860 -3.962 -1.686 3.155 PA YYY 6 YYY O1A O1A O 0 1 N N N 10.401 -8.937 24.900 -4.360 -2.613 4.267 O1A YYY 7 YYY O2A O2A O 0 1 N N N 9.197 -7.212 23.342 -4.951 -0.422 2.953 O2A YYY 8 YYY "O5'" O5* O 0 1 N N N 11.471 -6.586 24.510 -2.493 -1.028 3.315 "O5'" YYY 9 YYY "C5'" C5* C 0 1 N N N 12.633 -6.974 25.199 -2.005 -0.136 2.327 "C5'" YYY 10 YYY "C4'" C4* C 0 1 N N R 13.523 -5.772 25.463 -0.611 0.328 2.728 "C4'" YYY 11 YYY "O4'" O4* O 0 1 N N N 13.892 -5.032 24.291 0.247 -0.829 2.764 "O4'" YYY 12 YYY "C3'" C3* C 0 1 N N S 12.970 -4.801 26.511 0.008 1.286 1.720 "C3'" YYY 13 YYY "O3'" O3* O 0 1 N N N 13.557 -4.958 27.785 0.965 2.121 2.368 "O3'" YYY 14 YYY "C2'" C2* C 0 1 N N N 13.218 -3.427 25.942 0.710 0.360 0.754 "C2'" YYY 15 YYY "C1'" C1* C 0 1 N N R 13.775 -3.628 24.532 1.157 -0.778 1.657 "C1'" YYY 16 YYY N1 N1 N 0 1 N N N 12.886 -2.894 23.608 1.164 -2.047 0.989 N1 YYY 17 YYY C2 C2 C 0 1 N N N 13.417 -2.005 22.642 2.328 -2.561 0.367 C2 YYY 18 YYY O2 O2 O 0 1 N N N 14.663 -1.861 22.530 3.386 -1.929 0.379 O2 YYY 19 YYY N3 N3 N 0 1 N N N 12.558 -1.321 21.833 2.260 -3.794 -0.259 N3 YYY 20 YYY C4 C4 C 0 1 N N N 11.209 -1.456 21.929 1.147 -4.479 -0.282 C4 YYY 21 YYY N4 N4 N 0 1 N N N 10.373 -0.770 21.115 1.101 -5.702 -0.910 N4 YYY 22 YYY C5 C5 C 0 1 N N N 10.683 -2.319 22.878 -0.094 -3.972 0.359 C5 YYY 23 YYY C6 C6 C 0 1 N N N 11.544 -3.021 23.712 -0.008 -2.785 0.956 C6 YYY 24 YYY "H5'1" 1H5* H 0 0 N N N 13.180 -7.785 24.664 -1.971 -0.654 1.366 "H5'1" YYY 25 YYY "H5'2" 2H5* H 0 0 N N N 12.393 -7.526 26.138 -2.683 0.718 2.254 "H5'2" YYY 26 YYY "H4'" H4* H 0 1 N N N 14.472 -6.176 25.886 -0.644 0.753 3.736 "H4'" YYY 27 YYY "H3'" H3* H 0 1 N N N 11.870 -4.959 26.601 -0.722 1.941 1.236 "H3'" YYY 28 YYY "H1'" H1* H 0 1 N N N 14.792 -3.173 24.483 2.163 -0.604 2.054 "H1'" YYY 29 YYY HA HA H 0 1 N N N 13.214 -4.356 28.435 0.743 3.042 2.146 HA YYY 30 YYY "H2'1" 1H2* H 0 0 N N N 13.872 -2.795 26.587 -0.003 -0.001 0.003 "H2'1" YYY 31 YYY "H2'2" 2H2* H 0 0 N N N 12.317 -2.770 25.970 1.556 0.818 0.232 "H2'2" YYY 32 YYY H6 H6 H 0 1 N N N 11.124 -3.697 24.476 -0.867 -2.341 1.449 H6 YYY 33 YYY H4N1 1H4N H 0 0 N N N 9.361 -0.871 21.187 0.349 -6.310 -0.691 H4N1 YYY 34 YYY H4N2 2H4N H 0 0 N N N 10.760 -0.135 20.417 1.822 -5.923 -1.553 H4N2 YYY 35 YYY H5 H5 H 0 1 N N N 9.591 -2.447 22.970 -1.005 -4.554 0.330 H5 YYY 36 YYY H3B H3B H 0 1 N N N 10.533 -10.120 20.705 -6.213 -4.970 1.456 H3B YYY 37 YYY H2B H2B H 0 1 N N N 13.923 -9.899 21.497 -4.849 -4.118 -1.155 H2B YYY 38 YYY H2A H2A H 0 1 N N N 8.609 -7.103 24.080 -5.240 0.085 3.742 H2A YYY 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 YYY O3B H3B SING N N 1 YYY O3B PB SING N N 2 YYY PB O1B DOUB N N 3 YYY PB O2B SING N N 4 YYY PB O3A SING N N 5 YYY O2B H2B SING N N 6 YYY O3A PA SING N N 7 YYY PA O1A DOUB N N 8 YYY PA O2A SING N N 9 YYY PA "O5'" SING N N 10 YYY O2A H2A SING N N 11 YYY "O5'" "C5'" SING N N 12 YYY "C5'" "C4'" SING N N 13 YYY "C5'" "H5'1" SING N N 14 YYY "C5'" "H5'2" SING N N 15 YYY "C4'" "O4'" SING N N 16 YYY "C4'" "C3'" SING N N 17 YYY "C4'" "H4'" SING N N 18 YYY "O4'" "C1'" SING N N 19 YYY "C3'" "O3'" SING N N 20 YYY "C3'" "C2'" SING N N 21 YYY "C3'" "H3'" SING N N 22 YYY "O3'" HA SING N N 23 YYY "C2'" "C1'" SING N N 24 YYY "C2'" "H2'1" SING N N 25 YYY "C2'" "H2'2" SING N N 26 YYY "C1'" N1 SING N N 27 YYY "C1'" "H1'" SING N N 28 YYY N1 C2 SING N N 29 YYY N1 C6 SING N N 30 YYY C2 O2 DOUB N N 31 YYY C2 N3 SING N N 32 YYY N3 C4 DOUB N N 33 YYY C4 N4 SING N N 34 YYY C4 C5 SING N N 35 YYY N4 H4N1 SING N N 36 YYY N4 H4N2 SING N N 37 YYY C5 C6 DOUB N N 38 YYY C5 H5 SING N N 39 YYY C6 H6 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 YYY SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O" YYY SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P](O)(O)=O)O2" YYY SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2" YYY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)OP(=O)(O)O)O" YYY SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O" YYY InChI InChI 1.03 "InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" YYY InChIKey InChI 1.03 FTDHDKPUHBLBTL-SHYZEUOFSA-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 YYY "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxycytidine 5'-(trihydrogen diphosphate) ; YYY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 YYY "Create component" 2006-08-31 EBI YYY "Modify descriptor" 2011-06-04 RCSB #