data_8CP # _chem_comp.id 8CP _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H17 N4 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-01-19 _chem_comp.pdbx_modified_date 2017-07-21 _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 466.172 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8CP _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 5UGP _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 8CP N1 N1 N 0 1 N N N 6.770 7.972 10.405 5.069 -0.636 0.674 N1 8CP 1 8CP C2 C1 C 0 1 N N N 7.612 8.317 9.332 5.251 -0.771 -0.653 C2 8CP 2 8CP N3 N2 N 0 1 N N N 8.931 8.319 9.510 6.022 -1.738 -1.146 N3 8CP 3 8CP C4 C2 C 0 1 N N N 9.473 7.981 10.683 6.633 -2.595 -0.339 C4 8CP 4 8CP C5 C3 C 0 1 N N N 8.650 7.634 11.789 6.464 -2.481 1.056 C5 8CP 5 8CP C6 C4 C 0 1 N N N 7.299 7.590 11.573 5.676 -1.493 1.542 C6 8CP 6 8CP O2 O1 O 0 1 N N N 7.102 8.621 8.256 4.700 0.005 -1.416 O2 8CP 7 8CP N4 N3 N 0 1 N N N 10.804 7.974 10.852 7.428 -3.590 -0.860 N4 8CP 8 8CP "C1'" C5 C 0 1 N N R 5.362 7.914 10.083 4.219 0.441 1.187 "C1'" 8CP 9 8CP "C2'" C6 C 0 1 N N N 4.973 6.524 9.656 4.797 1.818 0.790 "C2'" 8CP 10 8CP "C3'" C7 C 0 1 N N S 4.471 5.806 10.907 3.548 2.676 0.488 "C3'" 8CP 11 8CP "C4'" C8 C 0 1 N N R 3.744 6.966 11.589 2.364 1.717 0.738 "C4'" 8CP 12 8CP "O4'" O2 O 0 1 N N N 4.592 8.127 11.264 2.917 0.394 0.563 "O4'" 8CP 13 8CP "O3'" O3 O 0 1 N N N 3.599 4.734 10.546 3.483 3.794 1.376 "O3'" 8CP 14 8CP "C5'" C9 C 0 1 N N N 3.552 6.809 13.088 1.251 1.968 -0.282 "C5'" 8CP 15 8CP "O5'" O4 O 0 1 N N N 4.816 6.649 13.661 0.121 1.154 0.036 "O5'" 8CP 16 8CP PA P1 P 0 1 N N N 5.074 5.498 14.787 -1.237 1.161 -0.830 PA 8CP 17 8CP O1A O5 O 0 1 N N N 6.430 5.702 15.412 -1.752 2.545 -0.928 O1A 8CP 18 8CP O2A O6 O 0 1 N N N 3.954 5.538 15.803 -0.934 0.595 -2.306 O2A 8CP 19 8CP O3A O7 O 0 1 N N N 5.073 4.086 13.975 -2.336 0.229 -0.112 O3A 8CP 20 8CP PB P2 P 0 1 N N N 3.919 3.021 13.784 -3.928 0.052 -0.272 PB 8CP 21 8CP O1B O8 O 0 1 N N N 2.604 3.456 14.231 -4.658 1.452 0.041 O1B 8CP 22 8CP O2B O9 O 0 1 N N N 3.845 2.607 12.329 -4.241 -0.369 -1.656 O2B 8CP 23 8CP PG P3 P 0 1 N N N 4.135 1.525 16.298 -6.137 -1.336 0.672 PG 8CP 24 8CP O1G O10 O 0 1 N N N 3.172 0.467 16.539 -6.826 -0.060 0.968 O1G 8CP 25 8CP O2G O11 O 0 1 N N N 5.483 1.173 16.976 -6.618 -2.461 1.719 O2G 8CP 26 8CP O3G O12 O 0 1 N N N 3.642 2.888 16.804 -6.497 -1.806 -0.825 O3G 8CP 27 8CP N3B N4 N 0 1 N N N 4.372 1.653 14.640 -4.473 -1.119 0.807 N3B 8CP 28 8CP H1 H1 H 0 1 N N N 9.073 7.414 12.758 6.955 -3.171 1.726 H1 8CP 29 8CP H2 H2 H 0 1 N N N 6.648 7.240 12.360 5.530 -1.385 2.607 H2 8CP 30 8CP H3 H3 H 0 1 N N N 11.406 8.224 10.093 7.542 -3.667 -1.821 H3 8CP 31 8CP H4 H4 H 0 1 N N N 11.194 7.719 11.737 7.873 -4.215 -0.268 H4 8CP 32 8CP H5 H5 H 0 1 N N N 5.104 8.640 9.298 4.124 0.365 2.270 H5 8CP 33 8CP H6 H6 H 0 1 N N N 4.176 6.569 8.899 5.364 2.246 1.617 H6 8CP 34 8CP H7 H7 H 0 1 N N N 5.845 5.997 9.240 5.423 1.728 -0.098 H7 8CP 35 8CP H8 H8 H 0 1 N N N 5.316 5.463 11.523 3.557 3.011 -0.549 H8 8CP 36 8CP H9 H9 H 0 1 N N N 2.758 7.090 11.117 1.983 1.840 1.752 H9 8CP 37 8CP H10 H10 H 0 1 N N N 3.699 4.021 11.166 4.234 4.398 1.304 H10 8CP 38 8CP H11 H11 H 0 1 N N N 3.064 7.705 13.500 0.962 3.018 -0.253 H11 8CP 39 8CP H12 H12 H 0 1 N N N 2.931 5.925 13.296 1.610 1.717 -1.280 H12 8CP 40 8CP H13 H13 H 0 1 N N N 4.316 5.688 16.668 -0.593 -0.309 -2.319 H13 8CP 41 8CP H14 H14 H 0 1 N N N 1.986 3.386 13.513 -4.496 1.789 0.933 H14 8CP 42 8CP H15 H15 H 0 1 N N N 5.408 0.333 17.414 -7.569 -2.638 1.696 H15 8CP 43 8CP H16 H16 H 0 1 N N N 2.780 2.790 17.190 -6.079 -2.637 -1.087 H16 8CP 44 8CP H17 H17 H 0 1 N N N 3.879 0.887 14.226 -3.983 -1.991 0.673 H17 8CP 45 # 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 8CP O2 C2 DOUB N N 1 8CP C2 N3 SING N N 2 8CP C2 N1 SING N N 3 8CP N3 C4 DOUB N N 4 8CP "C2'" "C1'" SING N N 5 8CP "C2'" "C3'" SING N N 6 8CP "C1'" N1 SING N N 7 8CP "C1'" "O4'" SING N N 8 8CP N1 C6 SING N N 9 8CP "O3'" "C3'" SING N N 10 8CP C4 N4 SING N N 11 8CP C4 C5 SING N N 12 8CP "C3'" "C4'" SING N N 13 8CP "O4'" "C4'" SING N N 14 8CP C6 C5 DOUB N N 15 8CP "C4'" "C5'" SING N N 16 8CP O2B PB DOUB N N 17 8CP "C5'" "O5'" SING N N 18 8CP "O5'" PA SING N N 19 8CP PB O3A SING N N 20 8CP PB O1B SING N N 21 8CP PB N3B SING N N 22 8CP O3A PA SING N N 23 8CP N3B PG SING N N 24 8CP PA O1A DOUB N N 25 8CP PA O2A SING N N 26 8CP PG O1G DOUB N N 27 8CP PG O3G SING N N 28 8CP PG O2G SING N N 29 8CP C5 H1 SING N N 30 8CP C6 H2 SING N N 31 8CP N4 H3 SING N N 32 8CP N4 H4 SING N N 33 8CP "C1'" H5 SING N N 34 8CP "C2'" H6 SING N N 35 8CP "C2'" H7 SING N N 36 8CP "C3'" H8 SING N N 37 8CP "C4'" H9 SING N N 38 8CP "O3'" H10 SING N N 39 8CP "C5'" H11 SING N N 40 8CP "C5'" H12 SING N N 41 8CP O2A H13 SING N N 42 8CP O1B H14 SING N N 43 8CP O2G H15 SING N N 44 8CP O3G H16 SING N N 45 8CP N3B H17 SING N N 46 # 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 8CP SMILES ACDLabs 12.01 "N1(C=CC(=NC1=O)N)C2OC(C(C2)O)COP(=O)(O)OP(O)(NP(=O)(O)O)=O" 8CP InChI InChI 1.03 "InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-28(21,22)25-27(19,20)12-26(16,17)18/h1-2,5-6,8,14H,3-4H2,(H,21,22)(H2,10,11,15)(H4,12,16,17,18,19,20)/t5-,6+,8+/m0/s1" 8CP InChIKey InChI 1.03 ICHPBSCTWPZUQK-SHYZEUOFSA-N 8CP SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2" 8CP SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2" 8CP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O" 8CP SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(NP(=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 8CP "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine" 8CP "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-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic 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 8CP "Create component" 2017-01-19 RCSB 8CP "Initial release" 2017-07-26 RCSB #