data_XCY # _chem_comp.id XCY _chem_comp.name "{5-[4-{[4-(AMINOMETHYL)BENZYL]AMINO}-2-OXOPYRIMIDIN-1(2H)- YL]-3-HYDROXYTETRAHYDROFURAN-2-YL}METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H23 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _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 426.361 _chem_comp.one_letter_code C _chem_comp.three_letter_code XCY _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1YFH _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 XCY P P P 0 1 N N N 9.155 41.209 46.859 5.782 0.466 -0.845 P XCY 1 XCY OP3 O3P O 0 1 N Y N 9.952 40.740 48.014 5.961 -1.114 -0.549 OP3 XCY 2 XCY OP2 O2P O 0 1 N N N 8.398 42.477 46.961 6.856 1.154 0.149 OP2 XCY 3 XCY "O5'" O5* O 0 1 N N N 8.119 40.075 46.430 4.365 0.828 -0.152 "O5'" XCY 4 XCY N1 N1 N 0 1 N N N 4.276 39.073 45.993 1.164 -2.047 0.989 N1 XCY 5 XCY C6 C6 C 0 1 N N N 4.607 39.927 47.004 2.243 -2.367 0.183 C6 XCY 6 XCY C2 C2 C 0 1 N N N 2.925 38.802 45.709 0.102 -2.974 1.133 C2 XCY 7 XCY O2 O2 O 0 1 N N N 2.646 38.012 44.788 -0.871 -2.720 1.844 O2 XCY 8 XCY N3 N3 N 0 1 N N N 1.958 39.404 46.446 0.176 -4.181 0.459 N3 XCY 9 XCY C4 C4 C 0 1 N N N 2.295 40.240 47.427 1.201 -4.469 -0.299 C4 XCY 10 XCY N4 N4 N 0 1 N N N 1.311 40.831 48.126 1.254 -5.674 -0.961 N4 XCY 11 XCY C5 C5 C 0 1 N N N 3.661 40.522 47.743 2.332 -3.522 -0.474 C5 XCY 12 XCY NZ NZ N 0 1 N N N -2.395 44.554 53.188 0.167 -12.444 -3.618 NZ XCY 13 XCY CB CB C 0 1 N N N -2.288 44.996 51.758 1.235 -11.486 -3.749 CB XCY 14 XCY CG CG C 0 1 Y N N -1.759 43.954 50.797 0.965 -10.229 -2.994 CG XCY 15 XCY CD1 CD1 C 0 1 Y N N -1.704 42.567 51.157 1.378 -10.110 -1.667 CD1 XCY 16 XCY CE1 CE1 C 0 1 Y N N -1.190 41.593 50.233 1.125 -8.934 -0.960 CE1 XCY 17 XCY CD2 CD2 C 0 1 Y N N -1.301 44.333 49.501 0.298 -9.172 -3.613 CD2 XCY 18 XCY CE2 CE2 C 0 1 Y N N -0.789 43.348 48.582 0.044 -7.996 -2.906 CE2 XCY 19 XCY CZ CZ C 0 1 Y N N -0.725 41.976 48.934 0.460 -7.886 -1.585 CZ XCY 20 XCY CH CH C 0 1 N N N -0.152 40.954 47.958 0.189 -6.620 -0.824 CH XCY 21 XCY "C2'" C2* C 0 1 N N N 6.117 39.335 44.293 1.881 -0.811 2.993 "C2'" XCY 22 XCY "C5'" C5* C 0 1 N N N 8.494 38.703 46.435 4.170 0.482 1.209 "C5'" XCY 23 XCY "C4'" C4* C 0 1 N N R 7.589 37.922 45.517 2.774 0.920 1.634 "C4'" XCY 24 XCY "O4'" O4* O 0 1 N N N 6.263 37.860 46.088 1.820 0.194 0.835 "O4'" XCY 25 XCY "C1'" C1* C 0 1 N N R 5.319 38.415 45.191 1.157 -0.778 1.657 "C1'" XCY 26 XCY "C3'" C3* C 0 1 N N S 7.421 38.571 44.149 2.463 0.581 3.084 "C3'" XCY 27 XCY "O3'" O3* O 0 1 N N N 7.338 37.560 43.154 1.479 1.479 3.592 "O3'" XCY 28 XCY OP1 O1P O 0 1 N N N ? ? ? 5.904 0.867 -2.286 OP1 XCY 29 XCY HOP3 3HOP H 0 0 N N N 10.438 39.926 47.949 6.729 -1.585 -0.936 HOP3 XCY 30 XCY HOP2 2HOP H 0 0 N N N 7.886 42.778 46.219 7.803 1.155 -0.103 HOP2 XCY 31 XCY H6 H6 H 0 1 N N N 5.665 40.142 47.229 3.025 -1.618 0.111 H6 XCY 32 XCY HN4 HN4 H 0 1 N N N 1.624 41.798 48.210 2.054 -5.832 -1.518 HN4 XCY 33 XCY H5 H5 H 0 1 N N N 3.984 41.196 48.554 3.172 -3.779 -1.106 H5 XCY 34 XCY HNZ1 1HNZ H 0 0 N N N -1.495 44.202 53.514 0.262 -13.344 -4.058 HNZ1 XCY 35 XCY HNZ2 2HNZ H 0 0 N N N -2.752 45.257 53.836 -0.726 -12.136 -3.272 HNZ2 XCY 36 XCY HB1 1HB H 0 1 N N N -1.676 45.926 51.689 1.366 -11.283 -4.821 HB1 XCY 37 XCY HB2 2HB H 0 1 N N N -3.272 45.381 51.402 2.157 -11.973 -3.403 HB2 XCY 38 XCY HD1 HD1 H 0 1 N N N -2.059 42.247 52.151 1.899 -10.928 -1.176 HD1 XCY 39 XCY HE1 HE1 H 0 1 N N N -1.152 40.531 50.527 1.451 -8.850 0.074 HE1 XCY 40 XCY HD2 HD2 H 0 1 N N N -1.343 45.395 49.207 -0.028 -9.256 -4.647 HD2 XCY 41 XCY HE2 HE2 H 0 1 N N N -0.437 43.652 47.582 -0.476 -7.178 -3.397 HE2 XCY 42 XCY HH1 1HH H 0 1 N N N -0.662 39.967 48.048 -0.732 -6.145 -1.181 HH1 XCY 43 XCY HH2 2HH H 0 1 N N N -0.428 41.190 46.904 0.057 -6.824 0.244 HH2 XCY 44 XCY "H2'" 1H2* H 0 1 N N N 6.220 40.383 44.659 2.692 -1.550 2.973 "H2'" XCY 45 XCY "H2''" 2H2* H 0 0 N N N 5.620 39.609 43.333 1.204 -1.067 3.813 "H2''" XCY 46 XCY "H5'" 1H5* H 0 1 N N N 8.513 38.278 47.466 4.278 -0.600 1.320 "H5'" XCY 47 XCY "H5''" 2H5* H 0 0 N N N 9.571 38.562 46.182 4.927 0.985 1.816 "H5''" XCY 48 XCY "H4'" H4* H 0 1 N N N 8.064 36.920 45.399 2.647 1.986 1.422 "H4'" XCY 49 XCY "H1'" H1* H 0 1 N N N 4.783 37.682 44.544 0.115 -0.466 1.773 "H1'" XCY 50 XCY "H3'" H3* H 0 1 N N N 8.264 39.234 43.843 3.333 0.642 3.743 "H3'" XCY 51 XCY "HO3'" H3T H 0 0 N Y N 8.154 37.082 43.064 1.828 1.850 4.422 "HO3'" XCY 52 # 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 XCY P OP3 SING N N 1 XCY P OP2 SING N N 2 XCY P "O5'" SING N N 3 XCY P OP1 DOUB N N 4 XCY OP3 HOP3 SING N N 5 XCY OP2 HOP2 SING N N 6 XCY "O5'" "C5'" SING N N 7 XCY N1 C6 SING N N 8 XCY N1 C2 SING N N 9 XCY N1 "C1'" SING N N 10 XCY C6 C5 DOUB N N 11 XCY C6 H6 SING N N 12 XCY C2 O2 DOUB N N 13 XCY C2 N3 SING N N 14 XCY N3 C4 DOUB N N 15 XCY C4 N4 SING N N 16 XCY C4 C5 SING N N 17 XCY N4 CH SING N N 18 XCY N4 HN4 SING N N 19 XCY C5 H5 SING N N 20 XCY NZ CB SING N N 21 XCY NZ HNZ1 SING N N 22 XCY NZ HNZ2 SING N N 23 XCY CB CG SING N N 24 XCY CB HB1 SING N N 25 XCY CB HB2 SING N N 26 XCY CG CD1 DOUB Y N 27 XCY CG CD2 SING Y N 28 XCY CD1 CE1 SING Y N 29 XCY CD1 HD1 SING N N 30 XCY CE1 CZ DOUB Y N 31 XCY CE1 HE1 SING N N 32 XCY CD2 CE2 DOUB Y N 33 XCY CD2 HD2 SING N N 34 XCY CE2 CZ SING Y N 35 XCY CE2 HE2 SING N N 36 XCY CZ CH SING N N 37 XCY CH HH1 SING N N 38 XCY CH HH2 SING N N 39 XCY "C2'" "C1'" SING N N 40 XCY "C2'" "C3'" SING N N 41 XCY "C2'" "H2'" SING N N 42 XCY "C2'" "H2''" SING N N 43 XCY "C5'" "C4'" SING N N 44 XCY "C5'" "H5'" SING N N 45 XCY "C5'" "H5''" SING N N 46 XCY "C4'" "O4'" SING N N 47 XCY "C4'" "C3'" SING N N 48 XCY "C4'" "H4'" SING N N 49 XCY "O4'" "C1'" SING N N 50 XCY "C1'" "H1'" SING N N 51 XCY "C3'" "O3'" SING N N 52 XCY "C3'" "H3'" SING N N 53 XCY "O3'" "HO3'" SING N N 54 # 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 XCY SMILES ACDLabs 10.04 "O=C2N=C(NCc1ccc(cc1)CN)C=CN2C3OC(C(O)C3)COP(=O)(O)O" XCY SMILES_CANONICAL CACTVS 3.341 "NCc1ccc(CNC2=NC(=O)N(C=C2)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)cc1" XCY SMILES CACTVS 3.341 "NCc1ccc(CNC2=NC(=O)N(C=C2)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)cc1" XCY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CN)CNC2=NC(=O)N(C=C2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" XCY SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CN)CNC2=NC(=O)N(C=C2)C3CC(C(O3)COP(=O)(O)O)O" XCY InChI InChI 1.03 "InChI=1S/C17H23N4O7P/c18-8-11-1-3-12(4-2-11)9-19-15-5-6-21(17(23)20-15)16-7-13(22)14(28-16)10-27-29(24,25)26/h1-6,13-14,16,22H,7-10,18H2,(H,19,20,23)(H2,24,25,26)/t13-,14+,16+/m0/s1" XCY InChIKey InChI 1.03 ATPQGDDDWMERDD-SQWLQELKSA-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 XCY "SYSTEMATIC NAME" ACDLabs 10.04 ;N-[4-(aminomethyl)benzyl]-2'-deoxycytidine 5'-(dihydrogen phosphate) ; XCY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[4-[[4-(aminomethyl)phenyl]methylamino]-2-oxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl dihydrogen 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 XCY "Create component" 2005-01-04 RCSB XCY "Modify descriptor" 2011-06-04 RCSB #