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 
# 
