data_YCO
# 
_chem_comp.id                                    YCO 
_chem_comp.name                                  "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C15 H16 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-02-10 
_chem_comp.pdbx_modified_date                    2012-02-03 
_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                        397.277 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YCO 
_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        3QNN 
_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 
YCO P      P      P 0 1 N N N -7.545 0.889  31.626 5.509  1.560  0.130  P      YCO 1  
YCO N1     N1     N 0 1 N N N -4.365 2.951  26.512 -0.733 -0.877 0.295  N1     YCO 2  
YCO C2     C2     C 0 1 N N N -3.557 3.250  25.393 -0.742 -0.473 -0.985 C2     YCO 3  
YCO O2     O2     O 0 1 N N N -3.574 2.405  24.342 0.276  -0.571 -1.644 O2     YCO 4  
YCO N3     N3     N 0 1 N N N -2.895 4.426  25.272 -1.848 0.038  -1.561 N3     YCO 5  
YCO C4     C4     C 0 1 N N N -2.876 5.320  26.278 -3.009 0.154  -0.820 C4     YCO 6  
YCO C5     C5     C 0 1 N N N -3.613 5.018  27.534 -2.998 -0.288 0.579  C5     YCO 7  
YCO C6     C6     C 0 1 N N N -4.291 3.809  27.639 -1.861 -0.794 1.091  C6     YCO 8  
YCO N7     N7     N 0 1 N N N -2.190 6.475  26.173 -4.109 0.645  -1.341 N7     YCO 9  
YCO C8     C8     C 0 1 Y N N -2.185 7.375  27.193 -5.244 0.748  -0.585 C8     YCO 10 
YCO C9     C9     C 0 1 Y N N -1.475 8.571  27.046 -6.407 1.273  -1.152 C9     YCO 11 
YCO "C1'"  "C1'"  C 0 1 N N R -4.878 1.554  26.657 0.502  -1.424 0.862  "C1'"  YCO 12 
YCO C10    C10    C 0 1 Y N N -1.448 9.504  28.086 -7.556 1.378  -0.394 C10    YCO 13 
YCO C11    C11    C 0 1 Y N N -2.141 9.249  29.274 -7.561 0.966  0.926  C11    YCO 14 
YCO C12    C12    C 0 1 Y N N -2.853 8.056  29.424 -6.414 0.444  1.499  C12    YCO 15 
YCO C13    C13    C 0 1 Y N N -2.878 7.114  28.388 -5.254 0.332  0.752  C13    YCO 16 
YCO O14    O14    O 0 1 N N N -3.583 5.938  28.553 -4.130 -0.182 1.323  O14    YCO 17 
YCO "C2'"  "C2'"  C 0 1 N N N -3.789 0.514  26.827 0.870  -2.738 0.146  "C2'"  YCO 18 
YCO "C3'"  "C3'"  C 0 1 N N S -3.823 0.265  28.314 2.280  -2.473 -0.434 "C3'"  YCO 19 
YCO "O3'"  "O3'"  O 0 1 N N N -3.412 -1.059 28.643 3.121  -3.618 -0.275 "O3'"  YCO 20 
YCO "C4'"  "C4'"  C 0 1 N N R -5.268 0.482  28.692 2.776  -1.296 0.445  "C4'"  YCO 21 
YCO "O4'"  "O4'"  O 0 1 N N N -5.753 1.487  27.800 1.587  -0.505 0.651  "O4'"  YCO 22 
YCO "C5'"  "C5'"  C 0 1 N N N -5.309 0.971  30.125 3.843  -0.485 -0.294 "C5'"  YCO 23 
YCO "O5'"  "O5'"  O 0 1 N N N -6.581 1.527  30.368 4.365  0.520  0.578  "O5'"  YCO 24 
YCO OP1    OP1    O 0 1 N N N -9.311 1.241  31.615 5.076  2.274  -1.092 OP1    YCO 25 
YCO OP2    OP2    O 0 1 N N N -6.887 -0.486 32.655 5.760  2.624  1.313  OP2    YCO 26 
YCO OP3    OP3    O 0 1 N Y N -7.160 2.060  32.825 6.874  0.761  -0.170 O8     YCO 27 
YCO HN3    HN3    H 0 1 N N N -2.412 4.633  24.421 -1.829 0.323  -2.488 HN3    YCO 28 
YCO H6     H6     H 0 1 N N N -4.757 3.525  28.571 -1.828 -1.130 2.117  H6     YCO 29 
YCO H9     H9     H 0 1 N N N -0.946 8.774  26.126 -6.407 1.596  -2.182 H9     YCO 30 
YCO "H1'"  "H1'"  H 0 1 N N N -5.405 1.320  25.720 0.371  -1.607 1.928  "H1'"  YCO 31 
YCO H10    H10    H 0 1 N N N -0.892 10.423 27.972 -8.455 1.785  -0.834 H10    YCO 32 
YCO H11    H11    H 0 1 N N N -2.126 9.974  30.075 -8.464 1.051  1.513  H11    YCO 33 
YCO H12    H12    H 0 1 N N N -3.386 7.860  30.342 -6.424 0.124  2.531  H12    YCO 34 
YCO "H2'"  "H2'"  H 0 1 N N N -3.997 -0.400 26.251 0.899  -3.565 0.856  "H2'"  YCO 35 
YCO "H2'A" "H2'A" H 0 0 N N N -2.809 0.884  26.493 0.161  -2.947 -0.655 "H2'A" YCO 36 
YCO "H3'"  "H3'"  H 0 1 N N N -3.132 0.929  28.854 2.221  -2.179 -1.482 "H3'"  YCO 37 
YCO "HO3'" "HO3'" H 0 0 N Y N -3.447 -1.177 29.585 2.802  -4.407 -0.734 "HO3'" YCO 38 
YCO "H4'"  "H4'"  H 0 1 N N N -5.879 -0.430 28.618 3.165  -1.664 1.395  "H4'"  YCO 39 
YCO "H5'"  "H5'"  H 0 1 N N N -5.132 0.130  30.812 4.649  -1.146 -0.610 "H5'"  YCO 40 
YCO "H5'A" "H5'A" H 0 0 N N N -4.532 1.734  30.282 3.397  -0.011 -1.168 "H5'A" YCO 41 
YCO HOP2   HOP2   H 0 0 N N N -6.987 -1.307 32.188 6.438  3.283  1.112  HOP2   YCO 42 
YCO HOP3   HOP3   H 0 0 N Y N -7.953 2.507  33.097 7.217  0.269  0.589  H17    YCO 43 
# 
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 
YCO P     OP2    SING N N 1  
YCO P     OP3    SING N N 2  
YCO N1    "C1'"  SING N N 3  
YCO N1    C6     SING N N 4  
YCO C2    N1     SING N N 5  
YCO O2    C2     DOUB N N 6  
YCO N3    C2     SING N N 7  
YCO N3    C4     SING N N 8  
YCO N3    HN3    SING N N 9  
YCO C4    C5     SING N N 10 
YCO C5    C6     DOUB N N 11 
YCO C5    O14    SING N N 12 
YCO C6    H6     SING N N 13 
YCO N7    C4     DOUB N N 14 
YCO N7    C8     SING N N 15 
YCO C8    C13    SING Y N 16 
YCO C9    C8     DOUB Y N 17 
YCO C9    C10    SING Y N 18 
YCO C9    H9     SING N N 19 
YCO "C1'" "C2'"  SING N N 20 
YCO "C1'" "O4'"  SING N N 21 
YCO "C1'" "H1'"  SING N N 22 
YCO C10   C11    DOUB Y N 23 
YCO C10   H10    SING N N 24 
YCO C11   C12    SING Y N 25 
YCO C11   H11    SING N N 26 
YCO C12   H12    SING N N 27 
YCO C13   C12    DOUB Y N 28 
YCO C13   O14    SING N N 29 
YCO "C2'" "C3'"  SING N N 30 
YCO "C2'" "H2'"  SING N N 31 
YCO "C2'" "H2'A" SING N N 32 
YCO "C3'" "O3'"  SING N N 33 
YCO "C3'" "C4'"  SING N N 34 
YCO "C3'" "H3'"  SING N N 35 
YCO "O3'" "HO3'" SING N N 36 
YCO "C4'" "C5'"  SING N N 37 
YCO "C4'" "H4'"  SING N N 38 
YCO "O4'" "C4'"  SING N N 39 
YCO "C5'" "O5'"  SING N N 40 
YCO "C5'" "H5'"  SING N N 41 
YCO "C5'" "H5'A" SING N N 42 
YCO "O5'" P      SING N N 43 
YCO OP1   P      DOUB N N 44 
YCO OP2   HOP2   SING N N 45 
YCO OP3   HOP3   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 
YCO SMILES           ACDLabs              12.01 "O=P(O)(O)OCC4OC(N2C(=O)NC1=Nc3ccccc3OC1=C2)CC4O"                                                                                                                              
YCO SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C3Oc4ccccc4N=C3NC2=O"                                                                                                                
YCO SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C3Oc4ccccc4N=C3NC2=O"                                                                                                                     
YCO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)N=C3C(=CN(C(=O)N3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)O2"                                                                                                         
YCO SMILES           "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)N=C3C(=CN(C(=O)N3)C4CC(C(O4)COP(=O)(O)O)O)O2"                                                                                                                      
YCO InChI            InChI                1.03  "InChI=1S/C15H16N3O8P/c19-9-5-13(26-12(9)7-24-27(21,22)23)18-6-11-14(17-15(18)20)16-8-3-1-2-4-10(8)25-11/h1-4,6,9,12-13,19H,5,7H2,(H,16,17,20)(H2,21,22,23)/t9-,12+,13+/m0/s1" 
YCO InChIKey         InChI                1.03  CEYLCTLUVICBGV-ZWKOPEQDSA-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 
YCO "SYSTEMATIC NAME" ACDLabs              12.01 "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one"           
YCO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-3-hydroxy-5-(2-oxo-1H-pyrimido[5,4-b][1,4]benzoxazin-3-yl)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 
YCO "Other modification" 2011-02-10 RCSB 
YCO "Modify descriptor"  2011-06-04 RCSB 
# 
