data_5PY
# 
_chem_comp.id                                    5PY 
_chem_comp.name                                  "1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-10-12 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        306.209 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     5PY 
_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        ? 
_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 
5PY P      P    P 0 1 N N N 20.049 5.359 53.620 -3.968 -1.665 3.118  P      5PY 1  
5PY OP2    O2P  O 0 1 N N N 19.790 4.980 52.234 -3.912 -2.311 1.636  OP2    5PY 2  
5PY OP1    O1P  O 0 1 N N N 19.043 5.020 54.628 -4.406 -2.599 4.208  OP1    5PY 3  
5PY "O5'"  O5*  O 0 1 N N N 21.432 4.574 53.729 -2.493 -1.028 3.315  "O5'"  5PY 4  
5PY "C5'"  C5*  C 0 1 N N N 22.401 4.741 54.638 -2.005 -0.136 2.327  "C5'"  5PY 5  
5PY "C4'"  C4*  C 0 1 N N R 23.503 5.614 54.058 -0.611 0.328  2.728  "C4'"  5PY 6  
5PY "O4'"  O4*  O 0 1 N N N 24.028 6.186 55.262 0.247  -0.829 2.764  "O4'"  5PY 7  
5PY "C1'"  C1*  C 0 1 N N R 25.423 5.949 55.303 1.157  -0.778 1.657  "C1'"  5PY 8  
5PY N1     N1   N 0 1 N N N 25.841 5.862 56.718 1.164  -2.047 0.989  N1     5PY 9  
5PY C2     C2   C 0 1 N N N 27.201 5.715 56.962 2.333  -2.557 0.365  C2     5PY 10 
5PY O2     O2   O 0 1 N N N 28.020 5.609 56.065 3.389  -1.922 0.376  O2     5PY 11 
5PY N3     N3   N 0 1 N N N 27.527 5.659 58.299 2.265  -3.790 -0.263 N3     5PY 12 
5PY C4     C4   C 0 1 N N N 26.660 5.780 59.359 1.144  -4.433 -0.261 C4     5PY 13 
5PY C5     C5   C 0 1 N N N 25.264 5.988 59.046 -0.110 -3.975 0.360  C5     5PY 14 
5PY C5M    C5M  C 0 1 N N N 24.292 6.282 60.145 -1.326 -4.827 0.280  C5M    5PY 15 
5PY C6     C6   C 0 1 N N N 24.915 6.019 57.747 -0.014 -2.785 0.958  C6     5PY 16 
5PY "C2'"  C2*  C 0 1 N N N 25.684 4.690 54.469 0.710  0.360  0.754  "C2'"  5PY 17 
5PY "C3'"  C3*  C 0 1 N N S 24.697 4.971 53.339 0.008  1.286  1.720  "C3'"  5PY 18 
5PY "O3'"  O3*  O 0 1 N N N 25.298 5.911 52.415 0.965  2.121  2.368  "O3'"  5PY 19 
5PY OP3    O3P  O 0 1 N Y N ?      ?     ?      -4.901 -0.360 2.920  OP3    5PY 20 
5PY H71    1H5M H 0 1 N N N 24.830 6.354 61.102 -2.065 -4.366 -0.379 H71    5PY 21 
5PY H72    2H5M H 0 1 N N N 23.782 7.235 59.938 -1.765 -4.953 1.272  H72    5PY 22 
5PY H73    3H5M H 0 1 N N N 23.549 5.473 60.203 -1.069 -5.814 -0.113 H73    5PY 23 
5PY H4     H4   H 0 1 N N N 27.006 5.722 60.380 1.099  -5.414 -0.763 H4     5PY 24 
5PY H6     H6   H 0 1 N N N 23.877 6.172 57.492 -0.865 -2.330 1.454  H6     5PY 25 
5PY "H1'"  H1*  H 0 1 N N N 26.027 6.758 54.867 2.163  -0.604 2.054  "H1'"  5PY 26 
5PY "H2'"  1H2* H 0 1 N N N 26.726 4.599 54.128 -0.003 -0.001 0.003  "H2'"  5PY 27 
5PY "H2''" 2H2* H 0 0 N N N 25.549 3.733 54.994 1.556  0.818  0.232  "H2''" 5PY 28 
5PY "H3'"  H3*  H 0 1 N N N 24.411 4.079 52.763 -0.722 1.941  1.236  "H3'"  5PY 29 
5PY "HO3'" H3T  H 0 0 N Y N 25.430 6.745 52.851 0.743  3.042  2.146  "HO3'" 5PY 30 
5PY "H4'"  H4*  H 0 1 N N N 23.062 6.238 53.266 -0.644 0.753  3.736  "H4'"  5PY 31 
5PY "H5'"  1H5* H 0 1 N N N 21.983 5.226 55.532 -1.971 -0.654 1.366  "H5'"  5PY 32 
5PY "H5''" 2H5* H 0 0 N N N 22.818 3.760 54.910 -2.683 0.718  2.254  "H5''" 5PY 33 
5PY HOP2   2HOP H 0 0 N N N 19.734 5.761 51.697 -4.684 -2.823 1.313  HOP2   5PY 34 
5PY HOP3   3HOP H 0 0 N N N ?      ?     ?      -5.874 -0.475 2.871  HOP3   5PY 35 
# 
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 
5PY P     "O5'"  SING N N 1  
5PY P     OP2    SING N N 2  
5PY P     OP3    SING N N 3  
5PY P     OP1    DOUB N N 4  
5PY OP2   HOP2   SING N N 5  
5PY "O5'" "C5'"  SING N N 6  
5PY "C5'" "C4'"  SING N N 7  
5PY "C5'" "H5'"  SING N N 8  
5PY "C5'" "H5''" SING N N 9  
5PY "C4'" "C3'"  SING N N 10 
5PY "C4'" "O4'"  SING N N 11 
5PY "C4'" "H4'"  SING N N 12 
5PY "O4'" "C1'"  SING N N 13 
5PY "C1'" N1     SING N N 14 
5PY "C1'" "C2'"  SING N N 15 
5PY "C1'" "H1'"  SING N N 16 
5PY N1    C2     SING N N 17 
5PY N1    C6     SING N N 18 
5PY C2    N3     SING N N 19 
5PY C2    O2     DOUB N N 20 
5PY N3    C4     DOUB N N 21 
5PY C4    C5     SING N N 22 
5PY C4    H4     SING N N 23 
5PY C5    C5M    SING N N 24 
5PY C5    C6     DOUB N N 25 
5PY C5M   H71    SING N N 26 
5PY C5M   H72    SING N N 27 
5PY C5M   H73    SING N N 28 
5PY C6    H6     SING N N 29 
5PY "C2'" "C3'"  SING N N 30 
5PY "C2'" "H2'"  SING N N 31 
5PY "C2'" "H2''" SING N N 32 
5PY "C3'" "O3'"  SING N N 33 
5PY "C3'" "H3'"  SING N N 34 
5PY "O3'" "HO3'" SING N N 35 
5PY OP3   HOP3   SING N N 36 
# 
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 
5PY SMILES           ACDLabs              10.04 "O=P(O)(O)OCC2OC(N1C(=O)N=CC(=C1)C)CC2O"                                                                                                     
5PY InChI            InChI                1.02b "InChI=1/C10H15N2O7P/c1-6-3-11-10(14)12(4-6)9-2-7(13)8(19-9)5-18-20(15,16)17/h3-4,7-9,13H,2,5H2,1H3,(H2,15,16,17)/t7-,8+,9+/m0/s1/f/h15-16H" 
5PY InChIKey         InChI                1.02b TWYWJJKQSULVQX-ZRPKJLBLDL                                                                                                                    
5PY SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1"                                                                                    
5PY SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1"                                                                                        
5PY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                      
5PY SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1)C2CC(C(O2)COP(=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 
5PY "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-2(1H)-one"            
5PY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
