data_4PD
# 
_chem_comp.id                                    4PD 
_chem_comp.name                                  "3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYL-1,3-DIHYDRO-2H-PYRROLO[2,3-D]PYRIMIDIN-2-ONE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H16 N3 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                     2006-04-18 
_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                        345.245 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     4PD 
_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 
4PD P      P    P 0 1 N N N 2.814  0.971  -9.697  -3.968 -1.665 3.118  P      4PD 1  
4PD OP1    O1P  O 0 1 N N N 2.972  2.472  -9.673  -4.406 -2.599 4.208  OP1    4PD 2  
4PD OP2    O2P  O 0 1 N N N 2.461  0.239  -10.969 -3.912 -2.311 1.636  OP2    4PD 3  
4PD "O5'"  O5*  O 0 1 N N N 1.735  0.573  -8.546  -2.493 -1.028 3.315  "O5'"  4PD 4  
4PD "C5'"  C5*  C 0 1 N N N 1.249  -0.762 -8.508  -2.005 -0.136 2.327  "C5'"  4PD 5  
4PD "C4'"  C4*  C 0 1 N N R 0.399  -1.029 -7.251  -0.611 0.328  2.728  "C4'"  4PD 6  
4PD "O4'"  O4*  O 0 1 N N N 1.133  -0.648 -6.068  0.247  -0.829 2.764  "O4'"  4PD 7  
4PD "C3'"  C3*  C 0 1 N N S -0.964 -0.326 -7.212  0.008  1.286  1.720  "C3'"  4PD 8  
4PD "O3'"  O3*  O 0 1 N N N -1.966 -1.185 -7.747  0.965  2.121  2.368  "O3'"  4PD 9  
4PD "C2'"  C2*  C 0 1 N N N -1.180 -0.105 -5.728  0.710  0.360  0.754  "C2'"  4PD 10 
4PD "C1'"  C1*  C 0 1 N N R 0.220  -0.067 -5.125  1.157  -0.778 1.657  "C1'"  4PD 11 
4PD N1     N1   N 0 1 N N N 0.696  1.270  -4.750  1.164  -2.047 0.989  N1     4PD 12 
4PD C2     C2   C 0 1 N N N 0.926  1.552  -3.391  2.366  -2.496 0.391  C2     4PD 13 
4PD O2     O2   O 0 1 N N N 0.851  0.723  -2.482  3.425  -1.863 0.403  O2     4PD 14 
4PD N3     N3   N 0 1 N N N 1.293  2.851  -3.091  2.283  -3.748 -0.241 N3     4PD 15 
4PD C4     C4   C 0 1 N N N 1.554  3.779  -4.033  1.147  -4.498 -0.291 C4     4PD 16 
4PD C5     C5   C 0 1 N N N 1.373  3.425  -5.433  -0.054 -3.969 0.349  C5     4PD 17 
4PD C6     C6   C 0 1 N N N 0.932  2.214  -5.743  -0.009 -2.788 0.955  C6     4PD 18 
4PD C14    C14  C 0 1 N N N 1.748  4.597  -6.143  -1.035 -4.973 0.118  C14    4PD 19 
4PD C15    C15  C 0 1 N N N 2.079  5.486  -5.185  -0.391 -5.932 -0.579 C15    4PD 20 
4PD C16    C16  C 0 1 N N N 2.542  6.881  -5.414  -0.985 -7.205 -1.069 C16    4PD 21 
4PD N17    N17  N 0 1 N N N 1.966  5.007  -3.874  0.955  -5.663 -0.845 N17    4PD 22 
4PD OP3    O3P  O 0 1 N Y N ?      ?      ?       -4.901 -0.360 2.920  OP3    4PD 23 
4PD HOP2   2HOP H 0 0 N N N 1.524  0.085  -10.997 -4.684 -2.823 1.313  HOP2   4PD 24 
4PD "H5'"  1H5* H 0 1 N N N 2.115  -1.441 -8.486  -1.971 -0.654 1.366  "H5'"  4PD 25 
4PD "H5''" 2H5* H 0 0 N N N 0.626  -0.935 -9.398  -2.683 0.718  2.254  "H5''" 4PD 26 
4PD "H4'"  H4*  H 0 1 N N N 0.192  -2.109 -7.286  -0.644 0.753  3.736  "H4'"  4PD 27 
4PD "H3'"  H3*  H 0 1 N N N -1.007 0.604  -7.799  -0.722 1.941  1.236  "H3'"  4PD 28 
4PD "HO3'" H3T  H 0 0 N Y N -1.606 -2.056 -7.866  0.561  3.000  2.469  "HO3'" 4PD 29 
4PD "H2'"  1H2* H 0 1 N N N -1.798 -0.897 -5.281  -0.003 -0.001 0.003  "H2'"  4PD 30 
4PD "H2''" 2H2* H 0 0 N N N -1.713 0.839  -5.544  1.556  0.818  0.232  "H2''" 4PD 31 
4PD "H1'"  H1*  H 0 1 N N N 0.170  -0.635 -4.184  2.163  -0.604 2.054  "H1'"  4PD 32 
4PD H19    H19  H 0 1 N N N 1.368  3.114  -2.129  3.118  -4.115 -0.686 H19    4PD 33 
4PD H6     H6   H 0 1 N N N 0.754  1.958  -6.777  -0.876 -2.357 1.442  H6     4PD 34 
4PD H14    H14  H 0 1 N N N 1.764  4.743  -7.213  -2.063 -4.961 0.434  H14    4PD 35 
4PD H161   1H16 H 0 0 N N N 3.104  6.930  -6.358  -1.620 -7.644 -0.297 H161   4PD 36 
4PD H162   2H16 H 0 0 N N N 3.192  7.193  -4.583  -0.195 -7.914 -1.325 H162   4PD 37 
4PD H163   3H16 H 0 0 N N N 1.672  7.552  -5.471  -1.587 -7.020 -1.961 H163   4PD 38 
4PD HOP3   3HOP H 0 0 N N N -0.099 -0.945 -0.015  -5.874 -0.475 2.871  HOP3   4PD 39 
# 
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 
4PD P     OP1    DOUB N N 1  
4PD P     OP2    SING N N 2  
4PD P     "O5'"  SING N N 3  
4PD P     OP3    SING N N 4  
4PD OP2   HOP2   SING N N 5  
4PD "O5'" "C5'"  SING N N 6  
4PD "C5'" "C4'"  SING N N 7  
4PD "C5'" "H5'"  SING N N 8  
4PD "C5'" "H5''" SING N N 9  
4PD "C4'" "O4'"  SING N N 10 
4PD "C4'" "C3'"  SING N N 11 
4PD "C4'" "H4'"  SING N N 12 
4PD "O4'" "C1'"  SING N N 13 
4PD "C3'" "O3'"  SING N N 14 
4PD "C3'" "C2'"  SING N N 15 
4PD "C3'" "H3'"  SING N N 16 
4PD "O3'" "HO3'" SING N N 17 
4PD "C2'" "C1'"  SING N N 18 
4PD "C2'" "H2'"  SING N N 19 
4PD "C2'" "H2''" SING N N 20 
4PD "C1'" N1     SING N N 21 
4PD "C1'" "H1'"  SING N N 22 
4PD N1    C2     SING N N 23 
4PD N1    C6     SING N N 24 
4PD C2    O2     DOUB N N 25 
4PD C2    N3     SING N N 26 
4PD N3    C4     SING N N 27 
4PD N3    H19    SING N N 28 
4PD C4    C5     SING N N 29 
4PD C4    N17    DOUB N N 30 
4PD C5    C6     DOUB N N 31 
4PD C5    C14    SING N N 32 
4PD C6    H6     SING N N 33 
4PD C14   C15    DOUB N N 34 
4PD C14   H14    SING N N 35 
4PD C15   C16    SING N N 36 
4PD C15   N17    SING N N 37 
4PD C16   H161   SING N N 38 
4PD C16   H162   SING N N 39 
4PD C16   H163   SING N N 40 
4PD OP3   HOP3   SING N N 41 
# 
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 
4PD SMILES           ACDLabs              10.04 "O=C2NC1=NC(=CC1=CN2C3OC(C(O)C3)COP(=O)(O)O)C"                                                                                                                
4PD SMILES_CANONICAL CACTVS               3.341 "CC1=CC2=CN([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)C(=O)NC2=N1"                                                                                               
4PD SMILES           CACTVS               3.341 "CC1=CC2=CN([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)C(=O)NC2=N1"                                                                                                   
4PD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CC2=CN(C(=O)NC2=N1)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O"                                                                                                 
4PD SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CC2=CN(C(=O)NC2=N1)C3CC(C(O3)COP(=O)(O)O)O"                                                                                                              
4PD InChI            InChI                1.03  "InChI=1S/C12H16N3O7P/c1-6-2-7-4-15(12(17)14-11(7)13-6)10-3-8(16)9(22-10)5-21-23(18,19)20/h2,4,8-10,16H,3,5H2,1H3,(H,13,14,17)(H2,18,19,20)/t8-,9+,10+/m0/s1" 
4PD InChIKey         InChI                1.03  VOKZMFPBFFRNPZ-IVZWLZJFSA-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 
4PD "SYSTEMATIC NAME" ACDLabs              10.04 "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methyl-1,3-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one"   
4PD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(6-methyl-2-oxo-1H-pyrrolo[2,3-d]pyrimidin-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 
4PD "Create component"  2006-04-18 RCSB 
4PD "Modify descriptor" 2011-06-04 RCSB 
# 
