data_5PC
# 
_chem_comp.id                                    5PC 
_chem_comp.name                                  "5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" 
_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                     2003-03-11 
_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                     5PC 
_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 
5PC OP3    O3P  O 0 1 N Y N ?      ?      ?       -3.912 -2.311 1.636  OP3    5PC 1  
5PC P      P    P 0 1 N N N 0.797  -6.110 -10.274 -3.968 -1.665 3.118  P      5PC 2  
5PC OP1    O1P  O 0 1 N N N 0.039  -5.056 -10.977 -4.406 -2.599 4.208  OP1    5PC 3  
5PC OP2    O2P  O 0 1 N N N 1.333  -7.259 -11.041 -4.901 -0.360 2.920  OP2    5PC 4  
5PC "C5'"  C5*  C 0 1 N N N 0.304  -7.807 -8.252  -2.005 -0.136 2.327  "C5'"  5PC 5  
5PC "O5'"  O5*  O 0 1 N N N -0.104 -6.688 -9.047  -2.493 -1.028 3.315  "O5'"  5PC 6  
5PC "C4'"  C4*  C 0 1 N N R -0.593 -8.011 -7.019  -0.611 0.328  2.728  "C4'"  5PC 7  
5PC "O4'"  O4*  O 0 1 N N N -0.533 -6.960 -6.073  0.247  -0.829 2.764  "O4'"  5PC 8  
5PC "C3'"  C3*  C 0 1 N N S -2.072 -8.287 -7.302  0.008  1.286  1.720  "C3'"  5PC 9  
5PC "O3'"  O3*  O 0 1 N N N -2.291 -9.671 -7.464  0.965  2.121  2.368  "O3'"  5PC 10 
5PC "C2'"  C2*  C 0 1 N N N -2.766 -7.662 -6.090  0.710  0.360  0.754  "C2'"  5PC 11 
5PC "C1'"  C1*  C 0 1 N N R -1.627 -7.172 -5.221  1.157  -0.778 1.657  "C1'"  5PC 12 
5PC N1     N1   N 0 1 N N N -1.948 -5.897 -4.640  1.164  -2.047 0.989  N1     5PC 13 
5PC C2     C2   C 0 1 N N N -2.468 -5.808 -3.441  2.327  -2.559 0.368  C2     5PC 14 
5PC O2     O2   O 0 1 N N N -2.746 -6.809 -2.805  3.384  -1.926 0.378  O2     5PC 15 
5PC N3     N3   N 0 1 N N N -2.750 -4.654 -2.918  2.259  -3.790 -0.258 N3     5PC 16 
5PC C4     C4   C 0 1 N N N -2.444 -3.607 -3.571  1.148  -4.482 -0.285 C4     5PC 17 
5PC N4     N4   N 0 1 N N N -2.686 -2.461 -3.079  1.142  -5.703 -0.923 N4     5PC 18 
5PC C5     C5   C 0 1 N N N -1.981 -3.581 -4.846  -0.103 -3.975 0.360  C5     5PC 19 
5PC C6     C6   C 0 1 N N N -1.812 -4.806 -5.327  -0.009 -2.784 0.957  C6     5PC 20 
5PC C7     C7   C 0 1 N N N -1.826 -2.360 -5.633  -1.320 -4.706 0.345  C7     5PC 21 
5PC C8     C8   C 0 1 N N N -1.848 -1.381 -6.331  -2.349 -5.324 0.333  C8     5PC 22 
5PC C9     C9   C 0 1 N N N -1.929 -0.231 -7.219  -3.602 -6.077 0.317  C9     5PC 23 
5PC HOP3   3HOP H 0 0 N N N 0.487  -0.678 0.452   -4.684 -2.823 1.313  HOP3   5PC 24 
5PC HOP2   2HOP H 0 0 N N N 1.396  -7.743 -11.855 -5.874 -0.475 2.871  HOP2   5PC 25 
5PC "H5'"  1H5* H 0 1 N N N 0.274  -8.702 -8.873  -1.971 -0.654 1.366  "H5'"  5PC 26 
5PC "H5''" 2H5* H 0 0 N N N 1.328  -7.647 -7.916  -2.683 0.718  2.254  "H5''" 5PC 27 
5PC "H4'"  H4*  H 0 1 N N N -0.206 -8.895 -6.511  -0.644 0.753  3.736  "H4'"  5PC 28 
5PC "H3'"  H3*  H 0 1 N N N -2.346 -7.743 -8.206  -0.722 1.941  1.236  "H3'"  5PC 29 
5PC "HO3'" H3T  H 0 0 N Y N -3.208 -9.842 -7.639  0.743  3.042  2.146  "HO3'" 5PC 30 
5PC "H2'"  1H2* H 0 1 N N N -3.351 -8.390 -5.527  -0.003 -0.001 0.003  "H2'"  5PC 31 
5PC "H2''" 2H2* H 0 0 N N N -3.402 -6.848 -6.436  1.556  0.818  0.232  "H2''" 5PC 32 
5PC "H1'"  H1*  H 0 1 N N N -1.373 -7.920 -4.469  2.163  -0.604 2.054  "H1'"  5PC 33 
5PC H41    H41  H 0 1 N N N -3.093 -2.462 -2.154  1.429  -5.732 -1.870 H41    5PC 34 
5PC H42    H42  H 0 1 N N N -2.461 -1.680 -3.678  0.850  -6.495 -0.405 H42    5PC 35 
5PC H6     H6   H 0 1 N N N -1.553 -4.883 -6.373  -0.859 -2.326 1.455  H6     5PC 36 
5PC H91    H91  H 0 1 N N N -0.916 0.054  -7.501  -4.371 -5.566 0.904  H91    5PC 37 
5PC H92    H92  H 0 1 N N N -2.460 -0.518 -8.127  -3.976 -6.190 -0.705 H92    5PC 38 
5PC H93    H93  H 0 1 N N N -2.424 0.596  -6.709  -3.461 -7.077 0.739  H93    5PC 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 
5PC OP3   P      SING N N 1  
5PC OP3   HOP3   SING N N 2  
5PC P     OP1    DOUB N N 3  
5PC P     OP2    SING N N 4  
5PC P     "O5'"  SING N N 5  
5PC OP2   HOP2   SING N N 6  
5PC "C5'" "O5'"  SING N N 7  
5PC "C5'" "C4'"  SING N N 8  
5PC "C5'" "H5'"  SING N N 9  
5PC "C5'" "H5''" SING N N 10 
5PC "C4'" "O4'"  SING N N 11 
5PC "C4'" "C3'"  SING N N 12 
5PC "C4'" "H4'"  SING N N 13 
5PC "O4'" "C1'"  SING N N 14 
5PC "C3'" "O3'"  SING N N 15 
5PC "C3'" "C2'"  SING N N 16 
5PC "C3'" "H3'"  SING N N 17 
5PC "O3'" "HO3'" SING N N 18 
5PC "C2'" "C1'"  SING N N 19 
5PC "C2'" "H2'"  SING N N 20 
5PC "C2'" "H2''" SING N N 21 
5PC "C1'" N1     SING N N 22 
5PC "C1'" "H1'"  SING N N 23 
5PC N1    C2     SING N N 24 
5PC N1    C6     SING N N 25 
5PC C2    O2     DOUB N N 26 
5PC C2    N3     SING N N 27 
5PC N3    C4     DOUB N N 28 
5PC C4    N4     SING N N 29 
5PC C4    C5     SING N N 30 
5PC N4    H41    SING N N 31 
5PC N4    H42    SING N N 32 
5PC C5    C6     DOUB N N 33 
5PC C5    C7     SING N N 34 
5PC C6    H6     SING N N 35 
5PC C7    C8     TRIP N N 36 
5PC C8    C9     SING N N 37 
5PC C9    H91    SING N N 38 
5PC C9    H92    SING N N 39 
5PC C9    H93    SING N N 40 
# 
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 
5PC SMILES           ACDLabs              10.04 "O=C1N=C(N)C(C#CC)=CN1C2OC(C(O)C2)COP(=O)(O)O"                                                                                                             
5PC SMILES_CANONICAL CACTVS               3.341 "CC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                              
5PC SMILES           CACTVS               3.341 "CC#CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                                  
5PC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC#CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                
5PC SMILES           "OpenEye OEToolkits" 1.5.0 "CC#CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O"                                                                                                             
5PC InChI            InChI                1.03  "InChI=1S/C12H16N3O7P/c1-2-3-7-5-15(12(17)14-11(7)13)10-4-8(16)9(22-10)6-21-23(18,19)20/h5,8-10,16H,4,6H2,1H3,(H2,13,14,17)(H2,18,19,20)/t8-,9+,10+/m0/s1" 
5PC InChIKey         InChI                1.03  JMXAJBGSEDAXSC-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 
5PC "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5-prop-1-yn-1-ylcytidine 5'-(dihydrogen phosphate)
;
5PC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-5-prop-1-ynyl-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 
5PC "Create component"  2003-03-11 RCSB 
5PC "Modify descriptor" 2011-06-04 RCSB 
# 
