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 #