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 #