data_3PD # _chem_comp.id 3PD _chem_comp.name "2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-04-14 _chem_comp.pdbx_modified_date 2020-06-17 _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 347.221 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3PD _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 3PD "O5'" "O5'" O 0 1 N N N 0.929 11.162 13.419 3.235 3.702 -2.745 "O5'" 3PD 1 3PD "C5'" "C5'" C 0 1 N N N 1.922 11.969 12.786 2.240 2.706 -2.896 "C5'" 3PD 2 3PD "C4'" "C4'" C 0 1 N N R 2.431 13.049 13.724 2.219 1.846 -1.646 "C4'" 3PD 3 3PD "O4'" "O4'" O 0 1 N N N 1.382 13.999 14.095 1.879 2.654 -0.508 "O4'" 3PD 4 3PD "C1'" "C1'" C 0 1 N N R 1.567 14.465 15.412 1.171 1.827 0.433 "C1'" 3PD 5 3PD "C2'" "C2'" C 0 1 N N N 2.807 13.768 16.007 0.970 0.461 -0.212 "C2'" 3PD 6 3PD "C3'" "C3'" C 0 1 N N S 3.019 12.553 15.059 1.177 0.741 -1.684 "C3'" 3PD 7 3PD "O3'" "O3'" O 0 1 N N N 4.418 12.253 14.819 1.636 -0.408 -2.366 "O3'" 3PD 8 3PD N9 N9 N 0 1 Y N N 0.267 14.282 16.183 -0.077 2.488 0.819 N9 3PD 9 3PD C4 C4 C 0 1 Y N N -0.407 13.104 16.516 -0.705 2.429 2.031 C4 3PD 10 3PD N3 N3 N 0 1 Y N N -0.006 11.798 16.192 -0.281 1.738 3.113 N3 3PD 11 3PD C2 C2 C 0 1 Y N N -0.858 10.835 16.654 -1.083 1.861 4.148 C2 3PD 12 3PD N2 N2 N 0 1 N N N -0.624 9.536 16.441 -0.830 1.237 5.342 N2 3PD 13 3PD N1 N1 N 0 1 Y N N -2.023 11.153 17.382 -2.263 2.641 4.111 N1 3PD 14 3PD C6 C6 C 0 1 Y N N -2.453 12.488 17.721 -2.721 3.365 3.001 C6 3PD 15 3PD O6 O6 O 0 1 N N N -3.493 12.639 18.363 -3.741 4.041 2.966 O6 3PD 16 3PD C5 C5 C 0 1 Y N N -1.550 13.505 17.234 -1.825 3.211 1.888 C5 3PD 17 3PD N7 N7 N 0 1 Y N N -1.600 14.885 17.352 -1.918 3.751 0.639 N7 3PD 18 3PD C8 C8 C 0 1 Y N N -0.523 15.291 16.725 -0.848 3.296 0.017 C8 3PD 19 3PD P P P 0 1 N N N 5.526 12.056 15.963 0.705 -1.727 -2.352 P 3PD 20 3PD O1P O1P O 0 1 N N N 6.284 13.310 16.097 1.453 -2.739 -3.368 O1P 3PD 21 3PD O2P O2P O 0 1 N N N 4.890 11.528 17.191 -0.594 -1.252 -3.188 O2P 3PD 22 3PD O1 O1 O 0 1 N N N ? ? ? 0.413 -2.287 -0.990 O1 3PD 23 3PD "H5'" "H5'" H 0 1 N N N 1.273 10.288 13.560 3.079 4.368 -3.436 "H5'" 3PD 24 3PD "H5'1" "1H5'" H 0 0 N N N 1.471 12.453 11.908 1.270 3.186 -3.037 "H5'1" 3PD 25 3PD "H5'2" "2H5'" H 0 0 N N N 2.765 11.328 12.489 2.475 2.094 -3.768 "H5'2" 3PD 26 3PD "H4'" "H4'" H 0 1 N N N 3.231 13.507 13.125 3.224 1.436 -1.487 "H4'" 3PD 27 3PD "H1'" "H1'" H 0 1 N N N 1.783 15.542 15.462 1.753 1.756 1.357 "H1'" 3PD 28 3PD "H2'1" "1H2'" H 0 0 N N N 2.671 13.474 17.058 -0.002 0.004 0.001 "H2'1" 3PD 29 3PD "H2'2" "2H2'" H 0 0 N N N 3.682 14.434 16.014 1.736 -0.240 0.147 "H2'2" 3PD 30 3PD "H3'" "H3'" H 0 1 N N N 2.567 11.646 15.487 0.241 1.086 -2.140 "H3'" 3PD 31 3PD HN21 1HN2 H 0 0 N N N 0.164 9.171 15.945 -1.587 0.804 5.817 HN21 3PD 32 3PD HN22 2HN2 H 0 0 N N N -1.349 8.981 16.849 0.102 1.241 5.687 HN22 3PD 33 3PD HN1 HN1 H 0 1 N N N -2.597 10.393 17.688 -2.824 2.680 4.958 HN1 3PD 34 3PD H8 H8 H 0 1 N N N -0.267 16.336 16.635 -0.576 3.514 -1.007 H8 3PD 35 3PD H1P H1P H 0 1 N N N 5.681 14.044 16.126 1.101 -3.648 -3.477 H1P 3PD 36 3PD H2P H2P H 0 1 N N N 5.549 11.415 17.866 -1.366 -1.854 -3.248 H2P 3PD 37 # # 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 3PD "O5'" "C5'" SING N N 1 3PD "O5'" "H5'" SING N N 2 3PD "C5'" "C4'" SING N N 3 3PD "C5'" "H5'1" SING N N 4 3PD "C5'" "H5'2" SING N N 5 3PD "C4'" "O4'" SING N N 6 3PD "C4'" "C3'" SING N N 7 3PD "C4'" "H4'" SING N N 8 3PD "O4'" "C1'" SING N N 9 3PD "C1'" "C2'" SING N N 10 3PD "C1'" N9 SING N N 11 3PD "C1'" "H1'" SING N N 12 3PD "C2'" "C3'" SING N N 13 3PD "C2'" "H2'1" SING N N 14 3PD "C2'" "H2'2" SING N N 15 3PD "C3'" "O3'" SING N N 16 3PD "C3'" "H3'" SING N N 17 3PD "O3'" P SING N N 18 3PD N9 C4 SING Y N 19 3PD N9 C8 SING Y N 20 3PD C4 N3 SING Y N 21 3PD C4 C5 DOUB Y N 22 3PD N3 C2 DOUB Y N 23 3PD C2 N2 SING N N 24 3PD C2 N1 SING Y N 25 3PD N2 HN21 SING N N 26 3PD N2 HN22 SING N N 27 3PD N1 C6 SING Y N 28 3PD N1 HN1 SING N N 29 3PD C6 O6 DOUB N N 30 3PD C6 C5 SING Y N 31 3PD C5 N7 SING Y N 32 3PD N7 C8 DOUB Y N 33 3PD C8 H8 SING N N 34 3PD P O1P SING N N 35 3PD P O2P SING N N 36 3PD P O1 DOUB N N 37 3PD O1P H1P SING N N 38 3PD O2P H2P SING N N 39 # # 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 3PD SMILES ACDLabs 10.04 "O=C1c2ncn(c2N=C(N)N1)C3OC(C(OP(=O)(O)O)C3)CO" 3PD SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O[P](O)(O)=O)[C@@H](CO)O3" 3PD SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O[P](O)(O)=O)[CH](CO)O3" 3PD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)OP(=O)(O)O)N=C(NC2=O)N" 3PD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CC(C(O3)CO)OP(=O)(O)O)N=C(NC2=O)N" 3PD InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(5(2-16)21-6)22-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1" 3PD InChIKey InChI 1.03 QQMSZHORHNORLP-KVQBGUIXSA-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 3PD "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-3'-guanylic acid" 3PD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] 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 3PD "Create component" 2006-04-14 RCSB 3PD "Modify descriptor" 2011-06-04 RCSB 3PD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3PD _pdbx_chem_comp_synonyms.name "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##