data_DG # _chem_comp.id DG _chem_comp.name "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-01 _chem_comp.pdbx_modified_date 2024-09-27 _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 G _chem_comp.three_letter_code DG _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _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 EBI _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 DG OP3 O3P O 0 1 N Y N N N N 1.807 -6.720 -10.410 -1.603 -1.547 5.624 OP3 DG 1 DG P P P 0 1 N N N N N N 0.961 -7.850 -11.142 -0.818 -0.321 4.935 P DG 2 DG OP1 O1P O 0 1 N N N N N N 0.170 -8.600 -10.123 -1.774 0.766 4.630 OP1 DG 3 DG OP2 O2P O 0 1 N N N N N N 1.852 -8.616 -12.064 0.312 0.224 5.941 OP2 DG 4 DG "O5'" O5* O 0 1 N N N N N N 0.048 -6.954 -12.084 -0.126 -0.826 3.572 "O5'" DG 5 DG "C5'" C5* C 0 1 N N N N N N -1.051 -6.223 -11.511 0.550 0.300 3.011 "C5'" DG 6 DG "C4'" C4* C 0 1 N N R N N N -1.328 -5.001 -12.351 1.233 -0.113 1.706 "C4'" DG 7 DG "O4'" O4* O 0 1 N N N N N N -0.272 -4.023 -12.145 0.253 -0.471 0.705 "O4'" DG 8 DG "C3'" C3* C 0 1 N N S N N N -1.390 -5.229 -13.845 1.976 1.091 1.073 "C3'" DG 9 DG "O3'" O3* O 0 1 N N N N N N -2.368 -4.320 -14.370 3.294 1.218 1.612 "O3'" DG 10 DG "C2'" C2* C 0 1 N N N N N N 0.027 -4.903 -14.329 2.026 0.692 -0.421 "C2'" DG 11 DG "C1'" C1* C 0 1 N N R N N N 0.517 -3.869 -13.327 0.897 -0.345 -0.573 "C1'" DG 12 DG N9 N9 N 0 1 Y N N N N N 1.928 -3.987 -12.970 -0.068 0.111 -1.575 N9 DG 13 DG C8 C8 C 0 1 Y N N N N N 2.740 -5.108 -12.939 -1.172 0.877 -1.341 C8 DG 14 DG N7 N7 N 0 1 Y N N N N N 3.900 -4.878 -12.390 -1.804 1.094 -2.458 N7 DG 15 DG C5 C5 C 0 1 Y N N N N N 3.852 -3.557 -12.017 -1.145 0.482 -3.472 C5 DG 16 DG C6 C6 C 0 1 N N N N N N 4.809 -2.738 -11.336 -1.361 0.377 -4.866 C6 DG 17 DG O6 O6 O 0 1 N N N N N N 5.900 -3.103 -10.856 -2.321 0.914 -5.391 O6 DG 18 DG N1 N1 N 0 1 N N N N N N 4.384 -1.424 -11.224 -0.473 -0.327 -5.601 N1 DG 19 DG C2 C2 C 0 1 N N N N N N 3.153 -0.949 -11.650 0.593 -0.928 -5.003 C2 DG 20 DG N2 N2 N 0 1 N N N N N N 2.928 0.356 -11.439 1.474 -1.643 -5.774 N2 DG 21 DG N3 N3 N 0 1 N N N N N N 2.236 -1.721 -12.198 0.804 -0.839 -3.709 N3 DG 22 DG C4 C4 C 0 1 Y N N N N N 2.641 -2.992 -12.372 -0.027 -0.152 -2.917 C4 DG 23 DG HOP3 3HOP H 0 0 N N N N N N 2.310 -6.242 -11.058 -2.002 -1.203 6.435 HOP3 DG 24 DG HOP2 2HOP H 0 0 N N N N N N 2.355 -8.138 -12.712 0.913 -0.513 6.114 HOP2 DG 25 DG "H5'" 1H5* H 0 1 N N N N N N -1.957 -6.858 -11.377 1.299 0.661 3.715 "H5'" DG 26 DG "H5''" 2H5* H 0 0 N N N N N N -0.876 -5.968 -10.439 -0.170 1.093 2.808 "H5''" DG 27 DG "H4'" H4* H 0 1 N N N N N N -2.337 -4.666 -12.015 1.921 -0.940 1.879 "H4'" DG 28 DG "H3'" H3* H 0 1 N N N N N N -1.682 -6.257 -14.160 1.411 2.013 1.211 "H3'" DG 29 DG "HO3'" H3T H 0 0 N Y N N N N -2.406 -4.463 -15.308 3.732 1.921 1.114 "HO3'" DG 30 DG "H2'" 1H2* H 0 1 N N N N N N 0.692 -5.790 -14.439 2.990 0.246 -0.665 "H2'" DG 31 DG "H2''" 2H2* H 0 0 N N N N N N 0.087 -4.578 -15.394 1.834 1.559 -1.053 "H2''" DG 32 DG "H1'" H1* H 0 1 N N N N N N 0.410 -2.866 -13.803 1.316 -1.306 -0.873 "H1'" DG 33 DG H8 H8 H 0 1 N N N N N N 2.482 -6.109 -13.322 -1.477 1.248 -0.373 H8 DG 34 DG H1 H1 H 0 1 N N N N N N 5.025 -0.756 -10.795 -0.601 -0.413 -6.559 H1 DG 35 DG H21 1H2 H 0 1 N N N N N N 2.022 0.705 -11.752 2.240 -2.073 -5.363 H21 DG 36 DG H22 2H2 H 0 1 N N N N N N 3.677 0.909 -11.854 1.329 -1.722 -6.730 H22 DG 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 DG OP3 P SING N N 1 DG OP3 HOP3 SING N N 2 DG P OP1 DOUB N N 3 DG P OP2 SING N N 4 DG P "O5'" SING N N 5 DG OP2 HOP2 SING N N 6 DG "O5'" "C5'" SING N N 7 DG "C5'" "C4'" SING N N 8 DG "C5'" "H5'" SING N N 9 DG "C5'" "H5''" SING N N 10 DG "C4'" "O4'" SING N N 11 DG "C4'" "C3'" SING N N 12 DG "C4'" "H4'" SING N N 13 DG "O4'" "C1'" SING N N 14 DG "C3'" "O3'" SING N N 15 DG "C3'" "C2'" SING N N 16 DG "C3'" "H3'" SING N N 17 DG "O3'" "HO3'" SING N N 18 DG "C2'" "C1'" SING N N 19 DG "C2'" "H2'" SING N N 20 DG "C2'" "H2''" SING N N 21 DG "C1'" N9 SING N N 22 DG "C1'" "H1'" SING N N 23 DG N9 C8 SING Y N 24 DG N9 C4 SING Y N 25 DG C8 N7 DOUB Y N 26 DG C8 H8 SING N N 27 DG N7 C5 SING Y N 28 DG C5 C6 SING N N 29 DG C5 C4 DOUB Y N 30 DG C6 O6 DOUB N N 31 DG C6 N1 SING N N 32 DG N1 C2 SING N N 33 DG N1 H1 SING N N 34 DG C2 N2 SING N N 35 DG C2 N3 DOUB N N 36 DG N2 H21 SING N N 37 DG N2 H22 SING N N 38 DG N3 C4 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 DG SMILES ACDLabs 10.04 "O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O" DG SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" DG SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" DG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N" DG SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N" DG InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1" DG InChIKey InChI 1.03 LTFMZDNNPPEQNG-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 DG "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-guanylic acid ; DG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-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 DG "Create component" 2001-06-01 EBI DG "Modify descriptor" 2011-06-04 RCSB DG "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 DG PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O1P ? ? 2 DG PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O3P ? ? 3 DG TYR None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OH ? ? #