data_D5M # _chem_comp.id D5M _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-05-03 _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 331.222 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D5M _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 1Z1C _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 D5M "O5'" O5* O 0 1 N N N -51.464 14.039 60.113 2.211 -1.232 -3.468 "O5'" D5M 1 D5M "C5'" C5* C 0 1 N N N -51.078 14.680 58.895 1.348 -1.500 -2.377 "C5'" D5M 2 D5M "C4'" C4* C 0 1 N N R -49.647 14.357 58.531 2.156 -1.432 -1.088 "C4'" D5M 3 D5M "O4'" O4* O 0 1 N N N -49.503 12.918 58.415 2.678 -0.093 -0.958 "O4'" D5M 4 D5M "C3'" C3* C 0 1 N N S -49.179 14.929 57.190 1.309 -1.697 0.152 "C3'" D5M 5 D5M "O3'" O3* O 0 1 N N N -47.747 15.116 57.200 2.127 -2.250 1.180 "O3'" D5M 6 D5M "C2'" C2* C 0 1 N N N -49.481 13.795 56.223 0.878 -0.312 0.578 "C2'" D5M 7 D5M "C1'" C1* C 0 1 N N R -49.156 12.570 57.073 2.101 0.516 0.211 "C1'" D5M 8 D5M N9 N9 N 0 1 Y N N -49.877 11.341 56.724 1.818 1.923 -0.049 N9 D5M 9 D5M C8 C8 C 0 1 Y N N -51.158 11.208 56.223 1.432 2.463 -1.249 C8 D5M 10 D5M N7 N7 N 0 1 Y N N -51.538 9.960 56.060 1.250 3.765 -1.175 N7 D5M 11 D5M C5 C5 C 0 1 Y N N -50.433 9.217 56.470 1.530 4.086 0.130 C5 D5M 12 D5M C6 C6 C 0 1 Y N N -50.200 7.826 56.554 1.519 5.292 0.822 C6 D5M 13 D5M N6 N6 N 0 1 N N N -51.110 6.903 56.229 1.171 6.489 0.173 N6 D5M 14 D5M N1 N1 N 0 1 Y N N -48.985 7.418 56.997 1.849 5.300 2.136 N1 D5M 15 D5M C2 C2 C 0 1 Y N N -48.075 8.350 57.338 2.176 4.115 2.707 C2 D5M 16 D5M N3 N3 N 0 1 Y N N -48.178 9.681 57.314 2.223 2.888 2.144 N3 D5M 17 D5M C4 C4 C 0 1 Y N N -49.397 10.056 56.866 1.886 2.954 0.847 C4 D5M 18 D5M P P P 0 1 N N N ? ? ? 1.592 -1.245 -4.964 P D5M 19 D5M O1P O1P O 0 1 N N N ? ? ? 2.575 -0.951 -6.059 O1P D5M 20 D5M O3P O3P O 0 1 N N N ? ? ? 0.339 -0.227 -4.868 O3P D5M 21 D5M O2P O2P O 0 1 N N N ? ? ? 0.886 -2.697 -5.051 O2P D5M 22 D5M "H5'1" 1H5* H 0 0 N N N -51.737 14.332 58.086 0.551 -0.756 -2.359 "H5'1" D5M 23 D5M "H5'2" 2H5* H 0 0 N N N -51.164 15.768 59.033 0.917 -2.495 -2.497 "H5'2" D5M 24 D5M "H4'" H4* H 0 1 N N N -49.041 14.809 59.330 3.008 -2.117 -1.157 "H4'" D5M 25 D5M H1 H1 H 0 1 N N N -49.653 15.892 56.950 0.475 -2.383 -0.018 H1 D5M 26 D5M "H3'" H3* H 0 1 N N N -47.426 15.157 56.307 2.928 -1.706 1.218 "H3'" D5M 27 D5M "H2'1" 1H2* H 0 0 N N N -50.529 13.802 55.889 0.008 0.008 -0.009 "H2'1" D5M 28 D5M "H2'2" 2H2* H 0 0 N N N -48.910 13.848 55.284 0.635 -0.225 1.641 "H2'2" D5M 29 D5M "H1'" H1* H 0 1 N N N -48.093 12.336 56.911 2.853 0.503 1.007 "H1'" D5M 30 D5M H8 H8 H 0 1 N N N -51.789 12.052 55.987 1.301 1.859 -2.137 H8 D5M 31 D5M HN61 1HN6 H 0 0 N N N -51.337 6.986 55.259 0.205 6.745 0.096 HN61 D5M 32 D5M HN62 2HN6 H 0 0 N N N -50.739 5.992 56.408 1.883 7.025 -0.286 HN62 D5M 33 D5M H2 H2 H 0 1 N N N -47.125 7.966 57.680 2.435 4.159 3.759 H2 D5M 34 D5M H3P H3P H 0 1 N N N ? ? ? -0.163 -0.014 -5.684 H3P D5M 35 D5M H2P H2P H 0 1 N N N ? ? ? 0.508 -2.990 -5.907 H2P D5M 36 # 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 D5M "O5'" "C5'" SING N N 1 D5M "O5'" P SING N N 2 D5M "C5'" "C4'" SING N N 3 D5M "C5'" "H5'1" SING N N 4 D5M "C5'" "H5'2" SING N N 5 D5M "C4'" "O4'" SING N N 6 D5M "C4'" "C3'" SING N N 7 D5M "C4'" "H4'" SING N N 8 D5M "O4'" "C1'" SING N N 9 D5M "C3'" "O3'" SING N N 10 D5M "C3'" "C2'" SING N N 11 D5M "C3'" H1 SING N N 12 D5M "O3'" "H3'" SING N N 13 D5M "C2'" "C1'" SING N N 14 D5M "C2'" "H2'1" SING N N 15 D5M "C2'" "H2'2" SING N N 16 D5M "C1'" N9 SING N N 17 D5M "C1'" "H1'" SING N N 18 D5M N9 C8 SING Y N 19 D5M N9 C4 SING Y N 20 D5M C8 N7 DOUB Y N 21 D5M C8 H8 SING N N 22 D5M N7 C5 SING Y N 23 D5M C5 C6 SING Y N 24 D5M C5 C4 DOUB Y N 25 D5M C6 N6 SING N N 26 D5M C6 N1 DOUB Y N 27 D5M N6 HN61 SING N N 28 D5M N6 HN62 SING N N 29 D5M N1 C2 SING Y N 30 D5M C2 N3 DOUB Y N 31 D5M C2 H2 SING N N 32 D5M N3 C4 SING Y N 33 D5M P O1P DOUB N N 34 D5M P O3P SING N N 35 D5M P O2P SING N N 36 D5M O3P H3P SING N N 37 D5M O2P H2P SING N N 38 # 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 D5M SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O" D5M SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" D5M SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" D5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N" D5M SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N" D5M InChI InChI 1.03 "InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1" D5M InChIKey InChI 1.03 KHWCHTKSEGGWEX-RRKCRQDMSA-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 D5M "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-adenylic acid ; D5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-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 D5M "Create component" 2005-05-03 RCSB D5M "Modify descriptor" 2011-06-04 RCSB #