data_AD2 # _chem_comp.id AD2 _chem_comp.name "2'-DEOXY-ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N5 O9 P2" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-03-06 _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 411.202 _chem_comp.one_letter_code A _chem_comp.three_letter_code AD2 _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 1L2B _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 AD2 P1 P1 P 0 1 N N N -14.899 53.873 36.894 3.461 4.758 -3.952 P1 AD2 1 AD2 OP1 O1P O 0 1 N N N -15.219 52.425 36.995 4.534 5.779 -3.708 OP1 AD2 2 AD2 OP2 O2P O 0 1 N N N -13.535 54.351 37.244 1.983 5.359 -4.217 OP2 AD2 3 AD2 "O5'" "O5'" O 0 1 N N N -15.241 54.360 35.417 3.235 3.702 -2.745 "O5'" AD2 4 AD2 P2 P2 P 0 1 N N N -13.893 51.893 31.198 0.705 -1.727 -2.352 P2 AD2 5 AD2 O5P O5P O 0 1 N N N -13.487 51.313 32.504 1.453 -2.739 -3.368 O5P AD2 6 AD2 O4P O4P O 0 1 N N N -12.860 52.452 30.294 0.413 -2.287 -0.990 O4P AD2 7 AD2 O6P O6P O 0 1 N N N -14.689 50.852 30.429 -0.594 -1.252 -3.188 O6P AD2 8 AD2 N9 N9 N 0 1 Y N N -15.037 57.371 32.985 -0.077 2.488 0.819 N9 AD2 9 AD2 C4 C4 C 0 1 Y N N -15.839 58.486 32.924 -0.699 2.425 2.036 C4 AD2 10 AD2 N3 N3 N 0 1 Y N N -17.033 58.604 32.320 -0.299 1.747 3.123 N3 AD2 11 AD2 C2 C2 C 0 1 Y N N -17.506 59.839 32.456 -1.173 1.925 4.138 C2 AD2 12 AD2 N1 N1 N 0 1 Y N N -16.963 60.891 33.078 -2.313 2.657 4.159 N1 AD2 13 AD2 C6 C6 C 0 1 Y N N -15.761 60.736 33.676 -2.655 3.315 3.026 C6 AD2 14 AD2 N6 N6 N 0 1 N N N -15.213 61.782 34.296 -3.826 4.091 2.985 N6 AD2 15 AD2 C5 C5 C 0 1 Y N N -15.157 59.476 33.607 -1.833 3.210 1.908 C5 AD2 16 AD2 N7 N7 N 0 1 Y N N -13.957 58.993 34.105 -1.913 3.746 0.647 N7 AD2 17 AD2 C8 C8 C 0 1 Y N N -13.935 57.743 33.715 -0.847 3.294 0.021 C8 AD2 18 AD2 "C2'" "C2'" C 0 1 N N N -14.174 55.065 32.636 0.970 0.461 -0.212 "C2'" AD2 19 AD2 "C5'" "C5'" C 0 1 N N N -16.420 53.904 34.755 2.240 2.706 -2.896 "C5'" AD2 20 AD2 "C4'" "C4'" C 0 1 N N R -16.286 54.120 33.268 2.219 1.846 -1.646 "C4'" AD2 21 AD2 "O4'" "O4'" O 0 1 N N N -16.459 55.527 32.980 1.879 2.654 -0.508 "O4'" AD2 22 AD2 "C1'" "C1'" C 0 1 N N R -15.291 56.063 32.379 1.171 1.827 0.433 "C1'" AD2 23 AD2 "C3'" "C3'" C 0 1 N N S -14.899 53.739 32.756 1.177 0.741 -1.684 "C3'" AD2 24 AD2 "O3'" "O3'" O 0 1 N N N -14.958 53.056 31.505 1.636 -0.408 -2.366 "O3'" AD2 25 AD2 OP3 O3P O 0 1 N Y N ? ? ? 3.708 3.799 -5.230 OP3 AD2 26 AD2 HOP2 2HOP H 0 0 N N N -13.330 55.277 37.179 1.875 6.082 -4.871 HOP2 AD2 27 AD2 HOP5 5HOP H 0 0 N N N -14.149 50.955 33.083 1.101 -3.648 -3.477 HOP5 AD2 28 AD2 HOP6 6HOP H 0 0 N N N -14.949 51.223 29.594 -1.366 -1.854 -3.248 HOP6 AD2 29 AD2 H2 H2 H 0 1 N N N -18.488 60.016 31.986 -0.929 1.412 5.062 H2 AD2 30 AD2 H61 1H6 H 0 1 N N N -15.877 62.145 34.980 -4.674 3.685 2.637 H61 AD2 31 AD2 H62 2H6 H 0 1 N N N -14.306 61.665 34.747 -3.779 5.065 3.215 H62 AD2 32 AD2 H8 H8 H 0 1 N N N -13.089 57.083 33.971 -0.579 3.514 -1.004 H8 AD2 33 AD2 "H2'1" "1H2'" H 0 0 N N N -13.524 55.315 33.507 -0.002 0.004 0.001 "H2'1" AD2 34 AD2 "H2'2" "2H2'" H 0 0 N N N -13.360 55.078 31.874 1.736 -0.240 0.147 "H2'2" AD2 35 AD2 "H5'1" "1H5'" H 0 0 N N N -17.342 54.378 35.166 1.270 3.186 -3.037 "H5'1" AD2 36 AD2 "H5'2" "2H5'" H 0 0 N N N -16.658 52.844 35.005 2.475 2.094 -3.768 "H5'2" AD2 37 AD2 "H4'" "H4'" H 0 1 N N N -17.055 53.483 32.772 3.224 1.436 -1.487 "H4'" AD2 38 AD2 "H1'" "H1'" H 0 1 N N N -15.384 56.217 31.279 1.753 1.756 1.357 "H1'" AD2 39 AD2 "H3'" "H3'" H 0 1 N N N -14.379 53.028 33.440 0.241 1.086 -2.140 "H3'" AD2 40 AD2 HOP3 3HOP H 0 0 N N N 0.205 0.926 -0.065 3.963 4.205 -6.086 HOP3 AD2 41 # 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 AD2 P1 OP1 DOUB N N 1 AD2 P1 OP2 SING N N 2 AD2 P1 "O5'" SING N N 3 AD2 P1 OP3 SING N N 4 AD2 OP2 HOP2 SING N N 5 AD2 "O5'" "C5'" SING N N 6 AD2 P2 O5P SING N N 7 AD2 P2 O4P DOUB N N 8 AD2 P2 O6P SING N N 9 AD2 P2 "O3'" SING N N 10 AD2 O5P HOP5 SING N N 11 AD2 O6P HOP6 SING N N 12 AD2 N9 C4 SING Y N 13 AD2 N9 C8 SING Y N 14 AD2 N9 "C1'" SING N N 15 AD2 C4 N3 DOUB Y N 16 AD2 C4 C5 SING Y N 17 AD2 N3 C2 SING Y N 18 AD2 C2 N1 DOUB Y N 19 AD2 C2 H2 SING N N 20 AD2 N1 C6 SING Y N 21 AD2 C6 N6 SING N N 22 AD2 C6 C5 DOUB Y N 23 AD2 N6 H61 SING N N 24 AD2 N6 H62 SING N N 25 AD2 C5 N7 SING Y N 26 AD2 N7 C8 DOUB Y N 27 AD2 C8 H8 SING N N 28 AD2 "C2'" "C1'" SING N N 29 AD2 "C2'" "C3'" SING N N 30 AD2 "C2'" "H2'1" SING N N 31 AD2 "C2'" "H2'2" SING N N 32 AD2 "C5'" "C4'" SING N N 33 AD2 "C5'" "H5'1" SING N N 34 AD2 "C5'" "H5'2" SING N N 35 AD2 "C4'" "O4'" SING N N 36 AD2 "C4'" "C3'" SING N N 37 AD2 "C4'" "H4'" SING N N 38 AD2 "O4'" "C1'" SING N N 39 AD2 "C1'" "H1'" SING N N 40 AD2 "C3'" "O3'" SING N N 41 AD2 "C3'" "H3'" SING N N 42 AD2 OP3 HOP3 SING N N 43 # 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 AD2 SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3OP(=O)(O)O" AD2 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O[P](O)(O)=O)[C@@H](CO[P](O)(O)=O)O3" AD2 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O3" AD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)OP(=O)(O)O)N" AD2 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)OP(=O)(O)O)N" AD2 InChI InChI 1.03 "InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(24-26(19,20)21)6(23-7)2-22-25(16,17)18/h3-7H,1-2H2,(H2,11,12,13)(H2,16,17,18)(H2,19,20,21)/t5-,6+,7+/m0/s1" AD2 InChIKey InChI 1.03 GOZKRKUVKAXOEP-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 AD2 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxyadenosine 3',5'-bis(dihydrogen phosphate) ; AD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-phosphonooxy-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 AD2 "Create component" 2002-03-06 RCSB AD2 "Modify descriptor" 2011-06-04 RCSB #