data_7DD # _chem_comp.id 7DD _chem_comp.name "7-deazaadenosine-5'-diphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N4 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-12-07 _chem_comp.pdbx_modified_date 2016-06-10 _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 426.213 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 7DD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5EX5 _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 7DD O1B O1 O 0 1 N N N 21.597 -0.190 3.474 -6.049 1.962 -1.900 O1B 7DD 1 7DD PB P1 P 0 1 N N N 20.265 -0.369 2.813 -5.541 1.502 -0.443 PB 7DD 2 7DD O2B O2 O 0 1 N N N 19.176 0.242 3.645 -5.089 2.796 0.401 O2B 7DD 3 7DD O3B O3 O 0 1 N N N 20.168 0.072 1.399 -6.640 0.809 0.267 O3B 7DD 4 7DD O3A O4 O 0 1 N N N 20.044 -1.942 2.953 -4.290 0.501 -0.602 O3A 7DD 5 7DD PA P2 P 0 1 N N N 18.906 -2.873 2.362 -3.604 -0.594 0.359 PA 7DD 6 7DD O1A O5 O 0 1 N N N 19.639 -3.985 1.667 -4.462 -1.955 0.320 O1A 7DD 7 7DD O2A O6 O 0 1 N N N 17.946 -2.118 1.541 -3.562 -0.076 1.745 O2A 7DD 8 7DD "O5'" O7 O 0 1 N N N 18.122 -3.440 3.617 -2.105 -0.889 -0.149 "O5'" 7DD 9 7DD "C5'" C1 C 0 1 N N N 18.852 -4.102 4.635 -1.198 -1.739 0.555 "C5'" 7DD 10 7DD "C4'" C2 C 0 1 N N R 17.878 -4.697 5.647 0.133 -1.801 -0.198 "C4'" 7DD 11 7DD "O4'" O8 O 0 1 N N N 17.046 -5.618 4.921 0.818 -0.533 -0.113 "O4'" 7DD 12 7DD "C1'" C3 C 0 1 N N R 16.898 -6.739 5.777 2.204 -0.829 -0.393 "C1'" 7DD 13 7DD N9 N1 N 0 1 Y N N 16.475 -7.931 5.022 3.068 0.233 0.127 N9 7DD 14 7DD C8 C4 C 0 1 Y N N 17.158 -8.510 4.027 2.739 1.085 1.149 C8 7DD 15 7DD C16 C5 C 0 1 Y N N 16.474 -9.596 3.653 3.754 1.933 1.380 C16 7DD 16 7DD C5 C6 C 0 1 Y N N 15.360 -9.700 4.392 4.812 1.594 0.430 C5 7DD 17 7DD C6 C7 C 0 1 Y N N 14.341 -10.601 4.436 6.097 2.086 0.156 C6 7DD 18 7DD N6 N2 N 0 1 N N N 14.314 -11.644 3.592 6.621 3.143 0.879 N6 7DD 19 7DD N1 N3 N 0 1 Y N N 13.360 -10.475 5.331 6.799 1.511 -0.816 N1 7DD 20 7DD C2 C8 C 0 1 Y N N 13.348 -9.399 6.231 6.303 0.502 -1.509 C2 7DD 21 7DD N3 N4 N 0 1 Y N N 14.390 -8.483 6.162 5.103 0.008 -1.286 N3 7DD 22 7DD C4 C9 C 0 1 Y N N 15.378 -8.666 5.260 4.325 0.517 -0.333 C4 7DD 23 7DD "C2'" C10 C 0 1 N N R 18.294 -6.898 6.411 2.480 -2.157 0.346 "C2'" 7DD 24 7DD "O2'" O9 O 0 1 N N N 18.273 -7.677 7.633 3.352 -2.987 -0.425 "O2'" 7DD 25 7DD "C3'" C11 C 0 1 N N S 18.613 -5.468 6.743 1.086 -2.811 0.477 "C3'" 7DD 26 7DD "O3'" O10 O 0 1 N N N 18.117 -5.068 8.040 1.055 -4.065 -0.208 "O3'" 7DD 27 7DD H1 H1 H 0 1 N N N 22.207 0.198 2.858 -6.803 2.567 -1.880 H1 7DD 28 7DD H2 H2 H 0 1 N N N 18.632 0.797 3.098 -4.371 3.300 -0.005 H2 7DD 29 7DD H3 H3 H 0 1 N N N 19.357 -4.033 0.761 -4.532 -2.351 -0.560 H3 7DD 30 7DD H4 H4 H 0 1 N N N 19.457 -4.906 4.190 -1.030 -1.341 1.556 H4 7DD 31 7DD H5 H5 H 0 1 N N N 19.513 -3.383 5.140 -1.621 -2.741 0.628 H5 7DD 32 7DD H6 H6 H 0 1 N N N 17.276 -3.895 6.099 -0.034 -2.075 -1.240 H6 7DD 33 7DD H7 H7 H 0 1 N N N 16.169 -6.524 6.572 2.356 -0.953 -1.465 H7 7DD 34 7DD H8 H8 H 0 1 N N N 18.090 -8.164 3.604 1.803 1.075 1.689 H8 7DD 35 7DD H9 H9 H 0 1 N N N 16.773 -10.284 2.876 3.783 2.715 2.124 H9 7DD 36 7DD H10 H10 H 0 1 N N N 13.506 -12.203 3.778 6.098 3.553 1.585 H10 7DD 37 7DD H11 H11 H 0 1 N N N 14.278 -11.310 2.650 7.511 3.473 0.679 H11 7DD 38 7DD H12 H12 H 0 1 N N N 12.554 -9.286 6.954 6.906 0.063 -2.289 H12 7DD 39 7DD H13 H13 H 0 1 N N N 19.007 -7.303 5.678 2.906 -1.965 1.331 H13 7DD 40 7DD H14 H14 H 0 1 N N N 19.154 -7.744 7.981 3.559 -3.835 -0.007 H14 7DD 41 7DD H15 H15 H 0 1 N N N 19.696 -5.291 6.662 0.823 -2.942 1.527 H15 7DD 42 7DD H16 H16 H 0 1 N N N 18.577 -5.550 8.718 1.636 -4.737 0.174 H16 7DD 43 # 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 7DD O3B PB DOUB N N 1 7DD O2A PA DOUB N N 2 7DD O1A PA SING N N 3 7DD PA O3A SING N N 4 7DD PA "O5'" SING N N 5 7DD PB O3A SING N N 6 7DD PB O1B SING N N 7 7DD PB O2B SING N N 8 7DD N6 C6 SING N N 9 7DD "O5'" "C5'" SING N N 10 7DD C16 C8 DOUB Y N 11 7DD C16 C5 SING Y N 12 7DD C8 N9 SING Y N 13 7DD C5 C6 DOUB Y N 14 7DD C5 C4 SING Y N 15 7DD C6 N1 SING Y N 16 7DD "C5'" "C4'" SING N N 17 7DD "O4'" "C4'" SING N N 18 7DD "O4'" "C1'" SING N N 19 7DD N9 C4 SING Y N 20 7DD N9 "C1'" SING N N 21 7DD C4 N3 DOUB Y N 22 7DD N1 C2 DOUB Y N 23 7DD "C4'" "C3'" SING N N 24 7DD "C1'" "C2'" SING N N 25 7DD N3 C2 SING Y N 26 7DD "C2'" "C3'" SING N N 27 7DD "C2'" "O2'" SING N N 28 7DD "C3'" "O3'" SING N N 29 7DD O1B H1 SING N N 30 7DD O2B H2 SING N N 31 7DD O1A H3 SING N N 32 7DD "C5'" H4 SING N N 33 7DD "C5'" H5 SING N N 34 7DD "C4'" H6 SING N N 35 7DD "C1'" H7 SING N N 36 7DD C8 H8 SING N N 37 7DD C16 H9 SING N N 38 7DD N6 H10 SING N N 39 7DD N6 H11 SING N N 40 7DD C2 H12 SING N N 41 7DD "C2'" H13 SING N N 42 7DD "O2'" H14 SING N N 43 7DD "C3'" H15 SING N N 44 7DD "O3'" H16 SING N N 45 # 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 7DD InChI InChI 1.03 "InChI=1S/C11H16N4O10P2/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(17)7(16)6(24-11)3-23-27(21,22)25-26(18,19)20/h1-2,4,6-8,11,16-17H,3H2,(H,21,22)(H2,12,13,14)(H2,18,19,20)/t6-,7-,8-,11-/m1/s1" 7DD InChIKey InChI 1.03 NCKAOCPROMQFJK-KCGFPETGSA-N 7DD SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(ccc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" 7DD SMILES CACTVS 3.385 "Nc1ncnc2n(ccc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" 7DD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O" 7DD SMILES "OpenEye OEToolkits" 2.0.4 "c1cn(c2c1c(ncn2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O" # 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 7DD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen 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 7DD "Create component" 2015-12-07 RCSB 7DD "Initial release" 2016-06-15 RCSB #