data_ND7 # _chem_comp.id ND7 _chem_comp.name "5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N6 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-05-10 _chem_comp.pdbx_modified_date 2019-05-17 _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 346.236 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ND7 _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 6OM4 _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 ND7 O1A O1 O 0 1 N N N -15.742 -5.500 -14.762 -5.162 2.116 -1.302 O1A ND7 1 ND7 PA P1 P 0 1 N N N -15.046 -5.189 -16.056 -4.866 1.015 -0.165 PA ND7 2 ND7 O2A O2 O 0 1 N N N -15.561 -5.865 -17.319 -4.789 1.679 1.156 O2A ND7 3 ND7 N3A N1 N 0 1 N N N -15.203 -3.505 -16.211 -6.104 -0.124 -0.150 N3A ND7 4 ND7 "O5'" O3 O 0 1 N N N -13.491 -5.498 -16.022 -3.467 0.283 -0.479 "O5'" ND7 5 ND7 "C5'" C1 C 0 1 N N N -12.751 -4.927 -14.900 -2.822 -0.594 0.447 "C5'" ND7 6 ND7 "C4'" C2 C 0 1 N N R -11.496 -5.824 -14.747 -1.520 -1.114 -0.165 "C4'" ND7 7 ND7 "C3'" C3 C 0 1 N N S -11.932 -7.186 -14.108 -0.868 -2.161 0.766 "C3'" ND7 8 ND7 "O3'" O4 O 0 1 N N N -11.440 -8.273 -14.791 -1.180 -3.484 0.328 "O3'" ND7 9 ND7 "C2'" C4 C 0 1 N N R -11.457 -6.982 -12.607 0.647 -1.889 0.633 "C2'" ND7 10 ND7 "O2'" O5 O 0 1 N N N -10.993 -8.267 -12.037 1.317 -3.037 0.109 "O2'" ND7 11 ND7 "C1'" C5 C 0 1 N N R -10.410 -6.149 -12.679 0.731 -0.711 -0.362 "C1'" ND7 12 ND7 "O4'" O6 O 0 1 N N N -10.693 -5.188 -13.953 -0.549 -0.050 -0.261 "O4'" ND7 13 ND7 N9 N2 N 0 1 Y N N -10.208 -5.247 -11.581 1.809 0.204 0.021 N9 ND7 14 ND7 C4 C6 C 0 1 Y N N -9.038 -5.055 -10.911 3.134 0.084 -0.315 C4 ND7 15 ND7 C5 C7 C 0 1 Y N N -9.261 -4.114 -9.970 3.784 1.183 0.271 C5 ND7 16 ND7 N7 N3 N 0 1 Y N N -10.551 -3.716 -10.063 2.840 1.904 0.922 N7 ND7 17 ND7 C8 C8 C 0 1 Y N N -11.100 -4.398 -11.049 1.679 1.334 0.771 C8 ND7 18 ND7 N3 N4 N 0 1 Y N N -7.826 -5.632 -11.051 3.848 -0.789 -1.020 N3 ND7 19 ND7 C2 C9 C 0 1 Y N N -6.855 -5.259 -10.273 5.146 -0.628 -1.168 C2 ND7 20 ND7 N1 N5 N 0 1 Y N N -7.050 -4.342 -9.319 5.800 0.389 -0.637 N1 ND7 21 ND7 C6 C10 C 0 1 Y N N -8.207 -3.758 -9.155 5.171 1.311 0.083 C6 ND7 22 ND7 N6 N6 N 0 1 N N N -8.392 -2.766 -8.111 5.865 2.374 0.636 N6 ND7 23 ND7 H1 H1 H 0 1 N N N -16.450 -6.113 -14.922 -5.991 2.598 -1.176 H1 ND7 24 ND7 H2 H2 H 0 1 N N N -14.865 -3.060 -15.382 -6.177 -0.591 -1.041 H2 ND7 25 ND7 H3 H3 H 0 1 N N N -14.671 -3.192 -16.998 -5.975 -0.789 0.598 H3 ND7 26 ND7 H4 H4 H 0 1 N N N -12.460 -3.889 -15.118 -2.600 -0.052 1.366 H4 ND7 27 ND7 H5 H5 H 0 1 N N N -13.358 -4.953 -13.983 -3.480 -1.434 0.671 H5 ND7 28 ND7 H6 H6 H 0 1 N N N -11.063 -6.015 -15.740 -1.710 -1.547 -1.148 H6 ND7 29 ND7 H7 H7 H 0 1 N N N -13.032 -7.211 -14.102 -1.195 -2.011 1.795 H7 ND7 30 ND7 H8 H8 H 0 1 N N N -11.730 -9.072 -14.367 -0.796 -4.181 0.877 H8 ND7 31 ND7 H9 H9 H 0 1 N N N -12.290 -6.574 -12.016 1.070 -1.608 1.598 H9 ND7 32 ND7 H10 H10 H 0 1 N N N -10.712 -8.133 -11.140 1.244 -3.824 0.667 H10 ND7 33 ND7 H11 H11 H 0 1 N N N -9.479 -6.698 -12.883 0.891 -1.081 -1.375 H11 ND7 34 ND7 H12 H12 H 0 1 N N N -12.122 -4.289 -11.381 0.751 1.702 1.183 H12 ND7 35 ND7 H13 H13 H 0 1 N N N -5.875 -5.696 -10.398 5.697 -1.355 -1.747 H13 ND7 36 ND7 H14 H14 H 0 1 N N N -7.536 -2.647 -7.608 5.394 3.040 1.160 H14 ND7 37 ND7 H15 H15 H 0 1 N N N -8.660 -1.895 -8.523 6.822 2.451 0.499 H15 ND7 38 # # 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 ND7 O2A PA DOUB N N 1 ND7 N3A PA SING N N 2 ND7 PA "O5'" SING N N 3 ND7 PA O1A SING N N 4 ND7 "O5'" "C5'" SING N N 5 ND7 "C5'" "C4'" SING N N 6 ND7 "O3'" "C3'" SING N N 7 ND7 "C4'" "C3'" SING N N 8 ND7 "C4'" "O4'" SING N N 9 ND7 "C3'" "C2'" SING N N 10 ND7 "O4'" "C1'" SING N N 11 ND7 "C1'" "C2'" SING N N 12 ND7 "C1'" N9 SING N N 13 ND7 "C2'" "O2'" SING N N 14 ND7 N9 C8 SING Y N 15 ND7 N9 C4 SING Y N 16 ND7 N3 C4 DOUB Y N 17 ND7 N3 C2 SING Y N 18 ND7 C8 N7 DOUB Y N 19 ND7 C4 C5 SING Y N 20 ND7 C2 N1 DOUB Y N 21 ND7 N7 C5 SING Y N 22 ND7 C5 C6 DOUB Y N 23 ND7 N1 C6 SING Y N 24 ND7 C6 N6 SING N N 25 ND7 O1A H1 SING N N 26 ND7 N3A H2 SING N N 27 ND7 N3A H3 SING N N 28 ND7 "C5'" H4 SING N N 29 ND7 "C5'" H5 SING N N 30 ND7 "C4'" H6 SING N N 31 ND7 "C3'" H7 SING N N 32 ND7 "O3'" H8 SING N N 33 ND7 "C2'" H9 SING N N 34 ND7 "O2'" H10 SING N N 35 ND7 "C1'" H11 SING N N 36 ND7 C8 H12 SING N N 37 ND7 C2 H13 SING N N 38 ND7 N6 H14 SING N N 39 ND7 N6 H15 SING N N 40 # # 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 ND7 SMILES ACDLabs 12.01 "OP(OCC3C(C(O)C(n1cnc2c1ncnc2N)O3)O)(=O)N" ND7 InChI InChI 1.03 "InChI=1S/C10H15N6O6P/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(22-10)1-21-23(12,19)20/h2-4,6-7,10,17-18H,1H2,(H2,11,13,14)(H3,12,19,20)/t4-,6-,7-,10-/m1/s1" ND7 InChIKey InChI 1.03 LDEMREUBLBGZBO-KQYNXXCUSA-N ND7 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](N)(O)=O)[C@@H](O)[C@H]3O" ND7 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](N)(O)=O)[CH](O)[CH]3O" ND7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N)O)O)O)N" ND7 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N)O)O)O)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 ND7 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine" ND7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphonamidic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ND7 "Create component" 2019-05-10 RCSB ND7 "Initial release" 2019-05-22 RCSB ##