data_9ZD # _chem_comp.id 9ZD _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[(2~{R})-1-methoxy-1-oxidanylidene-propan-2-yl]phosphonamidic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-06-28 _chem_comp.pdbx_modified_date 2017-10-13 _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 432.326 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9ZD _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 5WA9 _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 9ZD O3P O1 O 0 1 N N N -30.455 3.901 -22.546 3.409 -3.045 -0.993 O3P 9ZD 1 9ZD P P1 P 0 1 N N N -31.200 4.015 -23.840 3.194 -2.040 0.246 P 9ZD 2 9ZD O2P O2 O 0 1 N N N -32.046 2.849 -24.267 2.894 -2.819 1.468 O2P 9ZD 3 9ZD "O5'" O3 O 0 1 N N N -30.093 4.363 -24.933 1.966 -1.049 -0.074 "O5'" 9ZD 4 9ZD "C5'" C1 C 0 1 N N N -30.289 4.085 -26.308 1.392 -0.180 0.905 "C5'" 9ZD 5 9ZD "C4'" C2 C 0 1 N N R -29.309 4.971 -27.054 0.251 0.619 0.271 "C4'" 9ZD 6 9ZD "C3'" C3 C 0 1 N N S -29.701 6.458 -27.087 -0.329 1.627 1.288 "C3'" 9ZD 7 9ZD "O3'" O4 O 0 1 N N N -28.732 7.276 -26.405 0.220 2.929 1.070 "O3'" 9ZD 8 9ZD "C2'" C4 C 0 1 N N R -29.780 6.766 -28.582 -1.846 1.624 0.996 "C2'" 9ZD 9 9ZD "O2'" O5 O 0 1 N N N -29.325 8.076 -28.962 -2.281 2.924 0.593 "O2'" 9ZD 10 9ZD "C1'" C5 C 0 1 N N R -28.923 5.664 -29.184 -2.003 0.614 -0.162 "C1'" 9ZD 11 9ZD "O4'" O6 O 0 1 N N N -29.247 4.522 -28.405 -0.852 -0.253 -0.057 "O4'" 9ZD 12 9ZD N9 N1 N 0 1 Y N N -29.229 5.348 -30.587 -3.239 -0.156 -0.002 N9 9ZD 13 9ZD C4 C6 C 0 1 Y N N -28.295 5.158 -31.503 -4.491 0.221 -0.418 C4 9ZD 14 9ZD C5 C7 C 0 1 Y N N -29.019 4.847 -32.730 -5.353 -0.826 -0.053 C5 9ZD 15 9ZD N7 N2 N 0 1 Y N N -30.324 4.891 -32.443 -4.597 -1.772 0.555 N7 9ZD 16 9ZD C8 C8 C 0 1 Y N N -30.445 5.173 -31.128 -3.355 -1.383 0.582 C8 9ZD 17 9ZD N3 N3 N 0 1 Y N N -26.948 5.218 -31.490 -4.993 1.285 -1.038 N3 9ZD 18 9ZD C2 C9 C 0 1 Y N N -26.287 4.965 -32.632 -6.279 1.359 -1.308 C2 9ZD 19 9ZD N1 N4 N 0 1 Y N N -26.884 4.669 -33.803 -7.127 0.400 -0.985 N1 9ZD 20 9ZD C6 C10 C 0 1 Y N N -28.220 4.603 -33.933 -6.719 -0.699 -0.359 C6 9ZD 21 9ZD N6 N5 N 0 1 N N N -28.816 4.322 -35.118 -7.615 -1.698 -0.025 N6 9ZD 22 9ZD N2 N6 N 0 1 N N N -32.240 5.393 -23.843 4.595 -1.138 0.486 N2 9ZD 23 9ZD C3 C11 C 0 1 N N R -31.597 6.691 -23.716 4.924 -0.349 -0.709 C3 9ZD 24 9ZD C7 C12 C 0 1 N N N -32.241 7.687 -24.607 5.527 0.967 -0.292 C7 9ZD 25 9ZD C9 C13 C 0 1 N N N -31.675 7.199 -22.281 5.929 -1.121 -1.568 C9 9ZD 26 9ZD O10 O7 O 0 1 N N N -31.631 8.678 -24.971 5.668 1.223 0.881 O10 9ZD 27 9ZD O11 O8 O 0 1 N N N -33.615 7.497 -24.986 5.908 1.856 -1.222 O11 9ZD 28 9ZD C12 C14 C 0 1 N N N -34.622 8.337 -24.424 6.480 3.103 -0.748 C12 9ZD 29 9ZD H1 H1 H 0 1 N N N -30.632 3.055 -22.151 3.610 -2.602 -1.829 H1 9ZD 30 9ZD H2 H2 H 0 1 N N N -31.322 4.323 -26.603 1.004 -0.773 1.734 H2 9ZD 31 9ZD H3 H3 H 0 1 N N N -30.083 3.025 -26.517 2.154 0.505 1.275 H3 9ZD 32 9ZD H4 H4 H 0 1 N N N -28.320 4.881 -26.581 0.603 1.138 -0.620 H4 9ZD 33 9ZD H5 H5 H 0 1 N N N -30.697 6.580 -26.636 -0.133 1.297 2.308 H5 9ZD 34 9ZD H6 H6 H 0 1 N N N -28.719 7.049 -25.483 -0.110 3.602 1.681 H6 9ZD 35 9ZD H7 H7 H 0 1 N N N -30.819 6.623 -28.913 -2.402 1.291 1.872 H7 9ZD 36 9ZD H8 H8 H 0 1 N N N -29.885 8.733 -28.566 -2.149 3.608 1.263 H8 9ZD 37 9ZD H9 H9 H 0 1 N N N -27.860 5.925 -29.076 -2.000 1.132 -1.121 H9 9ZD 38 9ZD H10 H10 H 0 1 N N N -31.380 5.247 -30.592 -2.539 -1.946 1.009 H10 9ZD 39 9ZD H11 H11 H 0 1 N N N -25.208 5.001 -32.610 -6.654 2.237 -1.813 H11 9ZD 40 9ZD H12 H12 H 0 1 N N N -28.116 4.185 -35.819 -8.555 -1.601 -0.247 H12 9ZD 41 9ZD H13 H13 H 0 1 N N N -29.364 3.490 -35.027 -7.305 -2.496 0.432 H13 9ZD 42 9ZD H14 H14 H 0 1 N N N -32.748 5.388 -24.704 4.508 -0.545 1.298 H14 9ZD 43 9ZD H15 H15 H 0 1 N N N -30.537 6.599 -23.993 4.017 -0.167 -1.286 H15 9ZD 44 9ZD H16 H16 H 0 1 N N N -31.201 6.470 -21.607 6.835 -1.303 -0.991 H16 9ZD 45 9ZD H17 H17 H 0 1 N N N -31.151 8.163 -22.205 5.493 -2.073 -1.870 H17 9ZD 46 9ZD H18 H18 H 0 1 N N N -32.729 7.330 -21.995 6.173 -0.536 -2.454 H18 9ZD 47 9ZD H19 H19 H 0 1 N N N -35.605 8.050 -24.825 5.752 3.624 -0.126 H19 9ZD 48 9ZD H20 H20 H 0 1 N N N -34.625 8.224 -23.330 7.374 2.892 -0.161 H20 9ZD 49 9ZD H21 H21 H 0 1 N N N -34.412 9.385 -24.684 6.744 3.730 -1.600 H21 9ZD 50 # 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 9ZD N6 C6 SING N N 1 9ZD C6 N1 DOUB Y N 2 9ZD C6 C5 SING Y N 3 9ZD N1 C2 SING Y N 4 9ZD C5 N7 SING Y N 5 9ZD C5 C4 DOUB Y N 6 9ZD C2 N3 DOUB Y N 7 9ZD N7 C8 DOUB Y N 8 9ZD C4 N3 SING Y N 9 9ZD C4 N9 SING Y N 10 9ZD C8 N9 SING Y N 11 9ZD N9 "C1'" SING N N 12 9ZD "C1'" "C2'" SING N N 13 9ZD "C1'" "O4'" SING N N 14 9ZD "O2'" "C2'" SING N N 15 9ZD "C2'" "C3'" SING N N 16 9ZD "O4'" "C4'" SING N N 17 9ZD "C3'" "C4'" SING N N 18 9ZD "C3'" "O3'" SING N N 19 9ZD "C4'" "C5'" SING N N 20 9ZD "C5'" "O5'" SING N N 21 9ZD O11 C7 SING N N 22 9ZD O11 C12 SING N N 23 9ZD O10 C7 DOUB N N 24 9ZD "O5'" P SING N N 25 9ZD C7 C3 SING N N 26 9ZD O2P P DOUB N N 27 9ZD N2 P SING N N 28 9ZD N2 C3 SING N N 29 9ZD P O3P SING N N 30 9ZD C3 C9 SING N N 31 9ZD O3P H1 SING N N 32 9ZD "C5'" H2 SING N N 33 9ZD "C5'" H3 SING N N 34 9ZD "C4'" H4 SING N N 35 9ZD "C3'" H5 SING N N 36 9ZD "O3'" H6 SING N N 37 9ZD "C2'" H7 SING N N 38 9ZD "O2'" H8 SING N N 39 9ZD "C1'" H9 SING N N 40 9ZD C8 H10 SING N N 41 9ZD C2 H11 SING N N 42 9ZD N6 H12 SING N N 43 9ZD N6 H13 SING N N 44 9ZD N2 H14 SING N N 45 9ZD C3 H15 SING N N 46 9ZD C9 H16 SING N N 47 9ZD C9 H17 SING N N 48 9ZD C9 H18 SING N N 49 9ZD C12 H19 SING N N 50 9ZD C12 H20 SING N N 51 9ZD C12 H21 SING N N 52 # 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 9ZD SMILES ACDLabs 12.01 "OP(=O)(OCC1C(O)C(O)C(O1)n3c2ncnc(c2nc3)N)NC(C)C(=O)OC" 9ZD InChI InChI 1.03 "InChI=1S/C14H21N6O8P/c1-6(14(23)26-2)19-29(24,25)27-3-7-9(21)10(22)13(28-7)20-5-18-8-11(15)16-4-17-12(8)20/h4-7,9-10,13,21-22H,3H2,1-2H3,(H2,15,16,17)(H2,19,24,25)/t6-,7-,9-,10-,13-/m1/s1" 9ZD InChIKey InChI 1.03 KHSIAISBDZSYJB-KWGHVAAJSA-N 9ZD SMILES_CANONICAL CACTVS 3.385 "COC(=O)[C@@H](C)N[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 9ZD SMILES CACTVS 3.385 "COC(=O)[CH](C)N[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 9ZD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@H](C(=O)OC)NP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 9ZD SMILES "OpenEye OEToolkits" 2.0.6 "CC(C(=O)OC)NP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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 9ZD "SYSTEMATIC NAME" ACDLabs 12.01 "methyl (2R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}propanoate (non-preferred name)" 9ZD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[(2~{R})-1-methoxy-1-oxidanylidene-propan-2-yl]phosphonamidic 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 9ZD "Create component" 2017-06-28 RCSB 9ZD "Initial release" 2017-10-18 RCSB #