data_A1CWA # _chem_comp.id A1CWA _chem_comp.name "(2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N8 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-09-29 _chem_comp.pdbx_modified_date 2025-10-17 _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 412.298 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CWA _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 9YD4 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1CWA "C2'" C1 C 0 1 N N N N N N -17.304 14.748 -1.313 1.773 2.385 -0.408 "C2'" A1CWA 1 A1CWA "C1'" C2 C 0 1 N N R N N N -17.365 13.875 -0.019 1.597 1.009 0.273 "C1'" A1CWA 2 A1CWA C2 C3 C 0 1 N N N N N N -13.415 15.062 1.008 5.814 -0.118 1.273 C2 A1CWA 3 A1CWA C4 C4 C 0 1 Y N N N N N -15.002 13.572 0.431 3.811 -0.201 0.124 C4 A1CWA 4 A1CWA "C5'" C5 C 0 1 N N N N N N -20.024 12.511 -1.912 -1.867 1.713 -0.620 "C5'" A1CWA 5 A1CWA "O5'" O1 O 0 1 N N N N N N -18.830 11.812 -2.309 -2.706 0.771 0.052 "O5'" A1CWA 6 A1CWA C6 C6 C 0 1 N N N N N N -12.848 12.756 0.744 5.636 -1.663 -0.495 C6 A1CWA 7 A1CWA C11 C7 C 0 1 Y N N N N N -20.558 8.602 -2.584 -5.531 -0.659 1.625 C11 A1CWA 8 A1CWA O6 O2 O 0 1 N N N N N N -11.927 11.910 0.784 6.115 -2.539 -1.195 O6 A1CWA 9 A1CWA N1 N1 N 0 1 N N N N N N -12.531 14.032 1.031 6.359 -1.096 0.496 N1 A1CWA 10 A1CWA N2 N2 N 0 1 N N N N N N -13.001 16.262 1.266 6.572 0.440 2.272 N2 A1CWA 11 A1CWA N3 N3 N 0 1 N N N N N N -14.694 14.860 0.719 4.585 0.310 1.089 N3 A1CWA 12 A1CWA C5 C8 C 0 1 Y N N N N N -14.123 12.545 0.457 4.314 -1.208 -0.707 C5 A1CWA 13 A1CWA N7 N4 N 0 1 Y N N N N N -14.817 11.453 0.132 3.332 -1.535 -1.582 N7 A1CWA 14 A1CWA C8 C9 C 0 1 Y N N N N N -16.049 11.790 -0.074 2.282 -0.805 -1.342 C8 A1CWA 15 A1CWA N9 N5 N 0 1 Y N N N N N -16.180 13.074 0.109 2.530 0.035 -0.296 N9 A1CWA 16 A1CWA "O4'" O3 O 0 1 N N N N N N -18.514 12.969 -0.093 0.234 0.627 -0.014 "O4'" A1CWA 17 A1CWA "C3'" C10 C 0 1 N N S N N N -18.758 14.653 -1.810 0.337 2.945 -0.508 "C3'" A1CWA 18 A1CWA "O3'" O4 O 0 1 N N N N N N -19.402 15.893 -1.566 0.222 4.163 0.230 "O3'" A1CWA 19 A1CWA "C4'" C11 C 0 1 N N R N N N -19.485 13.599 -0.981 -0.539 1.839 0.130 "C4'" A1CWA 20 A1CWA P1 P1 P 0 1 N N N N N N -18.823 10.589 -3.353 -4.183 0.390 -0.462 P1 A1CWA 21 A1CWA O1 O5 O 0 1 N N N N N N -17.406 10.499 -3.750 -4.114 -0.064 -1.868 O1 A1CWA 22 A1CWA O2 O6 O 0 1 N N N N N N -19.764 11.087 -4.373 -5.137 1.684 -0.362 O2 A1CWA 23 A1CWA N10 N6 N 0 1 Y N N N N N -19.380 9.213 -2.412 -4.794 -0.812 0.472 N10 A1CWA 24 A1CWA C12 C12 C 0 1 Y N N N N N -20.641 7.587 -1.719 -5.826 -1.893 2.067 C12 A1CWA 25 A1CWA N13 N7 N 0 1 Y N N N N N -19.517 7.559 -0.997 -5.294 -2.786 1.215 N13 A1CWA 26 A1CWA C14 C13 C 0 1 Y N N N N N -18.755 8.550 -1.438 -4.667 -2.149 0.255 C14 A1CWA 27 A1CWA N14 N8 N 0 1 N N N N N N -17.551 8.819 -0.961 -3.994 -2.737 -0.803 N14 A1CWA 28 A1CWA "H2'" H1 H 0 1 N N N N N N -17.023 15.787 -1.085 2.396 3.037 0.204 "H2'" A1CWA 29 A1CWA "H2''" H2 H 0 0 N N N N N N -16.599 14.331 -2.047 2.207 2.266 -1.401 "H2''" A1CWA 30 A1CWA "H1'" H3 H 0 1 N N N N N N -17.470 14.542 0.849 1.750 1.097 1.349 "H1'" A1CWA 31 A1CWA "H5'" H4 H 0 1 N N N N N N -20.717 11.842 -1.381 -1.679 1.370 -1.638 "H5'" A1CWA 32 A1CWA "H5''" H5 H 0 0 N N N N N N -20.534 12.951 -2.782 -2.361 2.684 -0.649 "H5''" A1CWA 33 A1CWA H11 H6 H 0 1 N N N N N N -21.315 8.882 -3.302 -5.814 0.275 2.088 H11 A1CWA 34 A1CWA H1 H7 H 0 1 N N N N N N -11.583 14.234 1.277 7.271 -1.386 0.655 H1 A1CWA 35 A1CWA HN21 H8 H 0 0 N N N N N N -13.644 17.028 1.246 7.482 0.137 2.417 HN21 A1CWA 36 A1CWA HN22 H9 H 0 0 N N N N N N -12.039 16.423 1.485 6.198 1.137 2.833 HN22 A1CWA 37 A1CWA H8 H10 H 0 1 N N N N N N -16.844 11.114 -0.354 1.352 -0.857 -1.890 H8 A1CWA 38 A1CWA "H3'" H11 H 0 1 N N N N N N -18.777 14.382 -2.876 0.060 3.103 -1.550 "H3'" A1CWA 39 A1CWA "HO3'" H12 H 0 0 N N N N N N -20.301 15.848 -1.868 0.798 4.872 -0.089 "HO3'" A1CWA 40 A1CWA "H4'" H13 H 0 1 N N N N N N -20.308 14.058 -0.414 -0.716 2.055 1.183 "H4'" A1CWA 41 A1CWA H2 H14 H 0 1 N N N N N N -19.290 11.284 -5.172 -5.228 2.037 0.534 H2 A1CWA 42 A1CWA H12 H15 H 0 1 N N N N N N -21.474 6.906 -1.620 -6.393 -2.128 2.956 H12 A1CWA 43 A1CWA H141 H16 H 0 0 N N N N N N -17.326 8.168 -0.237 -3.562 -2.183 -1.471 H141 A1CWA 44 A1CWA H142 H17 H 0 0 N N N N N N -16.877 8.746 -1.696 -3.956 -3.704 -0.876 H142 A1CWA 45 # 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 A1CWA C6 O6 DOUB N N 1 A1CWA C6 N1 SING N N 2 A1CWA C6 C5 SING N N 3 A1CWA C2 N1 SING N N 4 A1CWA C2 N2 SING N N 5 A1CWA C2 N3 DOUB N N 6 A1CWA C4 N3 SING N N 7 A1CWA C4 C5 DOUB Y N 8 A1CWA C4 N9 SING Y N 9 A1CWA C5 N7 SING Y N 10 A1CWA C8 N7 DOUB Y N 11 A1CWA N9 C8 SING Y N 12 A1CWA "C1'" N9 SING N N 13 A1CWA "C1'" "O4'" SING N N 14 A1CWA "C1'" "C2'" SING N N 15 A1CWA "C4'" "O4'" SING N N 16 A1CWA "C3'" "C2'" SING N N 17 A1CWA "C3'" "O3'" SING N N 18 A1CWA "C3'" "C4'" SING N N 19 A1CWA "C4'" "C5'" SING N N 20 A1CWA "C5'" "O5'" SING N N 21 A1CWA P1 "O5'" SING N N 22 A1CWA P1 O1 DOUB N N 23 A1CWA P1 O2 SING N N 24 A1CWA N10 P1 SING N N 25 A1CWA N10 C11 SING Y N 26 A1CWA N10 C14 SING Y N 27 A1CWA C11 C12 DOUB Y N 28 A1CWA C12 N13 SING Y N 29 A1CWA C14 N13 DOUB Y N 30 A1CWA C14 N14 SING N N 31 A1CWA "C2'" "H2'" SING N N 32 A1CWA "C2'" "H2''" SING N N 33 A1CWA "C1'" "H1'" SING N N 34 A1CWA "C5'" "H5'" SING N N 35 A1CWA "C5'" "H5''" SING N N 36 A1CWA C11 H11 SING N N 37 A1CWA N1 H1 SING N N 38 A1CWA N2 HN21 SING N N 39 A1CWA N2 HN22 SING N N 40 A1CWA C8 H8 SING N N 41 A1CWA "C3'" "H3'" SING N N 42 A1CWA "O3'" "HO3'" SING N N 43 A1CWA "C4'" "H4'" SING N N 44 A1CWA O2 H2 SING N N 45 A1CWA C12 H12 SING N N 46 A1CWA N14 H141 SING N N 47 A1CWA N14 H142 SING N N 48 # 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 A1CWA SMILES ACDLabs 14.52 "Nc1nccn1P(=O)(O)OCC1OC(CC1O)n1cnc2c1N=C(N)NC2=O" A1CWA InChI InChI 1.06 "InChI=1S/C13H17N8O6P/c14-12-18-10-9(11(23)19-12)17-5-20(10)8-3-6(22)7(27-8)4-26-28(24,25)21-2-1-16-13(21)15/h1-2,5-8,22H,3-4H2,(H2,15,16)(H,24,25)(H3,14,18,19,23)/t6-,7+,8+/m0/s1" A1CWA InChIKey InChI 1.06 UDDIXTSYRLRNQW-XLPZGREQSA-N A1CWA SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)n4ccnc4N)O3" A1CWA SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)n4ccnc4N)O3" A1CWA SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1cn(c(n1)N)P(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)n3cnc4c3N=C(NC4=O)N)O" A1CWA SMILES "OpenEye OEToolkits" 3.1.0.0 "c1cn(c(n1)N)P(=O)(O)OCC2C(CC(O2)n3cnc4c3N=C(NC4=O)N)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 A1CWA "SYSTEMATIC NAME" ACDLabs 14.52 "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine" A1CWA "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1CWA _pdbx_chem_comp_synonyms.name "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type "systematic name from ACDLabs" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1CWA "Create component" 2025-09-29 RCSB A1CWA "Initial release" 2025-10-22 RCSB #