data_WVQ # _chem_comp.id WVQ _chem_comp.name "N-[(5E)-2-amino-5-(formylimino)-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-10-16 _chem_comp.pdbx_modified_date 2024-04-19 _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 363.221 _chem_comp.one_letter_code ? _chem_comp.three_letter_code WVQ _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 8UKQ _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 WVQ C5 C1 C 0 1 N N N N N N 14.808 1.898 49.374 -3.774 -0.155 0.687 C5 WVQ 1 WVQ C4 C2 C 0 1 N N N N N N 16.080 1.459 49.114 -2.549 -0.042 -0.155 C4 WVQ 2 WVQ N2 N1 N 0 1 N N N N N N 15.420 -1.641 47.300 -2.965 -2.809 -2.330 N2 WVQ 3 WVQ N7 N2 N 0 1 N N N N N N 14.456 3.118 50.099 -4.031 0.694 1.650 N7 WVQ 4 WVQ C8 C3 C 0 1 N N N N N N 15.351 4.201 50.477 -3.094 1.586 2.028 C8 WVQ 5 WVQ "C1'" C4 C 0 1 N N R N N N 18.557 1.567 49.278 -0.492 1.101 -0.846 "C1'" WVQ 6 WVQ C2 C5 C 0 1 N N N N N N 15.202 -0.403 48.027 -3.241 -1.925 -1.321 C2 WVQ 7 WVQ "C2'" C6 C 0 1 N N N N N N 19.237 2.219 48.094 -0.093 2.587 -0.978 "C2'" WVQ 8 WVQ "C3'" C7 C 0 1 N N S N N N 20.661 2.336 48.499 1.450 2.557 -1.046 "C3'" WVQ 9 WVQ "C4'" C8 C 0 1 N N R N N N 20.754 2.006 49.948 1.801 1.056 -0.948 "C4'" WVQ 10 WVQ "C5'" C9 C 0 1 N N N N N N 21.377 3.186 50.681 3.073 0.860 -0.120 "C5'" WVQ 11 WVQ C6 C10 C 0 1 N N N N N N 13.758 1.149 48.948 -4.699 -1.288 0.368 C6 WVQ 12 WVQ N1 N3 N 0 1 N N N N N N 13.947 0.022 48.285 -4.354 -2.104 -0.634 N1 WVQ 13 WVQ N3 N4 N 0 1 N N N N N N 16.254 0.328 48.448 -2.369 -0.940 -1.103 N3 WVQ 14 WVQ N9 N5 N 0 1 N N N N N N 17.286 2.165 49.515 -1.642 0.959 0.050 N9 WVQ 15 WVQ "O3'" O1 O 0 1 N N N N N N 21.470 1.420 47.765 1.907 3.098 -2.288 "O3'" WVQ 16 WVQ "O4'" O2 O 0 1 N N N N N N 19.430 1.770 50.405 0.670 0.456 -0.281 "O4'" WVQ 17 WVQ "O5'" O3 O 0 1 N N N N N N 21.981 4.026 49.740 3.445 -0.520 -0.139 "O5'" WVQ 18 WVQ O6 O4 O 0 1 N N N N N N 12.654 1.516 49.170 -5.727 -1.460 0.997 O6 WVQ 19 WVQ O8 O5 O 0 1 N N N N N N 14.925 5.136 51.069 -3.360 2.769 2.055 O8 WVQ 20 WVQ OP1 O6 O 0 1 N N N N N N 24.105 4.919 48.296 5.940 -0.343 0.194 OP1 WVQ 21 WVQ OP2 O7 O 0 1 N N N N N N 23.765 2.244 48.679 4.543 -0.909 2.219 OP2 WVQ 22 WVQ P P1 P 0 1 N N N N N N 23.550 3.749 49.314 4.739 -1.089 0.631 P WVQ 23 WVQ O1 O8 O 0 1 N Y N N N N 24.351 3.824 50.699 4.924 -2.651 0.287 O1 WVQ 24 WVQ H1 H1 H 0 1 N N N N N N 14.639 -2.182 46.988 -3.579 -3.536 -2.520 H1 WVQ 25 WVQ H2 H2 H 0 1 N N N N N N 16.351 -1.952 47.111 -2.156 -2.708 -2.856 H2 WVQ 26 WVQ H3 H3 H 0 1 N N N N N N 16.399 4.154 50.220 -2.107 1.248 2.307 H3 WVQ 27 WVQ H4 H4 H 0 1 N N N N N N 18.442 0.491 49.079 -0.721 0.679 -1.825 H4 WVQ 28 WVQ H5 H5 H 0 1 N N N N N N 18.806 3.212 47.897 -0.508 3.014 -1.891 H5 WVQ 29 WVQ H6 H6 H 0 1 N N N N N N 19.139 1.592 47.196 -0.426 3.151 -0.107 H6 WVQ 30 WVQ H7 H7 H 0 1 N N N N N N 21.006 3.368 48.335 1.880 3.106 -0.209 H7 WVQ 31 WVQ H8 H8 H 0 1 N N N N N N 21.382 1.114 50.089 1.925 0.629 -1.943 H8 WVQ 32 WVQ H9 H9 H 0 1 N N N N N N 22.133 2.823 51.393 3.879 1.459 -0.545 H9 WVQ 33 WVQ H10 H10 H 0 1 N N N N N N 20.597 3.739 51.225 2.890 1.173 0.907 H10 WVQ 34 WVQ H11 H11 H 0 1 N N N N N N 17.224 3.062 49.953 -1.759 1.576 0.789 H11 WVQ 35 WVQ H12 H12 H 0 1 N N N N N N 22.376 1.509 48.037 1.661 4.022 -2.429 H12 WVQ 36 WVQ H13 H13 H 0 1 N N N N N N 24.177 2.316 47.826 3.772 -1.372 2.575 H13 WVQ 37 WVQ H14 H14 H 0 1 N Y N N N N 24.988 4.528 50.659 5.686 -3.062 0.718 H14 WVQ 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 WVQ N2 C2 SING N N 1 WVQ "O3'" "C3'" SING N N 2 WVQ C2 N1 DOUB N N 3 WVQ C2 N3 SING N N 4 WVQ "C2'" "C3'" SING N N 5 WVQ "C2'" "C1'" SING N N 6 WVQ N1 C6 SING N N 7 WVQ OP1 P DOUB N N 8 WVQ N3 C4 DOUB N N 9 WVQ "C3'" "C4'" SING N N 10 WVQ OP2 P SING N N 11 WVQ C6 O6 DOUB N N 12 WVQ C6 C5 SING N N 13 WVQ C4 C5 SING N N 14 WVQ C4 N9 SING N N 15 WVQ "C1'" N9 SING N N 16 WVQ "C1'" "O4'" SING N N 17 WVQ P "O5'" SING N N 18 WVQ C5 N7 DOUB N N 19 WVQ "O5'" "C5'" SING N N 20 WVQ "C4'" "O4'" SING N N 21 WVQ "C4'" "C5'" SING N N 22 WVQ N7 C8 SING N N 23 WVQ C8 O8 DOUB N N 24 WVQ P O1 SING N N 25 WVQ N2 H1 SING N N 26 WVQ N2 H2 SING N N 27 WVQ C8 H3 SING N N 28 WVQ "C1'" H4 SING N N 29 WVQ "C2'" H5 SING N N 30 WVQ "C2'" H6 SING N N 31 WVQ "C3'" H7 SING N N 32 WVQ "C4'" H8 SING N N 33 WVQ "C5'" H9 SING N N 34 WVQ "C5'" H10 SING N N 35 WVQ N9 H11 SING N N 36 WVQ "O3'" H12 SING N N 37 WVQ OP2 H13 SING N N 38 WVQ O1 H14 SING N N 39 # 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 WVQ SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(NC\2=NC(N)=NC(=O)C/2=N\C=O)CC1O" WVQ InChI InChI 1.06 "InChI=1S/C10H14N5O8P/c11-10-14-8(7(12-3-16)9(18)15-10)13-6-1-4(17)5(23-6)2-22-24(19,20)21/h3-6,17H,1-2H2,(H2,19,20,21)(H3,11,13,14,15,18)/b12-7+/t4-,5+,6+/m0/s1" WVQ InChIKey InChI 1.06 ZSDJBOZQMXOVIY-CTYKPTQGSA-N WVQ SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)C(=NC=O)C(=N1)N[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" WVQ SMILES CACTVS 3.385 "NC1=NC(=O)C(=NC=O)C(=N1)N[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" WVQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1NC\2=NC(=NC(=O)/C2=N/C=O)N)COP(=O)(O)O)O" WVQ SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1NC2=NC(=NC(=O)C2=NC=O)N)COP(=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 WVQ "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(5E)-2-amino-5-(formylimino)-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" WVQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[[(5~{E})-2-azanyl-5-methanoylimino-6-oxidanylidene-pyrimidin-4-yl]amino]-3-oxidanyl-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 WVQ "Create component" 2023-10-16 RCSB WVQ "Modify linking type" 2023-10-17 RCSB WVQ "Initial release" 2024-04-24 RCSB #