data_DZ # _chem_comp.id DZ _chem_comp.name "[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-11-12 _chem_comp.pdbx_modified_date 2019-06-07 _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 351.207 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DZ _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 6I4O _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 DZ P P1 P 0 1 N N N N N N 40.099 20.048 20.447 4.648 1.157 0.341 P DZ 1 DZ OP1 O1 O 0 1 N N N N N N 39.989 18.607 20.107 5.985 0.282 0.147 OP1 DZ 2 DZ OP2 O2 O 0 1 N N N N N N 40.745 20.966 19.475 4.387 1.938 -0.888 OP2 DZ 3 DZ "O5'" O3 O 0 1 N N N N N N 38.633 20.600 20.757 3.403 0.177 0.628 "O5'" DZ 4 DZ "C5'" C1 C 0 1 N N N N N N 37.821 19.926 21.706 2.913 -0.761 -0.332 "C5'" DZ 5 DZ "C4'" C2 C 0 1 N N R N N N 36.659 20.801 22.193 1.730 -1.528 0.261 "C4'" DZ 6 DZ "O4'" O4 O 0 1 N N N N N N 37.127 22.046 22.698 0.623 -0.635 0.468 "O4'" DZ 7 DZ "C1'" C3 C 0 1 N N R N N N 36.092 22.990 22.525 -0.582 -1.394 0.229 "C1'" DZ 8 DZ C1 C4 C 0 1 N N N N N N 36.708 24.374 22.541 -1.732 -0.475 -0.093 C1 DZ 9 DZ C2 C5 C 0 1 N N N N N N 36.155 25.385 23.355 -1.615 0.469 -1.119 C2 DZ 10 DZ O2 O5 O 0 1 N N N N N N 35.152 25.238 24.053 -0.575 0.548 -1.755 O2 DZ 11 DZ N3 N1 N 0 1 N N N N N N 36.781 26.576 23.348 -2.641 1.290 -1.408 N3 DZ 12 DZ C4 C6 C 0 1 N N N N N N 37.863 26.856 22.642 -3.809 1.219 -0.710 C4 DZ 13 DZ C5 C7 C 0 1 N N N N N N 38.465 25.906 21.797 -3.960 0.301 0.308 C5 DZ 14 DZ C6 C8 C 0 1 N N N N N N 37.842 24.640 21.752 -2.911 -0.563 0.618 C6 DZ 15 DZ N N2 N 1 1 N N N N N N 39.677 26.164 20.973 -5.231 0.228 1.062 N DZ 16 DZ ON1 O6 O -1 1 N N N N N N 39.905 25.398 20.045 -5.324 -0.507 2.029 ON1 DZ 17 DZ ON2 O7 O 0 1 N N N N N N 40.441 27.074 21.284 -6.183 0.905 0.717 ON2 DZ 18 DZ N4 N3 N 0 1 N N N N N N 38.338 28.081 22.783 -4.845 2.068 -1.023 N4 DZ 19 DZ "C2'" C9 C 0 1 N N N N N N 35.425 22.600 21.211 -0.221 -2.267 -1.000 "C2'" DZ 20 DZ "C3'" C10 C 0 1 N N S N N N 35.608 21.085 21.107 1.262 -2.616 -0.725 "C3'" DZ 21 DZ "O3'" O8 O 0 1 N N N N N N 34.424 20.343 21.390 1.369 -3.911 -0.130 "O3'" DZ 22 DZ OP3 O9 O 0 1 N Y N N N N 40.835 20.174 21.881 4.838 2.161 1.585 OP3 DZ 23 DZ H1 H1 H 0 1 N N N N N N 40.374 18.453 19.252 6.218 -0.257 0.916 H1 DZ 24 DZ "H5''" H2 H 0 0 N N N N N N 37.411 19.018 21.241 2.590 -0.230 -1.227 "H5''" DZ 25 DZ "H5'" H3 H 0 1 N N N N N N 38.442 19.647 22.570 3.706 -1.462 -0.593 "H5'" DZ 26 DZ "H4'" H4 H 0 1 N N N N N N 36.154 20.256 23.004 2.020 -1.984 1.208 "H4'" DZ 27 DZ "H1'" H5 H 0 1 N N N N N N 35.356 22.912 23.339 -0.820 -2.018 1.090 "H1'" DZ 28 DZ H3 H6 H 0 1 N N N N N N 36.400 27.303 23.919 -2.549 1.941 -2.121 H3 DZ 29 DZ H6 H7 H 0 1 N N N N N N 38.239 23.870 21.107 -3.016 -1.287 1.413 H6 DZ 30 DZ H42 H8 H 0 1 N N N N N N 37.765 28.589 23.426 -4.716 2.768 -1.681 H42 DZ 31 DZ H41 H9 H 0 1 N N N N N N 39.274 28.037 23.134 -5.704 1.967 -0.584 H41 DZ 32 DZ "H2''" H10 H 0 0 N N N N N N 35.912 23.107 20.365 -0.833 -3.168 -1.030 "H2''" DZ 33 DZ "H2'" H11 H 0 1 N N N N N N 34.356 22.860 21.228 -0.322 -1.699 -1.924 "H2'" DZ 34 DZ "H3'" H12 H 0 1 N N N N N N 36.016 20.826 20.119 1.842 -2.572 -1.647 "H3'" DZ 35 DZ H2 H13 H 0 1 N N N N N N 34.605 19.414 21.308 1.034 -4.628 -0.685 H2 DZ 36 DZ H4 H14 H 0 1 N N N N N N 41.537 20.811 21.822 5.572 2.782 1.481 H4 DZ 37 # 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 DZ OP2 P DOUB N N 1 DZ ON1 N SING N N 2 DZ OP1 P SING N N 3 DZ P "O5'" SING N N 4 DZ "O5'" "C5'" SING N N 5 DZ N ON2 DOUB N N 6 DZ N C5 SING N N 7 DZ "C3'" "C2'" SING N N 8 DZ "C3'" "O3'" SING N N 9 DZ "C3'" "C4'" SING N N 10 DZ "C2'" "C1'" SING N N 11 DZ "C5'" "C4'" SING N N 12 DZ C6 C5 SING N N 13 DZ C6 C1 DOUB N N 14 DZ C5 C4 DOUB N N 15 DZ "C4'" "O4'" SING N N 16 DZ "C1'" C1 SING N N 17 DZ "C1'" "O4'" SING N N 18 DZ C1 C2 SING N N 19 DZ C4 N4 SING N N 20 DZ C4 N3 SING N N 21 DZ N3 C2 SING N N 22 DZ C2 O2 DOUB N N 23 DZ P OP3 SING N N 24 DZ OP1 H1 SING N N 25 DZ "C5'" "H5''" SING N N 26 DZ "C5'" "H5'" SING N N 27 DZ "C4'" "H4'" SING N N 28 DZ "C1'" "H1'" SING N N 29 DZ N3 H3 SING N N 30 DZ C6 H6 SING N N 31 DZ N4 H42 SING N N 32 DZ N4 H41 SING N N 33 DZ "C2'" "H2''" SING N N 34 DZ "C2'" "H2'" SING N N 35 DZ "C3'" "H3'" SING N N 36 DZ "O3'" H2 SING N N 37 DZ OP3 H4 SING N N 38 # 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 DZ InChI InChI 1.03 InChI=1S/C10H14N3O9P/c11-9-5(13(16)17)1-4(10(15)12-9)7-2-6(14)8(22-7)3-21-23(18,19)20/h1,6-8,14H,2-3H2,(H3,11,12,15)(H2,18,19,20)/t6-,7+,8+/m0/s1 DZ InChIKey InChI 1.03 IUUXEDXPTYNSEU-XLPZGREQSA-N DZ SMILES_CANONICAL CACTVS 3.385 NC1=C(C=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N1)[N+]([O-])=O DZ SMILES CACTVS 3.385 NC1=C(C=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1)[N+]([O-])=O DZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1[C@@H]([C@H](O[C@H]1C2=CC(=C(NC2=O)N)[N+](=O)[O-])COP(=O)(O)O)O DZ SMILES "OpenEye OEToolkits" 2.0.6 C1C(C(OC1C2=CC(=C(NC2=O)N)[N+](=O)[O-])COP(=O)(O)O)O # _pdbx_chem_comp_identifier.comp_id DZ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-yl)-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 DZ 'Create component' 2018-11-12 EBI DZ 'Initial release' 2019-06-12 RCSB # loop_ _software.name _software.version _software.description rdkit 2025.03.3 'Core functionality.' pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal DZ P P 11.458 3.783 1 DZ OP1 O 10.088 4.393 2 DZ OP2 O 12.068 5.153 3 DZ "O5'" O 10.848 2.412 4 DZ "C5'" C 11.729 1.199 5 DZ "C4'" C 11.119 -0.172 6 DZ "O4'" O 9.652 -0.483 7 DZ "C1'" C 9.495 -1.975 8 DZ C1 C 8.196 -2.725 9 DZ C2 C 8.196 -4.225 10 DZ O2 O 9.495 -4.975 11 DZ N3 N 6.897 -4.975 12 DZ C4 C 5.598 -4.225 13 DZ C5 C 5.598 -2.725 14 DZ C6 C 6.897 -1.975 15 DZ N N 4.299 -1.975 16 DZ ON1 O 4.299 -0.475 17 DZ ON2 O 3.000 -2.725 18 DZ N4 N 4.299 -4.975 19 DZ "C2'" C 10.866 -2.585 20 DZ "C3'" C 11.869 -1.471 21 DZ "O3'" O 13.361 -1.627 22 DZ OP3 O 12.828 3.172 23 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal DZ OP2 P DOUBLE NONE 1 DZ ON1 N SINGLE NONE 2 DZ OP1 P SINGLE NONE 3 DZ P "O5'" SINGLE NONE 4 DZ "O5'" "C5'" SINGLE NONE 5 DZ N ON2 DOUBLE NONE 6 DZ N C5 SINGLE NONE 7 DZ "C3'" "C2'" SINGLE NONE 8 DZ "C3'" "O3'" SINGLE BEGINWEDGE 9 DZ "C3'" "C4'" SINGLE NONE 10 DZ "C2'" "C1'" SINGLE NONE 11 DZ "C4'" "C5'" SINGLE BEGINDASH 12 DZ C6 C5 SINGLE NONE 13 DZ C6 C1 DOUBLE NONE 14 DZ C5 C4 DOUBLE NONE 15 DZ "C4'" "O4'" SINGLE NONE 16 DZ "C1'" C1 SINGLE BEGINDASH 17 DZ "C1'" "O4'" SINGLE NONE 18 DZ C1 C2 SINGLE NONE 19 DZ C4 N4 SINGLE NONE 20 DZ C4 N3 SINGLE NONE 21 DZ N3 C2 SINGLE NONE 22 DZ C2 O2 DOUBLE NONE 23 DZ P OP3 SINGLE NONE 24 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys DZ MurckoScaffold S1 scaffold 'O=c1[nH]cccc1[C@H]1CCCO1' InChI=1S/C9H11NO2/c11-9-7(3-1-5-10-9)8-4-2-6-12-8/h1,3,5,8H,2,4,6H2,(H,10,11)/t8-/m1/s1 UOAHMBKAEFQQDN-MRVPVSSYSA-N DZ deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N DZ phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N DZ pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal DZ "C4'" S1 1 DZ "O4'" S1 1 DZ "C1'" S1 1 DZ C1 S1 1 DZ C2 S1 1 DZ O2 S1 1 DZ N3 S1 1 DZ C4 S1 1 DZ C5 S1 1 DZ C6 S1 1 DZ "C2'" S1 1 DZ "C3'" S1 1 DZ "C1'" F1 1 DZ "C2'" F1 1 DZ "C3'" F1 1 DZ "O3'" F1 1 DZ "C4'" F1 1 DZ "O4'" F1 1 DZ "C5'" F1 1 DZ "O5'" F1 1 DZ OP1 F2 1 DZ P F2 1 DZ OP2 F2 1 DZ "O5'" F2 1 DZ OP3 F2 1 DZ C2 F3 1 DZ C1 F3 1 DZ C6 F3 1 DZ C5 F3 1 DZ C4 F3 1 DZ N3 F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id DZ _pdbe_chem_comp_rdkit_properties.exactmw 351.047 _pdbe_chem_comp_rdkit_properties.amw 351.208 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 12 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 6 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 10 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23 _pdbe_chem_comp_rdkit_properties.NumAtoms 37 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 147.887 _pdbe_chem_comp_rdkit_properties.tpsa 198.240 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.751 _pdbe_chem_comp_rdkit_properties.CrippenMR 72.557 _pdbe_chem_comp_rdkit_properties.chi0v 11.358 _pdbe_chem_comp_rdkit_properties.chi1v 6.721 _pdbe_chem_comp_rdkit_properties.chi2v 2.489 _pdbe_chem_comp_rdkit_properties.chi3v 2.489 _pdbe_chem_comp_rdkit_properties.chi4v 1.521 _pdbe_chem_comp_rdkit_properties.chi0n 24.463 _pdbe_chem_comp_rdkit_properties.chi1n 11.827 _pdbe_chem_comp_rdkit_properties.chi2n 2.174 _pdbe_chem_comp_rdkit_properties.chi3n 2.174 _pdbe_chem_comp_rdkit_properties.chi4n 1.326 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.820 _pdbe_chem_comp_rdkit_properties.kappa1 6.589 _pdbe_chem_comp_rdkit_properties.kappa2 6.354 _pdbe_chem_comp_rdkit_properties.kappa3 4.131 _pdbe_chem_comp_rdkit_properties.Phi 1.820 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id DZ UniChem ZINC ZINC000263620573 DZ UniChem PubChem 137348000 DZ UniChem BRENDA 257597 # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal DZ P -2.809 -1.228 2.115 ETKDGv3 1 DZ OP1 -2.635 -0.005 3.275 ETKDGv3 2 DZ OP2 -2.124 -2.474 2.624 ETKDGv3 3 DZ "O5'" -2.061 -0.759 0.656 ETKDGv3 4 DZ "C5'" -2.837 0.246 0.046 ETKDGv3 5 DZ "C4'" -2.093 0.810 -1.173 ETKDGv3 6 DZ "O4'" -0.890 1.416 -0.745 ETKDGv3 7 DZ "C1'" 0.169 0.829 -1.468 ETKDGv3 8 DZ C1 1.396 0.648 -0.596 ETKDGv3 9 DZ C2 2.747 0.716 -1.185 ETKDGv3 10 DZ O2 2.909 0.962 -2.410 ETKDGv3 11 DZ N3 3.882 0.489 -0.347 ETKDGv3 12 DZ C4 3.715 0.171 1.044 ETKDGv3 13 DZ C5 2.471 0.122 1.576 ETKDGv3 14 DZ C6 1.284 0.346 0.710 ETKDGv3 15 DZ N 2.262 -0.122 2.977 ETKDGv3 16 DZ ON1 3.010 0.551 3.915 ETKDGv3 17 DZ ON2 1.257 -0.759 3.354 ETKDGv3 18 DZ N4 4.878 -0.144 1.820 ETKDGv3 19 DZ "C2'" -0.305 -0.497 -2.036 ETKDGv3 20 DZ "C3'" -1.781 -0.271 -2.215 ETKDGv3 21 DZ "O3'" -2.045 0.223 -3.504 ETKDGv3 22 DZ OP3 -4.450 -1.578 1.866 ETKDGv3 23 DZ H1 -3.351 0.649 3.080 ETKDGv3 24 DZ "H5''" -3.811 -0.170 -0.296 ETKDGv3 25 DZ "H5'" -3.026 1.092 0.745 ETKDGv3 26 DZ "H4'" -2.739 1.595 -1.625 ETKDGv3 27 DZ "H1'" 0.416 1.513 -2.311 ETKDGv3 28 DZ H3 4.841 0.529 -0.759 ETKDGv3 29 DZ H6 0.304 0.271 1.161 ETKDGv3 30 DZ H42 5.828 -0.012 1.408 ETKDGv3 31 DZ H41 4.819 -0.621 2.746 ETKDGv3 32 DZ "H2''" -0.145 -1.324 -1.308 ETKDGv3 33 DZ "H2'" 0.210 -0.744 -2.991 ETKDGv3 34 DZ "H3'" -2.357 -1.211 -2.039 ETKDGv3 35 DZ H2 -2.026 -0.558 -4.117 ETKDGv3 36 DZ H4 -4.913 -0.703 1.893 ETKDGv3 37 #