data_ZDU # _chem_comp.id ZDU _chem_comp.name "5-(3-AMINOPROPYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H20 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-04-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 365.276 _chem_comp.one_letter_code U _chem_comp.three_letter_code ZDU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1Z5T _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.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 ZDU P P P 0 1 N N N 3.248 -12.692 45.584 -3.968 -1.665 3.118 P ZDU 1 ZDU OP1 O1P O 0 1 N N N 2.650 -11.716 44.693 -4.406 -2.599 4.208 OP1 ZDU 2 ZDU OP2 O2P O 0 1 N N N 4.484 -12.387 46.320 -3.912 -2.311 1.636 OP2 ZDU 3 ZDU "O5'" O5* O 0 1 N N N 3.476 -14.042 44.773 -2.493 -1.028 3.315 "O5'" ZDU 4 ZDU N1 N1 N 0 1 N N N 0.941 -17.102 42.324 1.164 -2.047 0.989 N1 ZDU 5 ZDU C6 C6 C 0 1 N N N 0.285 -15.887 42.306 -0.013 -2.784 0.958 C6 ZDU 6 ZDU C2 C2 C 0 1 N N N 0.306 -18.265 41.929 2.333 -2.544 0.374 C2 ZDU 7 ZDU O2 O2 O 0 1 N N N 0.878 -19.347 41.885 3.410 -1.945 0.363 O2 ZDU 8 ZDU N3 N3 N 0 1 N N N -1.029 -18.102 41.581 2.194 -3.793 -0.240 N3 ZDU 9 ZDU C4 C4 C 0 1 N N N -1.766 -16.897 41.579 1.047 -4.570 -0.300 C4 ZDU 10 ZDU O4 O4 O 0 1 N N N -2.976 -16.899 41.258 0.995 -5.663 -0.857 O4 ZDU 11 ZDU C5 C5 C 0 1 N N N -1.003 -15.717 41.973 -0.143 -3.980 0.369 C5 ZDU 12 ZDU C5A C5A C 0 1 N N N -1.650 -14.354 41.988 -1.420 -4.757 0.347 C5A ZDU 13 ZDU C5B C5B C 0 1 N N N -1.910 -13.795 40.570 -2.254 -4.400 -0.880 C5B ZDU 14 ZDU C5G C5G C 0 1 N N N -2.747 -12.545 40.656 -3.558 -5.188 -0.993 C5G ZDU 15 ZDU N5D N5D N 0 1 N N N -2.852 -11.826 39.340 -4.335 -4.808 -2.141 N5D ZDU 16 ZDU "C2'" C2* C 0 1 N N N 3.446 -16.434 42.118 0.710 0.360 0.754 "C2'" ZDU 17 ZDU "C5'" C5* C 0 1 N N N 3.788 -15.226 45.465 -2.005 -0.136 2.327 "C5'" ZDU 18 ZDU "C4'" C4* C 0 1 N N R 3.680 -16.407 44.535 -0.611 0.328 2.728 "C4'" ZDU 19 ZDU "O4'" O4* O 0 1 N N N 2.320 -16.611 44.133 0.247 -0.829 2.764 "O4'" ZDU 20 ZDU "C1'" C1* C 0 1 N N R 2.329 -17.182 42.841 1.157 -0.778 1.657 "C1'" ZDU 21 ZDU "C3'" C3* C 0 1 N N S 4.464 -16.232 43.245 0.008 1.286 1.720 "C3'" ZDU 22 ZDU "O3'" O3* O 0 1 N N N 5.469 -17.239 43.239 0.965 2.121 2.368 "O3'" ZDU 23 ZDU OP3 O3P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 OP3 ZDU 24 ZDU HOP2 2HOP H 0 0 N N N 4.875 -13.026 46.903 -4.684 -2.823 1.313 HOP2 ZDU 25 ZDU H6 H6 H 0 1 N N N 0.837 -14.973 42.581 -0.857 -2.318 1.458 H6 ZDU 26 ZDU HN3 HN3 H 0 1 N N N -1.516 -18.952 41.298 3.023 -4.171 -0.689 HN3 ZDU 27 ZDU H5A1 1H5A H 0 0 N N N -2.588 -14.364 42.590 -1.153 -5.818 0.312 H5A1 ZDU 28 ZDU H5A2 2H5A H 0 0 N N N -1.052 -13.635 42.596 -1.963 -4.568 1.277 H5A2 ZDU 29 ZDU H5B1 1H5B H 0 0 N N N -0.962 -13.626 40.006 -2.493 -3.329 -0.861 H5B1 ZDU 30 ZDU H5B2 2H5B H 0 0 N N N -2.365 -14.558 39.896 -1.647 -4.578 -1.776 H5B2 ZDU 31 ZDU H5G1 1H5G H 0 0 N N N -3.757 -12.767 41.071 -3.373 -6.264 -1.056 H5G1 ZDU 32 ZDU H5G2 2H5G H 0 0 N N N -2.369 -11.864 41.454 -4.181 -5.003 -0.112 H5G2 ZDU 33 ZDU H5D1 1H5D H 0 0 N N N -3.418 -10.979 39.398 -5.310 -4.580 -2.022 H5D1 ZDU 34 ZDU H5D2 2H5D H 0 0 N N N -3.197 -12.448 38.609 -3.961 -4.969 -3.063 H5D2 ZDU 35 ZDU "H2'" 1H2* H 0 1 N N N 3.841 -16.938 41.205 -0.003 -0.001 0.003 "H2'" ZDU 36 ZDU "H2''" 2H2* H 0 0 N N N 3.130 -15.503 41.591 1.556 0.818 0.232 "H2''" ZDU 37 ZDU "H5'" 1H5* H 0 1 N N N 4.786 -15.171 45.958 -1.971 -0.654 1.366 "H5'" ZDU 38 ZDU "H5''" 2H5* H 0 0 N N N 3.162 -15.354 46.378 -2.683 0.718 2.254 "H5''" ZDU 39 ZDU "H4'" H4* H 0 1 N N N 4.090 -17.265 45.116 -0.644 0.753 3.736 "H4'" ZDU 40 ZDU "H1'" H1* H 0 1 N N N 2.569 -18.265 42.735 2.163 -0.604 2.054 "H1'" ZDU 41 ZDU "H3'" H3* H 0 1 N N N 4.957 -15.238 43.131 -0.722 1.941 1.236 "H3'" ZDU 42 ZDU "HO3'" H3T H 0 0 N Y N 6.100 -17.113 43.937 0.743 3.042 2.146 "HO3'" ZDU 43 ZDU HOP3 3HOP H 0 0 N N N 0.391 -0.639 0.583 -5.874 -0.475 2.871 HOP3 ZDU 44 # 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 ZDU P OP1 DOUB N N 1 ZDU P OP2 SING N N 2 ZDU P "O5'" SING N N 3 ZDU P OP3 SING N N 4 ZDU OP2 HOP2 SING N N 5 ZDU "O5'" "C5'" SING N N 6 ZDU N1 C6 SING N N 7 ZDU N1 C2 SING N N 8 ZDU N1 "C1'" SING N N 9 ZDU C6 C5 DOUB N N 10 ZDU C6 H6 SING N N 11 ZDU C2 O2 DOUB N N 12 ZDU C2 N3 SING N N 13 ZDU N3 C4 SING N N 14 ZDU N3 HN3 SING N N 15 ZDU C4 O4 DOUB N N 16 ZDU C4 C5 SING N N 17 ZDU C5 C5A SING N N 18 ZDU C5A C5B SING N N 19 ZDU C5A H5A1 SING N N 20 ZDU C5A H5A2 SING N N 21 ZDU C5B C5G SING N N 22 ZDU C5B H5B1 SING N N 23 ZDU C5B H5B2 SING N N 24 ZDU C5G N5D SING N N 25 ZDU C5G H5G1 SING N N 26 ZDU C5G H5G2 SING N N 27 ZDU N5D H5D1 SING N N 28 ZDU N5D H5D2 SING N N 29 ZDU "C2'" "C1'" SING N N 30 ZDU "C2'" "C3'" SING N N 31 ZDU "C2'" "H2'" SING N N 32 ZDU "C2'" "H2''" SING N N 33 ZDU "C5'" "C4'" SING N N 34 ZDU "C5'" "H5'" SING N N 35 ZDU "C5'" "H5''" SING N N 36 ZDU "C4'" "O4'" SING N N 37 ZDU "C4'" "C3'" SING N N 38 ZDU "C4'" "H4'" SING N N 39 ZDU "O4'" "C1'" SING N N 40 ZDU "C1'" "H1'" SING N N 41 ZDU "C3'" "O3'" SING N N 42 ZDU "C3'" "H3'" SING N N 43 ZDU "O3'" "HO3'" SING N N 44 ZDU OP3 HOP3 SING N N 45 # 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 ZDU SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1CCCN)C2OC(C(O)C2)COP(=O)(O)O" ZDU SMILES_CANONICAL CACTVS 3.341 "NCCCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" ZDU SMILES CACTVS 3.341 "NCCCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" ZDU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)CCCN)COP(=O)(O)O)O" ZDU SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)CCCN)COP(=O)(O)O)O" ZDU InChI InChI 1.03 "InChI=1S/C12H20N3O8P/c13-3-1-2-7-5-15(12(18)14-11(7)17)10-4-8(16)9(23-10)6-22-24(19,20)21/h5,8-10,16H,1-4,6,13H2,(H,14,17,18)(H2,19,20,21)/t8-,9+,10+/m0/s1" ZDU InChIKey InChI 1.03 DPQBGKUKUKNQCZ-IVZWLZJFSA-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 ZDU "SYSTEMATIC NAME" ACDLabs 10.04 ;5-(3-aminopropyl)-2'-deoxyuridine 5'-(dihydrogen phosphate) ; ZDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[5-(3-aminopropyl)-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-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 ZDU "Create component" 2005-04-08 EBI ZDU "Modify descriptor" 2011-06-04 RCSB #