data_SDH # _chem_comp.id SDH _chem_comp.name "(5S)-7-amino-1-[2-deoxy-5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-erythro-pentofuranosyl]-1,3,6,8-tetraazaspiro[4.4]non-7-ene-2,4,9-trione" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N5 O9 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-02-28 _chem_comp.pdbx_modified_date 2014-03-28 _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 381.236 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SDH _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4PPX _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 SDH P P P 0 1 N N N 20.461 8.973 0.570 5.014 -0.536 -0.315 P SDH 1 SDH OP1 OP1 O 0 1 N N N 20.113 7.545 1.177 6.604 -1.030 0.117 OP1 SDH 2 SDH OP2 OP2 O 0 1 N N N 20.614 8.934 -0.901 4.436 -1.055 1.220 OP2 SDH 3 SDH "O5'" "O5'" O 0 1 N N N 19.305 9.971 1.117 3.423 -0.043 -0.746 "O5'" SDH 4 SDH N9 N9 N 0 1 N N N 17.133 10.914 6.158 -1.713 -0.072 0.562 N9 SDH 5 SDH C8 C8 C 0 1 N N N 16.010 10.637 6.971 -1.568 -0.617 1.786 C8 SDH 6 SDH O8 O8 O 0 1 N N N 14.850 10.934 6.753 -0.592 -0.447 2.491 O8 SDH 7 SDH N7 N7 N 0 1 N N N 16.436 9.940 8.151 -2.621 -1.368 2.139 N7 SDH 8 SDH C5 C5 C 0 1 N N N 17.809 9.733 8.132 -3.564 -1.386 1.171 C5 SDH 9 SDH O5 O5 O 0 1 N N N 18.491 9.184 8.972 -4.626 -1.971 1.189 O5 SDH 10 SDH C4 C4 C 0 1 N N R 18.331 10.366 6.819 -3.012 -0.524 0.067 C4 SDH 11 SDH C6 C6 C 0 1 N N N 19.095 9.161 6.152 -3.926 0.628 -0.254 C6 SDH 12 SDH O6 O6 O 0 1 N N N 18.524 8.191 5.725 -4.302 1.503 0.503 O6 SDH 13 SDH N1 N1 N 0 1 N N N 20.488 9.448 6.163 -4.237 0.488 -1.543 N1 SDH 14 SDH C2 C2 C 0 1 N N N 20.625 10.674 6.755 -3.666 -0.568 -2.086 C2 SDH 15 SDH N2 N2 N 0 1 N N N 21.834 11.275 6.938 -3.824 -0.930 -3.390 N2 SDH 16 SDH N3 N3 N 0 1 N N N 19.413 11.309 7.173 -2.897 -1.258 -1.194 N3 SDH 17 SDH "C2'" "C2'" C 0 1 N N N 18.301 12.579 4.612 -0.605 2.136 0.633 "C2'" SDH 18 SDH "C5'" "C5'" C 0 1 N N N 19.159 10.251 2.475 2.871 0.955 0.115 "C5'" SDH 19 SDH "C4'" "C4'" C 0 1 N N R 17.937 11.174 2.691 1.462 1.316 -0.360 "C4'" SDH 20 SDH "O4'" "O4'" O 0 1 N N N 17.137 10.707 3.756 0.556 0.216 -0.127 "O4'" SDH 21 SDH "C1'" "C1'" C 0 1 N N R 17.154 11.591 4.846 -0.764 0.803 -0.131 "C1'" SDH 22 SDH "C3'" "C3'" C 0 1 N N S 18.354 12.620 3.079 0.893 2.481 0.479 "C3'" SDH 23 SDH "O3'" "O3'" O 0 1 N N N 17.349 13.471 2.634 1.053 3.721 -0.213 "O3'" SDH 24 SDH H1 H1 H 0 1 N N N 20.024 7.615 2.120 6.957 -0.580 0.896 H1 SDH 25 SDH H2 H2 H 0 1 N N N 21.308 8.328 -1.132 4.464 -0.370 1.903 H2 SDH 26 SDH H3 H3 H 0 1 N N N 15.827 9.644 8.887 -2.696 -1.840 2.983 H3 SDH 27 SDH H4 H4 H 0 1 N N N 22.670 10.819 6.634 -4.385 -0.398 -3.976 H4 SDH 28 SDH H5 H5 H 0 1 N N N 21.885 12.173 7.376 -3.376 -1.720 -3.732 H5 SDH 29 SDH H6 H6 H 0 1 N N N 19.318 12.202 7.612 -2.383 -2.063 -1.360 H6 SDH 30 SDH H7 H7 H 0 1 N N N 19.245 12.208 5.038 -1.224 2.912 0.182 H7 SDH 31 SDH H8 H8 H 0 1 N N N 18.072 13.569 5.034 -0.863 2.007 1.685 H8 SDH 32 SDH H9 H9 H 0 1 N N N 19.009 9.312 3.028 2.823 0.570 1.134 H9 SDH 33 SDH H10 H10 H 0 1 N N N 20.066 10.753 2.844 3.501 1.844 0.092 H10 SDH 34 SDH H11 H11 H 0 1 N N N 17.355 11.214 1.758 1.476 1.581 -1.418 H11 SDH 35 SDH H12 H12 H 0 1 N N N 16.232 12.189 4.793 -1.094 0.989 -1.153 H12 SDH 36 SDH H13 H13 H 0 1 N N N 19.359 12.868 2.707 1.378 2.522 1.454 H13 SDH 37 SDH H14 H14 H 0 1 N Y N 17.572 14.368 2.855 0.712 4.488 0.269 H14 SDH 38 SDH OP3 OP3 O 0 1 N Y N ? ? ? 5.033 -1.631 -1.641 OP3 SDH 39 SDH H15 H15 H 0 1 N N N ? ? ? 5.490 0.843 -0.493 H15 SDH 40 SDH H16 H16 H 0 1 N Y N ? ? ? 5.374 -1.249 -2.461 H16 SDH 41 # 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 SDH OP2 P SING N N 1 SDH P "O5'" SING N N 2 SDH P OP1 SING N N 3 SDH "O5'" "C5'" SING N N 4 SDH "C5'" "C4'" SING N N 5 SDH "O3'" "C3'" SING N N 6 SDH "C4'" "C3'" SING N N 7 SDH "C4'" "O4'" SING N N 8 SDH "C3'" "C2'" SING N N 9 SDH "O4'" "C1'" SING N N 10 SDH "C2'" "C1'" SING N N 11 SDH "C1'" N9 SING N N 12 SDH O6 C6 DOUB N N 13 SDH C6 N1 SING N N 14 SDH C6 C4 SING N N 15 SDH N9 C4 SING N N 16 SDH N9 C8 SING N N 17 SDH N1 C2 DOUB N N 18 SDH O8 C8 DOUB N N 19 SDH C2 N2 SING N N 20 SDH C2 N3 SING N N 21 SDH C4 N3 SING N N 22 SDH C4 C5 SING N N 23 SDH C8 N7 SING N N 24 SDH C5 N7 SING N N 25 SDH C5 O5 DOUB N N 26 SDH OP1 H1 SING N N 27 SDH OP2 H2 SING N N 28 SDH N7 H3 SING N N 29 SDH N2 H4 SING N N 30 SDH N2 H5 SING N N 31 SDH N3 H6 SING N N 32 SDH "C2'" H7 SING N N 33 SDH "C2'" H8 SING N N 34 SDH "C5'" H9 SING N N 35 SDH "C5'" H10 SING N N 36 SDH "C4'" H11 SING N N 37 SDH "C1'" H12 SING N N 38 SDH "C3'" H13 SING N N 39 SDH "O3'" H14 SING N N 40 SDH P OP3 SING N N 41 SDH P H15 SING N N 42 SDH OP3 H16 SING N N 43 # 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 SDH SMILES ACDLabs 12.01 "O=C2NC(=O)N(C21NC(=NC1=O)N)C3OC(C(O)C3)COP(O)(O)O" SDH InChI InChI 1.03 "InChI=1S/C10H16N5O9P/c11-8-12-6(17)10(14-8)7(18)13-9(19)15(10)5-1-3(16)4(24-5)2-23-25(20,21)22/h3-5,16,20-22,25H,1-2H2,(H,13,18,19)(H3,11,12,14,17)/t3-,4+,5+,10+/m0/s1" SDH InChIKey InChI 1.03 BTPRAWLYZNCXOI-XPCBYELVSA-N SDH SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)[C@@]2(N1)N([C@H]3C[C@H](O)[C@@H](CO[PH](O)(O)O)O3)C(=O)NC2=O" SDH SMILES CACTVS 3.385 "NC1=NC(=O)[C]2(N1)N([CH]3C[CH](O)[CH](CO[PH](O)(O)O)O3)C(=O)NC2=O" SDH SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C(=O)NC(=O)[C@@]23C(=O)N=C(N3)N)COP(O)(O)O)O" SDH SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C(=O)NC(=O)C23C(=O)N=C(N3)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 SDH "SYSTEMATIC NAME" ACDLabs 12.01 "(5S)-7-amino-1-[2-deoxy-5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-erythro-pentofuranosyl]-1,3,6,8-tetraazaspiro[4.4]non-7-ene-2,4,9-trione" SDH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(5S)-7-azanyl-1-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,3,6,8-tetrazaspiro[4.4]non-7-ene-2,4,9-trione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SDH "Create component" 2014-02-28 RCSB SDH "Initial release" 2014-04-02 RCSB #