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 
# 
