data_5DB
# 
_chem_comp.id                                    5DB 
_chem_comp.name                                  "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-09-08 
_chem_comp.pdbx_modified_date                    2016-08-05 
_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                        336.235 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        5DLF 
_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 
5DB P     P1  P 0 1 N N N 27.769 -59.537 19.709 4.398  -1.142 -0.168 P     5DB 1  
5DB OP1   O1  O 0 1 N N N 28.397 -58.283 20.278 3.873  -2.310 0.807  OP1   5DB 2  
5DB "O5'" O2  O 0 1 N N N 26.296 -59.196 19.159 3.180  -0.152 -0.525 "O5'" 5DB 3  
5DB "C5'" C1  C 0 1 N N N 25.623 -60.043 18.224 2.523  0.658  0.452  "C5'" 5DB 4  
5DB "C4'" C2  C 0 1 N N R 24.471 -59.251 17.625 1.418  1.474  -0.221 "C4'" 5DB 5  
5DB "C3'" C3  C 0 1 N N S 24.927 -58.162 16.662 0.696  2.374  0.814  "C3'" 5DB 6  
5DB "O3'" O3  O 0 1 N N N 23.930 -58.063 15.648 1.380  3.618  0.974  "O3'" 5DB 7  
5DB "C2'" C4  C 0 1 N N N 24.951 -56.869 17.451 -0.687 2.585  0.152  "C2'" 5DB 8  
5DB "C1'" C5  C 0 1 N N R 23.850 -57.151 18.454 -0.812 1.415  -0.844 "C1'" 5DB 9  
5DB "O4'" O4  O 0 1 N N N 23.854 -58.556 18.704 0.369  0.607  -0.703 "O4'" 5DB 10 
5DB N1    N1  N 0 1 N N N 24.061 -56.501 19.735 -2.001 0.618  -0.530 N1    5DB 11 
5DB C6    C6  C 0 1 N N N 25.218 -56.652 20.396 -3.030 0.557  -1.420 C6    5DB 12 
5DB C5    C7  C 0 1 N N N 25.393 -56.028 21.626 -4.124 -0.184 -1.117 C5    5DB 13 
5DB C7    C8  C 0 1 N N N 26.695 -56.171 22.387 -5.278 -0.272 -2.081 C7    5DB 14 
5DB C4    C9  C 0 1 N N N 24.259 -55.224 22.168 -4.165 -0.870 0.111  C4    5DB 15 
5DB N3    N2  N 0 1 N N N 23.113 -55.119 21.455 -3.141 -0.781 0.946  N3    5DB 16 
5DB C2    C10 C 0 1 N N N 22.991 -55.740 20.256 -2.069 -0.054 0.634  C2    5DB 17 
5DB O2    O5  O 0 1 N N N 21.931 -55.655 19.581 -1.136 0.008  1.418  O2    5DB 18 
5DB O4    O6  O 0 1 N N N 24.368 -54.581 23.378 -5.245 -1.615 0.437  O4    5DB 19 
5DB OP2   O7  O 0 1 N N N 28.604 -60.151 18.613 5.471  -0.379 0.510  OP2   5DB 20 
5DB C1    C11 C 0 1 N N N 23.201 -54.266 24.141 -5.215 -2.282 1.701  C1    5DB 21 
5DB H1    H1  H 0 1 N N N 29.218 -58.109 19.832 3.167  -2.851 0.428  H1    5DB 22 
5DB H2    H2  H 0 1 N N N 25.236 -60.935 18.738 2.087  0.020  1.220  H2    5DB 23 
5DB H3    H3  H 0 1 N N N 26.319 -60.351 17.429 3.246  1.334  0.909  H3    5DB 24 
5DB H4    H4  H 0 1 N N N 23.765 -59.929 17.123 1.826  2.073  -1.035 H4    5DB 25 
5DB H5    H5  H 0 1 N N N 25.921 -58.392 16.252 0.595  1.862  1.771  H5    5DB 26 
5DB H6    H6  H 0 1 N N N 23.906 -58.870 15.147 0.920  4.250  1.543  H6    5DB 27 
5DB H7    H7  H 0 1 N N N 25.921 -56.710 17.944 -1.480 2.536  0.899  H7    5DB 28 
5DB H8    H8  H 0 1 N N N 24.714 -56.001 16.819 -0.716 3.539  -0.375 H8    5DB 29 
5DB H9    H9  H 0 1 N N N 22.885 -56.840 18.028 -0.879 1.799  -1.861 H9    5DB 30 
5DB H10   H10 H 0 1 N N N 26.009 -57.255 19.975 -2.975 1.092  -2.356 H10   5DB 31 
5DB H11   H11 H 0 1 N N N 26.634 -55.606 23.329 -5.124 -1.114 -2.757 H11   5DB 32 
5DB H12   H12 H 0 1 N N N 26.876 -57.233 22.607 -6.205 -0.417 -1.526 H12   5DB 33 
5DB H13   H13 H 0 1 N N N 27.521 -55.777 21.777 -5.341 0.650  -2.658 H13   5DB 34 
5DB H15   H15 H 0 1 N N N 23.496 -53.757 25.070 -4.367 -2.967 1.730  H15   5DB 35 
5DB H16   H16 H 0 1 N N N 22.546 -53.606 23.553 -5.115 -1.546 2.498  H16   5DB 36 
5DB H17   H17 H 0 1 N N N 22.662 -55.193 24.386 -6.139 -2.843 1.837  H17   5DB 37 
5DB OP3   OP3 O 0 1 N Y N ?      ?       ?      4.976  -1.792 -1.522 OP3   5DB 38 
5DB H19   H19 H 0 1 N Y N ?      ?       ?      5.714  -2.401 -1.383 H19   5DB 39 
# 
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 
5DB "O3'" "C3'" SING N N 1  
5DB "C3'" "C2'" SING N N 2  
5DB "C3'" "C4'" SING N N 3  
5DB "C2'" "C1'" SING N N 4  
5DB "C4'" "C5'" SING N N 5  
5DB "C4'" "O4'" SING N N 6  
5DB "C5'" "O5'" SING N N 7  
5DB "C1'" "O4'" SING N N 8  
5DB "C1'" N1    SING N N 9  
5DB OP2   P     DOUB N N 10 
5DB "O5'" P     SING N N 11 
5DB O2    C2    DOUB N N 12 
5DB P     OP1   SING N N 13 
5DB N1    C2    SING N N 14 
5DB N1    C6    SING N N 15 
5DB C2    N3    SING N N 16 
5DB C6    C5    DOUB N N 17 
5DB N3    C4    DOUB N N 18 
5DB C5    C4    SING N N 19 
5DB C5    C7    SING N N 20 
5DB C4    O4    SING N N 21 
5DB O4    C1    SING N N 22 
5DB OP1   H1    SING N N 23 
5DB "C5'" H2    SING N N 24 
5DB "C5'" H3    SING N N 25 
5DB "C4'" H4    SING N N 26 
5DB "C3'" H5    SING N N 27 
5DB "O3'" H6    SING N N 28 
5DB "C2'" H7    SING N N 29 
5DB "C2'" H8    SING N N 30 
5DB "C1'" H9    SING N N 31 
5DB C6    H10   SING N N 32 
5DB C7    H11   SING N N 33 
5DB C7    H12   SING N N 34 
5DB C7    H13   SING N N 35 
5DB C1    H15   SING N N 36 
5DB C1    H16   SING N N 37 
5DB C1    H17   SING N N 38 
5DB P     OP3   SING N N 39 
5DB OP3   H19   SING N N 40 
# 
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 
5DB SMILES           ACDLabs              12.01 "P(O)(O)(OCC1OC(CC1O)N2C(N=C(C(=C2)C)OC)=O)=O"                                                                                            
5DB InChI            InChI                1.03  "InChI=1S/C11H17N2O8P/c1-6-4-13(11(15)12-10(6)19-2)9-3-7(14)8(21-9)5-20-22(16,17)18/h4,7-9,14H,3,5H2,1-2H3,(H2,16,17,18)/t7-,8+,9+/m0/s1" 
5DB InChIKey         InChI                1.03  ZEXYXJZBCLRLBU-DJLDLDEBSA-N                                                                                                               
5DB SMILES_CANONICAL CACTVS               3.385 "COC1=NC(=O)N(C=C1C)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                               
5DB SMILES           CACTVS               3.385 "COC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                   
5DB SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1OC)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                 
5DB SMILES           "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1OC)C2CC(C(O2)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 
5DB "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one"                        
5DB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(4-methoxy-5-methyl-2-oxidanylidene-pyrimidin-1-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 
5DB "Create component" 2015-09-08 RCSB 
5DB "Initial release"  2016-08-10 RCSB 
# 
