data_D1F
# 
_chem_comp.id                                    D1F 
_chem_comp.name                                  "1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H24 N2 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-04-10 
_chem_comp.pdbx_modified_date                    2012-07-20 
_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                        368.382 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D1F 
_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        4EJ2 
_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 
D1F N1     N1     N 0 1 N N N 34.060 23.776 28.953 -0.771 -0.761 -0.031 N1     D1F 1  
D1F C2     C2     C 0 1 N N N 33.252 24.437 29.833 -1.205 -2.032 -0.021 C2     D1F 2  
D1F O2     O2     O 0 1 N N N 32.017 24.421 29.703 -2.401 -2.247 -0.044 O2     D1F 3  
D1F N3     N3     N 0 1 N N N 33.798 25.193 30.904 -0.355 -3.072 0.011  N3     D1F 4  
D1F C4     C4     C 0 1 N N N 35.186 25.246 31.067 0.978  -2.863 0.036  C4     D1F 5  
D1F O4     O4     O 0 1 N N N 35.738 25.874 31.977 1.754  -3.801 0.066  O4     D1F 6  
D1F C5     C5     C 0 1 N N N 35.992 24.566 30.189 1.475  -1.479 0.027  C5     D1F 7  
D1F C6     C6     C 0 1 N N N 35.494 23.815 29.110 0.561  -0.464 -0.007 C6     D1F 8  
D1F C7     C7     C 0 1 N N N 37.395 24.824 30.652 2.880  -1.202 0.053  C7     D1F 9  
D1F C8     C8     C 0 1 N N N 38.476 24.974 31.004 4.031  -0.976 0.074  C8     D1F 10 
D1F C9     C9     C 0 1 N N N 39.868 25.270 31.533 5.475  -0.691 0.101  C9     D1F 11 
D1F "C1'"  "C1'"  C 0 1 N N R 33.337 23.008 27.871 -1.747 0.330  -0.073 "C1'"  D1F 12 
D1F C10    C10    C 0 1 N N N 40.656 23.977 31.880 5.697  0.822  0.084  C10    D1F 13 
D1F C11    C11    C 0 1 N N N 42.102 24.179 32.372 7.198  1.118  0.111  C11    D1F 14 
D1F C12    C12    C 0 1 N N N 42.925 22.920 32.698 7.420  2.632  0.094  C12    D1F 15 
D1F C13    C13    C 0 1 N N N 44.194 22.820 31.847 8.921  2.927  0.122  C13    D1F 16 
D1F "C2'"  "C2'"  C 0 1 N N R 33.873 23.137 26.424 -2.509 0.282  -1.401 "C2'"  D1F 17 
D1F "O2'"  "O2'"  O 0 1 N N N 34.265 24.520 26.161 -1.596 0.484  -2.482 "O2'"  D1F 18 
D1F "C3'"  "C3'"  C 0 1 N N S 32.761 22.532 25.448 -3.568 1.388  -1.413 "C3'"  D1F 19 
D1F "O3'"  "O3'"  O 0 1 N N N 33.125 22.536 24.042 -4.332 1.305  -2.618 "O3'"  D1F 20 
D1F "C4'"  "C4'"  C 0 1 N N S 32.435 21.078 25.873 -4.494 1.207  -0.206 "C4'"  D1F 21 
D1F "O4'"  "O4'"  O 0 1 N N N 31.339 20.526 25.062 -5.442 2.275  -0.166 "O4'"  D1F 22 
D1F "C5'"  "C5'"  C 0 1 N N R 32.165 20.960 27.426 -3.656 1.219  1.076  "C5'"  D1F 23 
D1F "O5'"  "O5'"  O 0 1 N N N 33.199 21.602 28.204 -2.670 0.187  1.008  "O5'"  D1F 24 
D1F "C6'"  "C6'"  C 0 1 N N N 32.107 19.498 27.879 -4.565 0.979  2.282  "C6'"  D1F 25 
D1F "O6'"  "O6'"  O 0 1 N N N 33.209 18.762 27.334 -3.804 1.105  3.485  "O6'"  D1F 26 
D1F HN3    HN3    H 0 1 N N N 33.196 25.682 31.535 -0.701 -3.978 0.017  HN3    D1F 27 
D1F H6     H6     H 0 1 N N N 36.152 23.293 28.432 0.891  0.564  -0.015 H6     D1F 28 
D1F H9     H9     H 0 1 N N N 40.426 25.829 30.767 5.912  -1.112 1.006  H9     D1F 29 
D1F H9A    H9A    H 0 1 N N N 39.778 25.883 32.442 5.950  -1.138 -0.773 H9A    D1F 30 
D1F "H1'"  "H1'"  H 0 1 N N N 32.318 23.422 27.842 -1.230 1.285  0.014  "H1'"  D1F 31 
D1F H10    H10    H 0 1 N N N 40.103 23.447 32.670 5.261  1.244  -0.822 H10    D1F 32 
D1F H10A   H10A   H 0 0 N N N 40.692 23.352 30.975 5.223  1.269  0.958  H10A   D1F 33 
D1F H11    H11    H 0 1 N N N 42.642 24.732 31.589 7.635  0.697  1.017  H11    D1F 34 
D1F H11A   H11A   H 0 0 N N N 42.057 24.789 33.286 7.673  0.672  -0.763 H11A   D1F 35 
D1F H12    H12    H 0 1 N N N 43.212 22.950 33.759 6.984  3.053  -0.811 H12    D1F 36 
D1F H12A   H12A   H 0 0 N N N 42.303 22.032 32.511 6.946  3.078  0.968  H12A   D1F 37 
D1F H13    H13    H 0 1 N N N 44.746 21.907 32.116 9.358  2.506  1.027  H13    D1F 38 
D1F H13A   H13A   H 0 0 N N N 43.919 22.782 30.783 9.396  2.481  -0.752 H13A   D1F 39 
D1F H13B   H13B   H 0 0 N N N 44.829 23.699 32.031 9.079  4.006  0.110  H13B   D1F 40 
D1F "H2'"  "H2'"  H 0 1 N N N 34.762 22.495 26.339 -2.993 -0.688 -1.509 "H2'"  D1F 41 
D1F "HO2'" "HO2'" H 0 0 N N N 34.593 24.593 25.272 -2.011 0.466  -3.355 "HO2'" D1F 42 
D1F "H3'"  "H3'"  H 0 1 N N N 31.849 23.133 25.583 -3.080 2.362  -1.357 "H3'"  D1F 43 
D1F "HO3'" "HO3'" H 0 0 N N N 32.417 22.163 23.530 -5.024 1.977  -2.692 "HO3'" D1F 44 
D1F "H4'"  "H4'"  H 0 1 N N N 33.335 20.479 25.668 -5.019 0.256  -0.289 "H4'"  D1F 45 
D1F "HO4'" "HO4'" H 0 0 N N N 31.157 19.636 25.339 -6.005 2.331  -0.951 "HO4'" D1F 46 
D1F "H5'"  "H5'"  H 0 1 N N N 31.194 21.431 27.638 -3.163 2.186  1.179  "H5'"  D1F 47 
D1F "H6'"  "H6'"  H 0 1 N N N 32.151 19.457 28.977 -5.370 1.713  2.282  "H6'"  D1F 48 
D1F "H6'A" "H6'A" H 0 0 N N N 31.164 19.049 27.533 -4.989 -0.024 2.224  "H6'A" D1F 49 
D1F "HO6'" "HO6'" H 0 0 N N N 33.160 17.858 27.623 -4.318 0.965  4.292  "HO6'" D1F 50 
# 
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 
D1F N1    C2     SING N N 1  
D1F N1    C6     SING N N 2  
D1F N1    "C1'"  SING N N 3  
D1F C2    O2     DOUB N N 4  
D1F C2    N3     SING N N 5  
D1F N3    C4     SING N N 6  
D1F C4    O4     DOUB N N 7  
D1F C4    C5     SING N N 8  
D1F C5    C6     DOUB N N 9  
D1F C5    C7     SING N N 10 
D1F C7    C8     TRIP N N 11 
D1F C8    C9     SING N N 12 
D1F C9    C10    SING N N 13 
D1F "C1'" "C2'"  SING N N 14 
D1F "C1'" "O5'"  SING N N 15 
D1F C10   C11    SING N N 16 
D1F C11   C12    SING N N 17 
D1F C12   C13    SING N N 18 
D1F "C2'" "O2'"  SING N N 19 
D1F "C2'" "C3'"  SING N N 20 
D1F "C3'" "O3'"  SING N N 21 
D1F "C3'" "C4'"  SING N N 22 
D1F "C4'" "O4'"  SING N N 23 
D1F "C4'" "C5'"  SING N N 24 
D1F "C5'" "O5'"  SING N N 25 
D1F "C5'" "C6'"  SING N N 26 
D1F "C6'" "O6'"  SING N N 27 
D1F N3    HN3    SING N N 28 
D1F C6    H6     SING N N 29 
D1F C9    H9     SING N N 30 
D1F C9    H9A    SING N N 31 
D1F "C1'" "H1'"  SING N N 32 
D1F C10   H10    SING N N 33 
D1F C10   H10A   SING N N 34 
D1F C11   H11    SING N N 35 
D1F C11   H11A   SING N N 36 
D1F C12   H12    SING N N 37 
D1F C12   H12A   SING N N 38 
D1F C13   H13    SING N N 39 
D1F C13   H13A   SING N N 40 
D1F C13   H13B   SING N N 41 
D1F "C2'" "H2'"  SING N N 42 
D1F "O2'" "HO2'" SING N N 43 
D1F "C3'" "H3'"  SING N N 44 
D1F "O3'" "HO3'" SING N N 45 
D1F "C4'" "H4'"  SING N N 46 
D1F "O4'" "HO4'" SING N N 47 
D1F "C5'" "H5'"  SING N N 48 
D1F "C6'" "H6'"  SING N N 49 
D1F "C6'" "H6'A" SING N N 50 
D1F "O6'" "HO6'" SING N N 51 
# 
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 
D1F SMILES           ACDLabs              12.01 "O=C1NC(=O)N(C=C1C#CCCCCC)C2OC(C(O)C(O)C2O)CO"                                                                                                                           
D1F InChI            InChI                1.03  "InChI=1S/C17H24N2O7/c1-2-3-4-5-6-7-10-8-19(17(25)18-15(10)24)16-14(23)13(22)12(21)11(9-20)26-16/h8,11-14,16,20-23H,2-5,9H2,1H3,(H,18,24,25)/t11-,12-,13+,14-,16-/m1/s1" 
D1F InChIKey         InChI                1.03  ZIAKFTYLGUACKB-XYFZXANASA-N                                                                                                                                              
D1F SMILES_CANONICAL CACTVS               3.370 "CCCCCC#CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O"                                                                                                     
D1F SMILES           CACTVS               3.370 "CCCCCC#CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O"                                                                                                            
D1F SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCC#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O"                                                                                                   
D1F SMILES           "OpenEye OEToolkits" 1.7.6 "CCCCCC#CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)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 
D1F "SYSTEMATIC NAME" ACDLabs              12.01 "1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione"                                
D1F "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-hept-1-ynyl-1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D1F "Create component" 2012-04-10 RCSB 
# 
