data_CKB
# 
_chem_comp.id                                    CKB 
_chem_comp.name                                  1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H16 N2 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         1-D-glucopyranosyl-thymine 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-11-16 
_chem_comp.pdbx_modified_date                    2008-11-14 
_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                        288.254 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CKB 
_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        3BD7 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
CKB C2     C2     C 0 1 N N N 38.516 36.823 30.391 1.498  -0.191 -1.064 C2     CKB 1  
CKB C4     C4     C 0 1 N N N 37.145 35.569 31.982 3.760  -0.247 -0.484 C4     CKB 2  
CKB C5     C5     C 0 1 N N N 37.531 36.445 33.154 3.406  -0.043 0.872  C5     CKB 3  
CKB C6     C6     C 0 1 N N N 38.397 37.467 32.850 2.102  0.080  1.199  C6     CKB 4  
CKB C7     C7     C 0 1 N N N 37.033 36.249 34.576 4.470  0.037  1.936  C7     CKB 5  
CKB N1     N1     N 0 1 N N N 38.896 37.674 31.491 1.148  0.004  0.220  N1     CKB 6  
CKB N3     N3     N 0 1 N N N 37.651 35.804 30.684 2.791  -0.316 -1.418 N3     CKB 7  
CKB "C1'"  "C1'"  C 0 1 N N R 39.840 38.744 31.044 -0.267 0.136  0.575  "C1'"  CKB 8  
CKB "C2'"  "C2'"  C 0 1 N N R 39.428 40.134 31.715 -0.837 1.406  -0.063 "C2'"  CKB 9  
CKB "C3'"  "C3'"  C 0 1 N N S 40.474 41.175 31.211 -2.330 1.505  0.262  "C3'"  CKB 10 
CKB "C4'"  "C4'"  C 0 1 N N S 41.897 40.724 31.546 -3.035 0.239  -0.234 "C4'"  CKB 11 
CKB "C5'"  "C5'"  C 0 1 N N R 42.176 39.337 30.869 -2.381 -0.986 0.410  "C5'"  CKB 12 
CKB "C6'"  "C6'"  C 0 1 N N N 43.595 38.787 31.169 -3.040 -2.258 -0.126 "C6'"  CKB 13 
CKB "O6'"  "O6'"  O 0 1 N N N 43.697 38.544 32.624 -2.510 -3.395 0.559  "O6'"  CKB 14 
CKB "O2'"  "O2'"  O 0 1 N N N 38.077 40.519 31.416 -0.157 2.549  0.460  "O2'"  CKB 15 
CKB "O3'"  "O3'"  O 0 1 N N N 40.182 42.452 31.810 -2.886 2.648  -0.390 "O3'"  CKB 16 
CKB "O4'"  "O4'"  O 0 1 N N N 42.862 41.715 31.076 -4.417 0.288  0.128  "O4'"  CKB 17 
CKB "O5'"  "O5'"  O 0 1 N N N 41.215 38.288 31.306 -0.987 -1.001 0.094  "O5'"  CKB 18 
CKB O2     O2     O 0 1 N N N 38.890 36.916 29.214 0.634  -0.261 -1.917 O2     CKB 19 
CKB O4     O4     O 0 1 N N N 36.372 34.607 32.118 4.930  -0.360 -0.803 O4     CKB 20 
CKB H6     H6     H 0 1 N N N 38.718 38.135 33.635 1.812  0.236  2.227  H6     CKB 21 
CKB H7     H7     H 0 1 N N N 37.891 36.202 35.262 5.452  -0.083 1.477  H7     CKB 22 
CKB H7A    H7A    H 0 1 N N N 36.385 37.092 34.857 4.417  1.007  2.430  H7A    CKB 23 
CKB H7B    H7B    H 0 1 N N N 36.462 35.311 34.638 4.312  -0.754 2.668  H7B    CKB 24 
CKB HN3    HN3    H 0 1 N N N 37.363 35.196 29.944 3.026  -0.456 -2.349 HN3    CKB 25 
CKB "H1'"  "H1'"  H 0 1 N N N 39.786 38.931 29.961 -0.366 0.197  1.658  "H1'"  CKB 26 
CKB "H2'"  "H2'"  H 0 1 N N N 39.442 40.058 32.812 -0.701 1.363  -1.144 "H2'"  CKB 27 
CKB "H3'"  "H3'"  H 0 1 N N N 40.409 41.262 30.116 -2.464 1.598  1.340  "H3'"  CKB 28 
CKB "H4'"  "H4'"  H 0 1 N N N 42.000 40.624 32.637 -2.944 0.172  -1.319 "H4'"  CKB 29 
CKB "H5'"  "H5'"  H 0 1 N N N 42.069 39.542 29.794 -2.508 -0.939 1.492  "H5'"  CKB 30 
CKB "H6'"  "H6'"  H 0 1 N N N 43.756 37.848 30.620 -4.116 -2.205 0.035  "H6'"  CKB 31 
CKB "H6'A" "H6'A" H 0 0 N N N 44.359 39.512 30.851 -2.836 -2.351 -1.193 "H6'A" CKB 32 
CKB "HO6'" "HO6'" H 0 0 N N N 43.719 37.609 32.789 -2.884 -4.238 0.270  "HO6'" CKB 33 
CKB "HO2'" "HO2'" H 0 0 N N N 37.585 40.604 32.224 -0.468 3.390  0.098  "HO2'" CKB 34 
CKB "HO3'" "HO3'" H 0 0 N N N 40.118 42.353 32.753 -3.832 2.773  -0.228 "HO3'" CKB 35 
CKB "HO4'" "HO4'" H 0 0 N N N 43.071 42.314 31.783 -4.894 1.043  -0.242 "HO4'" CKB 36 
# 
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 
CKB C2    N1     SING N N 1  
CKB C2    N3     SING N N 2  
CKB C2    O2     DOUB N N 3  
CKB C4    C5     SING N N 4  
CKB C4    N3     SING N N 5  
CKB C4    O4     DOUB N N 6  
CKB C5    C6     DOUB N N 7  
CKB C5    C7     SING N N 8  
CKB C6    N1     SING N N 9  
CKB N1    "C1'"  SING N N 10 
CKB "C1'" "C2'"  SING N N 11 
CKB "C1'" "O5'"  SING N N 12 
CKB "C2'" "C3'"  SING N N 13 
CKB "C2'" "O2'"  SING N N 14 
CKB "C3'" "C4'"  SING N N 15 
CKB "C3'" "O3'"  SING N N 16 
CKB "C4'" "C5'"  SING N N 17 
CKB "C4'" "O4'"  SING N N 18 
CKB "C5'" "C6'"  SING N N 19 
CKB "C5'" "O5'"  SING N N 20 
CKB "C6'" "O6'"  SING N N 21 
CKB C6    H6     SING N N 22 
CKB C7    H7     SING N N 23 
CKB C7    H7A    SING N N 24 
CKB C7    H7B    SING N N 25 
CKB N3    HN3    SING N N 26 
CKB "C1'" "H1'"  SING N N 27 
CKB "C2'" "H2'"  SING N N 28 
CKB "C3'" "H3'"  SING N N 29 
CKB "C4'" "H4'"  SING N N 30 
CKB "C5'" "H5'"  SING N N 31 
CKB "C6'" "H6'"  SING N N 32 
CKB "C6'" "H6'A" SING N N 33 
CKB "O6'" "HO6'" SING N N 34 
CKB "O2'" "HO2'" SING N N 35 
CKB "O3'" "HO3'" SING N N 36 
CKB "O4'" "HO4'" SING N N 37 
# 
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 
CKB SMILES           ACDLabs              10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C(O)C2O)CO                                                                                                           
CKB InChI            InChI                1.02b InChI=1/C11H16N2O7/c1-4-2-13(11(19)12-9(4)18)10-8(17)7(16)6(15)5(3-14)20-10/h2,5-8,10,14-17H,3H2,1H3,(H,12,18,19)/t5-,6-,7+,8-,10-/m1/s1/f/h12H 
CKB InChIKey         InChI                1.02b RMXUFBPORJBBEZ-AHTCHRBJDA                                                                                                                       
CKB SMILES_CANONICAL CACTVS               3.341 CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O                                                                                     
CKB SMILES           CACTVS               3.341 CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O                                                                                            
CKB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O                                                                                   
CKB SMILES           "OpenEye OEToolkits" 1.5.0 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 
CKB "SYSTEMATIC NAME" ACDLabs              10.04 1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione                                   
CKB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 5-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidine-2,4-dione 
# 
