data_MDK
# 
_chem_comp.id                                    MDK 
_chem_comp.name                                  "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-methylpyridin-2(1H)-one" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-07-23 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        320.236 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     MDK 
_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        3O1R 
_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 
MDK P      P    P 0 1 N N N 0.680  0.731  -1.299 4.339  1.041  0.101  P    MDK 1  
MDK N1     N1   N 0 1 N N N 1.144  -2.182 3.156  -2.233 -0.278 0.118  N1   MDK 2  
MDK C2     C2   C 0 1 N N N 0.816  -3.135 4.100  -3.308 -0.065 0.900  C2   MDK 3  
MDK O2     O2   O 0 1 N N N 1.717  -3.851 4.603  -3.346 -0.541 2.024  O2   MDK 4  
MDK C3     C3   C 0 1 N N N -0.527 -3.332 4.525  -4.380 0.698  0.428  C3   MDK 5  
MDK C4     C4   C 0 1 N N N -1.533 -2.516 3.953  -4.318 1.229  -0.850 C4   MDK 6  
MDK N4     N4   N 0 1 N N N -2.887 -2.662 4.293  -5.361 1.989  -1.347 N4   MDK 7  
MDK C5     C5   C 0 1 N N N -1.184 -1.528 3.020  -3.173 0.982  -1.637 C5   MDK 8  
MDK C6     C6   C 0 1 N N N 0.159  -1.376 2.645  -2.163 0.239  -1.137 C6   MDK 9  
MDK "C1'"  C1*  C 0 1 N N R 2.522  -2.050 2.688  -1.116 -1.075 0.631  C1*  MDK 10 
MDK O1P    O1P  O 0 1 N N N 0.079  -0.241 -2.234 4.045  1.913  -1.059 O1P  MDK 11 
MDK "C2'"  C2*  C 0 1 N N N 2.967  -3.270 1.842  -0.978 -2.372 -0.188 C2*  MDK 12 
MDK C21    C21  C 0 1 N N N -0.902 -4.351 5.543  -5.586 0.940  1.298  C21  MDK 13 
MDK O2P    O2P  O 0 1 N N N 1.136  1.956  -2.059 4.763  1.949  1.361  O2P  MDK 14 
MDK "C3'"  C3*  C 0 1 N N S 3.927  -2.665 0.814  0.461  -2.312 -0.756 C3*  MDK 15 
MDK "O3'"  O3*  O 0 1 N N N 5.255  -2.592 1.337  1.088  -3.594 -0.693 O3*  MDK 16 
MDK "C4'"  C4*  C 0 1 N N R 3.349  -1.248 0.626  1.149  -1.312 0.209  C4*  MDK 17 
MDK "O4'"  O4*  O 0 1 N N N 2.814  -0.871 1.906  0.114  -0.345 0.485  O4*  MDK 18 
MDK "C5'"  C5*  C 0 1 N N N 2.254  -1.137 -0.469 2.345  -0.643 -0.471 C5*  MDK 19 
MDK "O5'"  O5*  O 0 1 N N N 1.881  0.143  -0.575 3.029  0.183  0.473  O5*  MDK 20 
MDK HN4    HN4  H 0 1 N N N -3.433 -1.996 3.784  -6.144 2.154  -0.799 HN4  MDK 21 
MDK HN4A   HN4A H 0 0 N N N -3.190 -3.587 4.063  -5.310 2.357  -2.243 HN4A MDK 22 
MDK H5     H5   H 0 1 N N N -1.944 -0.889 2.594  -3.104 1.387  -2.636 H5   MDK 23 
MDK H6     H6   H 0 1 N N N 0.424  -0.605 1.936  -1.289 0.053  -1.742 H6   MDK 24 
MDK "H1'"  H1*  H 0 1 N N N 3.081  -1.974 3.632  -1.284 -1.316 1.681  H1*  MDK 25 
MDK "H2'"  H2*  H 0 1 N N N 3.467  -4.029 2.462  -1.098 -3.244 0.455  H2*  MDK 26 
MDK "H2'A" H2*A H 0 0 N N N 2.109  -3.756 1.354  -1.707 -2.391 -0.998 H2*A MDK 27 
MDK H21    H21  H 0 1 N N N -1.989 -4.321 5.710  -5.437 1.848  1.882  H21  MDK 28 
MDK H21A   H21A H 0 0 N N N -0.614 -5.350 5.185  -6.470 1.053  0.670  H21A MDK 29 
MDK H21B   H21B H 0 0 N N N -0.380 -4.135 6.487  -5.725 0.093  1.971  H21B MDK 30 
MDK "H3'"  H3*  H 0 1 N N N 4.001  -3.249 -0.115 0.461  -1.930 -1.777 H3*  MDK 31 
MDK "HO3'" HO3* H 0 0 N N N 5.833  -2.214 0.684  0.640  -4.277 -1.211 HO3* MDK 32 
MDK "H4'"  H4*  H 0 1 N N N 4.150  -0.581 0.276  1.459  -1.815 1.125  H4*  MDK 33 
MDK "H5'"  H5*  H 0 1 N N N 2.655  -1.488 -1.432 3.025  -1.408 -0.844 H5*  MDK 34 
MDK "H5'A" H5*A H 0 0 N N N 1.387  -1.754 -0.191 1.994  -0.032 -1.302 H5*A MDK 35 
MDK O7     O7   O 0 1 N N N -0.341 1.151  -0.267 5.546  0.042  -0.271 O7   MDK 36 
MDK H16    H16  H 0 1 N N N 0.941  1.847  -2.982 5.547  2.493  1.208  H16  MDK 37 
MDK H17    H17  H 0 1 N N N -1.162 0.702  -0.432 5.793  -0.560 0.444  H17  MDK 38 
# 
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 
MDK P     O1P    DOUB N N 1  
MDK P     O2P    SING N N 2  
MDK P     "O5'"  SING N N 3  
MDK N1    C2     SING N N 4  
MDK N1    C6     SING N N 5  
MDK N1    "C1'"  SING N N 6  
MDK C2    O2     DOUB N N 7  
MDK C2    C3     SING N N 8  
MDK C3    C4     DOUB N N 9  
MDK C3    C21    SING N N 10 
MDK C4    N4     SING N N 11 
MDK C4    C5     SING N N 12 
MDK N4    HN4    SING N N 13 
MDK N4    HN4A   SING N N 14 
MDK C5    C6     DOUB N N 15 
MDK C5    H5     SING N N 16 
MDK C6    H6     SING N N 17 
MDK "C1'" "C2'"  SING N N 18 
MDK "C1'" "O4'"  SING N N 19 
MDK "C1'" "H1'"  SING N N 20 
MDK "C2'" "C3'"  SING N N 21 
MDK "C2'" "H2'"  SING N N 22 
MDK "C2'" "H2'A" SING N N 23 
MDK C21   H21    SING N N 24 
MDK C21   H21A   SING N N 25 
MDK C21   H21B   SING N N 26 
MDK "C3'" "O3'"  SING N N 27 
MDK "C3'" "C4'"  SING N N 28 
MDK "C3'" "H3'"  SING N N 29 
MDK "O3'" "HO3'" SING N N 30 
MDK "C4'" "O4'"  SING N N 31 
MDK "C4'" "C5'"  SING N N 32 
MDK "C4'" "H4'"  SING N N 33 
MDK "C5'" "O5'"  SING N N 34 
MDK "C5'" "H5'"  SING N N 35 
MDK "C5'" "H5'A" SING N N 36 
MDK O7    P      SING N N 37 
MDK O2P   H16    SING N N 38 
MDK O7    H17    SING N N 39 
# 
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 
MDK SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)C(=C(N)C=C1)C)CC2O"                                                                                                  
MDK SMILES_CANONICAL CACTVS               3.370 "CC1=C(N)C=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C1=O"                                                                                   
MDK SMILES           CACTVS               3.370 "CC1=C(N)C=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C1=O"                                                                                       
MDK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=C(C=CN(C1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)N"                                                                                     
MDK SMILES           "OpenEye OEToolkits" 1.7.0 "CC1=C(C=CN(C1=O)C2CC(C(O2)COP(=O)(O)O)O)N"                                                                                                  
MDK InChI            InChI                1.03  "InChI=1S/C11H17N2O7P/c1-6-7(12)2-3-13(11(6)15)10-4-8(14)9(20-10)5-19-21(16,17)18/h2-3,8-10,14H,4-5,12H2,1H3,(H2,16,17,18)/t8-,9+,10+/m0/s1" 
MDK InChIKey         InChI                1.03  OHKFCCHWVFFUOJ-IVZWLZJFSA-N                                                                                                                  
# 
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 
MDK "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-methylpyridin-2(1H)-one"              
MDK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyridin-1-yl)-3-hydroxy-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 
MDK "Create component"  2010-07-23 RCSB 
MDK "Modify descriptor" 2011-06-04 RCSB 
# 
