data_12A
# 
_chem_comp.id                                    12A 
_chem_comp.name                                  "2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H23 N6 O11 P S" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-08-09 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        538.426 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     12A 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1FIR 
_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 
12A OP3    O3P  O 0 1 N Y N 17.331 20.018 -1.562 -2.878 1.720  -7.838 OP3    12A 1  
12A P      P    P 0 1 N N N 17.138 21.317 -0.657 -2.012 0.414  -7.469 P      12A 2  
12A OP1    O1P  O 0 1 N N N 17.941 22.427 -1.245 -2.916 -0.662 -7.007 OP1    12A 3  
12A OP2    O2P  O 0 1 N N N 15.687 21.501 -0.408 -1.208 -0.082 -8.773 OP2    12A 4  
12A "O5'"  O5*  O 0 1 N N N 17.832 20.896 0.707  -0.967 0.776  -6.300 "O5'"  12A 5  
12A "C5'"  C5*  C 0 1 N N N 18.260 21.879 1.610  -0.232 -0.416 -6.019 "C5'"  12A 6  
12A "C4'"  C4*  C 0 1 N N R 18.565 21.264 2.941  0.783  -0.140 -4.909 "C4'"  12A 7  
12A "O4'"  O4*  O 0 1 N N N 19.647 20.316 2.805  0.108  0.259  -3.697 "O4'"  12A 8  
12A "C3'"  C3*  C 0 1 N N S 19.021 22.296 3.958  1.537  -1.435 -4.533 "C3'"  12A 9  
12A "O3'"  O3*  O 0 1 N N N 17.874 22.660 4.714  2.805  -1.485 -5.189 "O3'"  12A 10 
12A "C2'"  C2*  C 0 1 N N R 20.040 21.524 4.782  1.723  -1.330 -3.001 "C2'"  12A 11 
12A "O2'"  O2*  O 0 1 N N N 19.452 20.704 5.771  3.112  -1.315 -2.665 "O2'"  12A 12 
12A "C1'"  C1*  C 0 1 N N R 20.674 20.651 3.703  1.056  0.014  -2.635 "C1'"  12A 13 
12A N9     N9   N 0 1 Y N N 21.642 21.390 2.921  0.364  -0.093 -1.348 N9     12A 14 
12A C8     C8   C 0 1 Y N N 21.521 21.717 1.604  -0.925 -0.494 -1.156 C8     12A 15 
12A N7     N7   N 0 1 Y N N 22.538 22.383 1.132  -1.214 -0.471 0.111  N7     12A 16 
12A C5     C5   C 0 1 Y N N 23.384 22.501 2.218  -0.131 -0.056 0.813  C5     12A 17 
12A C6     C6   C 0 1 Y N N 24.620 23.092 2.364  0.138  0.155  2.175  C6     12A 18 
12A N6     N6   N 0 1 N N N 25.272 23.674 1.383  -0.838 -0.072 3.135  N6     12A 19 
12A N1     N1   N 0 1 Y N N 25.197 23.048 3.574  1.346  0.579  2.525  N1     12A 20 
12A C2     C2   C 0 1 Y N N 24.562 22.419 4.563  2.286  0.801  1.615  C2     12A 21 
12A N3     N3   N 0 1 Y N N 23.384 21.820 4.549  2.073  0.619  0.321  N3     12A 22 
12A C4     C4   C 0 1 Y N N 22.842 21.897 3.328  0.894  0.191  -0.115 C4     12A 23 
12A S2     S2   S 0 1 N N N 25.169 22.353 5.752  3.870  1.363  2.145  S2     12A 24 
12A C2M    C2M  C 0 1 N N N 26.447 23.647 5.613  3.594  1.437  3.933  C2M    12A 25 
12A CC     CC   C 0 1 N N N 26.582 23.549 1.361  -0.564 0.135  4.438  CC     12A 26 
12A OO     OO   O 0 1 N N N 27.160 22.913 2.239  0.538  0.523  4.773  OO     12A 27 
12A N      N    N 0 1 N N N 27.248 24.126 0.375  -1.512 -0.086 5.370  N      12A 28 
12A CA     CA   C 0 1 N N S 28.700 24.021 0.300  -1.214 0.140  6.786  CA     12A 29 
12A C      C    C 0 1 N N N 29.332 23.725 1.677  -0.676 -1.128 7.396  C      12A 30 
12A O      O    O 0 1 N N N 29.722 22.549 1.886  0.107  -1.072 8.314  O      12A 31 
12A OXT    OXT  O 0 1 N N N 29.398 24.640 2.534  -1.066 -2.320 6.918  OXT    12A 32 
12A CB     CB   C 0 1 N N R 29.307 25.315 -0.332 -2.493 0.553  7.517  CB     12A 33 
12A OG1    OG1  O 0 1 N N N 30.688 25.432 0.037  -3.468 -0.483 7.395  OG1    12A 34 
12A CG2    CG2  C 0 1 N N N 28.515 26.563 0.099  -3.040 1.842  6.898  CG2    12A 35 
12A HOP3   3HOP H 0 0 N N N 16.819 19.310 -1.187 -3.490 1.461  -8.541 HOP3   12A 36 
12A HOP2   2HOP H 0 0 N N N 15.572 22.274 0.131  -0.632 0.647  -9.041 HOP2   12A 37 
12A "H5'"  1H5* H 0 1 N N N 19.124 22.460 1.212  0.290  -0.742 -6.918 "H5'"  12A 38 
12A "H5''" 2H5* H 0 0 N N N 17.525 22.713 1.695  -0.919 -1.198 -5.695 "H5''" 12A 39 
12A "H4'"  H4*  H 0 1 N N N 17.623 20.780 3.290  1.487  0.630  -5.224 "H4'"  12A 40 
12A "H3'"  H3*  H 0 1 N N N 19.462 23.235 3.550  0.941  -2.311 -4.787 "H3'"  12A 41 
12A "HO3'" H3T  H 0 0 N Y N 18.159 23.305 5.350  3.228  -2.311 -4.918 "HO3'" 12A 42 
12A "H2'"  H2*  H 0 1 N N N 20.732 22.189 5.348  1.219  -2.155 -2.497 "H2'"  12A 43 
12A "HO2'" 2HO* H 0 0 N N N 20.088 20.221 6.285  3.483  -2.153 -2.972 "HO2'" 12A 44 
12A "H1'"  H1*  H 0 1 N N N 21.167 19.778 4.191  1.800  0.809  -2.599 "H1'"  12A 45 
12A H8     H8   H 0 1 N N N 20.659 21.460 0.964  -1.606 -0.787 -1.942 H8     12A 46 
12A HN6    HN6  H 0 1 N N N 25.028 24.664 1.358  -1.718 -0.382 2.868  HN6    12A 47 
12A H2M1   1H2M H 0 0 N N N 26.953 23.591 6.604  4.504  1.778  4.427  H2M1   12A 48 
12A H2M2   2H2M H 0 0 N N N 27.124 23.544 4.733  2.782  2.133  4.147  H2M2   12A 49 
12A H2M3   3H2M H 0 0 N N N 26.063 24.657 5.337  3.329  0.446  4.301  H2M3   12A 50 
12A H      H    H 0 1 N N N 26.668 24.629 -0.296 -2.392 -0.395 5.103  H      12A 51 
12A HA     HA   H 0 1 N N N 28.942 23.154 -0.359 -0.471 0.931  6.879  HA     12A 52 
12A HXT    HXT  H 0 1 N N N 29.786 24.457 3.381  -0.721 -3.134 7.309  HXT    12A 53 
12A HB     HB   H 0 1 N N N 29.236 25.239 -1.442 -2.272 0.722  8.571  HB     12A 54 
12A HG1    HG1  H 0 1 N N N 31.057 26.218 -0.347 -3.635 -0.600 6.450  HG1    12A 55 
12A HG21   1HG2 H 0 0 N N N 28.948 27.486 -0.351 -3.951 2.136  7.419  HG21   12A 56 
12A HG22   2HG2 H 0 0 N N N 27.429 26.461 -0.133 -2.296 2.633  6.991  HG22   12A 57 
12A HG23   3HG2 H 0 0 N N N 28.443 26.641 1.208  -3.262 1.673  5.845  HG23   12A 58 
# 
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 
12A OP3   P      SING N N 1  
12A OP3   HOP3   SING N N 2  
12A P     OP1    DOUB N N 3  
12A P     OP2    SING N N 4  
12A P     "O5'"  SING N N 5  
12A OP2   HOP2   SING N N 6  
12A "O5'" "C5'"  SING N N 7  
12A "C5'" "C4'"  SING N N 8  
12A "C5'" "H5'"  SING N N 9  
12A "C5'" "H5''" SING N N 10 
12A "C4'" "O4'"  SING N N 11 
12A "C4'" "C3'"  SING N N 12 
12A "C4'" "H4'"  SING N N 13 
12A "O4'" "C1'"  SING N N 14 
12A "C3'" "O3'"  SING N N 15 
12A "C3'" "C2'"  SING N N 16 
12A "C3'" "H3'"  SING N N 17 
12A "O3'" "HO3'" SING N N 18 
12A "C2'" "O2'"  SING N N 19 
12A "C2'" "C1'"  SING N N 20 
12A "C2'" "H2'"  SING N N 21 
12A "O2'" "HO2'" SING N N 22 
12A "C1'" N9     SING N N 23 
12A "C1'" "H1'"  SING N N 24 
12A N9    C8     SING Y N 25 
12A N9    C4     SING Y N 26 
12A C8    N7     DOUB Y N 27 
12A C8    H8     SING N N 28 
12A N7    C5     SING Y N 29 
12A C5    C6     SING Y N 30 
12A C5    C4     DOUB Y N 31 
12A C6    N6     SING N N 32 
12A C6    N1     DOUB Y N 33 
12A N6    CC     SING N N 34 
12A N6    HN6    SING N N 35 
12A N1    C2     SING Y N 36 
12A C2    N3     DOUB Y N 37 
12A C2    S2     SING N N 38 
12A N3    C4     SING Y N 39 
12A S2    C2M    SING N N 40 
12A C2M   H2M1   SING N N 41 
12A C2M   H2M2   SING N N 42 
12A C2M   H2M3   SING N N 43 
12A CC    OO     DOUB N N 44 
12A CC    N      SING N N 45 
12A N     CA     SING N N 46 
12A N     H      SING N N 47 
12A CA    C      SING N N 48 
12A CA    CB     SING N N 49 
12A CA    HA     SING N N 50 
12A C     O      DOUB N N 51 
12A C     OXT    SING N N 52 
12A OXT   HXT    SING N N 53 
12A CB    OG1    SING N N 54 
12A CB    CG2    SING N N 55 
12A CB    HB     SING N N 56 
12A OG1   HG1    SING N N 57 
12A CG2   HG21   SING N N 58 
12A CG2   HG22   SING N N 59 
12A CG2   HG23   SING N N 60 
# 
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 
12A SMILES           ACDLabs              10.04 "O=C(O)C(NC(=O)Nc3nc(SC)nc1c3ncn1C2OC(C(O)C2O)COP(=O)(O)O)C(O)C" 
12A InChI            InChI                1.02b 
"InChI=1/C16H23N6O11PS/c1-5(23)7(14(26)27)18-15(28)19-11-8-12(21-16(20-11)35-2)22(4-17-8)13-10(25)9(24)6(33-13)3-32-34(29,30)31/h4-7,9-10,13,23-25H,3H2,1-2H3,(H,26,27)(H2,29,30,31)(H2,18,19,20,21,28)/t5-,6-,7+,9-,10-,13-/m1/s1/f/h18-19,26,29-30H" 
12A InChIKey         InChI                1.02b CVAJCPGRFVTHBT-UWVNBYKYDP 
12A SMILES_CANONICAL CACTVS               3.341 "CSc1nc(NC(=O)N[C@@H]([C@@H](C)O)C(O)=O)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1" 
12A SMILES           CACTVS               3.341 "CSc1nc(NC(=O)N[CH]([CH](C)O)C(O)=O)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c2n1" 
12A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]([C@@H](C(=O)O)NC(=O)Nc1c2c(nc(n1)SC)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)O" 
12A SMILES           "OpenEye OEToolkits" 1.5.0 "CC(C(C(=O)O)NC(=O)Nc1c2c(nc(n1)SC)n(cn2)C3C(C(C(O3)COP(=O)(O)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 
12A "SYSTEMATIC NAME" ACDLabs              10.04 "(2S,3R)-2-({[9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2-(methylsulfanyl)-9H-purin-6-yl]carbamoyl}amino)-3-hydroxybutanoic acid (non-preferred name)" 
12A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R)-2-[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-methylsulfanyl-purin-6-yl]carbamoylamino]-3-hydroxy-butanoic acid"                                       
# 
