data_AKM
#

_chem_comp.id                                   AKM
_chem_comp.name                                 "[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H29 N3 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-04-29
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       561.371
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    AKM
_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       4KCF
_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
AKM  O2P    O2P  O  0  1  N  N  N  18.197  21.532  -15.712  -0.380   1.543   2.171  O2P  AKM   1  
AKM  P      P    P  0  1  N  N  N  19.384  22.392  -16.156  -0.140   2.007   0.648  P    AKM   2  
AKM  O1P    O1P  O  0  1  N  N  N  20.763  21.992  -15.719   0.109   3.466   0.610  O1P  AKM   3  
AKM  OPP    OPP  O  0  1  N  N  N  19.438  22.426  -17.749   1.133   1.229   0.044  OPP  AKM   4  
AKM  P2     P2   P  0  1  N  N  N  18.238  22.566  -18.799   2.725   1.368   0.241  P2   AKM   5  
AKM  O3P    O3P  O  0  1  N  N  N  18.939  23.008  -20.077   3.033   1.513   1.681  O3P  AKM   6  
AKM  O1     O1   O  0  1  N  N  N  17.741  21.066  -19.038   3.453   0.052  -0.334  O1   AKM   7  
AKM  C1     C1   C  0  1  N  N  R  16.524  20.523  -18.557   4.863  -0.176  -0.212  C1   AKM   8  
AKM  C2     C2   C  0  1  N  N  N  16.577  18.986  -18.599   5.337  -1.019  -1.396  C2   AKM   9  
AKM  C3     C3   C  0  1  N  N  S  15.169  18.406  -18.468   6.829  -1.313  -1.270  C3   AKM  10  
AKM  C3M    C3M  C  0  1  N  N  N  14.914  18.506  -16.960   7.643  -0.050  -1.562  C3M  AKM  11  
AKM  N3     N3   N  0  1  N  N  N  15.139  16.990  -18.862   7.184  -2.323  -2.294  N3   AKM  12  
AKM  C4     C4   C  0  1  N  N  N  14.140  19.078  -19.390   7.183  -1.882   0.098  C4   AKM  13  
AKM  O4A    O4A  O  0  1  N  N  N  14.162  18.493  -20.703   6.865  -3.285   0.109  O4A  AKM  14  
AKM  O4B    O4B  O  0  1  N  N  N  12.810  18.810  -18.911   8.604  -1.758   0.292  O4B  AKM  15  
AKM  C5     C5   C  0  1  N  N  R  14.435  20.493  -19.890   6.473  -1.210   1.262  C5   AKM  16  
AKM  C6     C6   C  0  1  N  N  N  13.307  21.495  -20.102   7.237   0.027   1.736  C6   AKM  17  
AKM  O5     O5   O  0  1  N  N  N  15.604  21.167  -19.429   5.119  -0.893   0.991  O5   AKM  18  
AKM  O4P    O4P  O  0  1  N  N  N  17.045  23.404  -18.368   3.253   2.664  -0.555  O4P  AKM  19  
AKM  "O5'"  O5*  O  0  1  N  N  N  19.091  23.883  -15.632  -1.446   1.663  -0.229  O5*  AKM  20  
AKM  "C5'"  C5*  C  0  1  N  N  N  20.100  24.857  -15.892  -2.716   2.280  -0.010  C5*  AKM  21  
AKM  "C4'"  C4*  C  0  1  N  N  R  19.304  26.139  -16.062  -3.731   1.727  -1.013  C4*  AKM  22  
AKM  "C3'"  C3*  C  0  1  N  N  S  20.154  27.339  -16.494  -5.117   2.389  -0.807  C3*  AKM  23  
AKM  "O3'"  O3*  O  0  1  N  N  N  19.998  27.496  -17.897  -5.211   3.614  -1.537  O3*  AKM  24  
AKM  "C2'"  C2*  C  0  1  N  N  N  19.551  28.542  -15.789  -6.076   1.323  -1.391  C2*  AKM  25  
AKM  "C1'"  C1*  C  0  1  N  N  R  18.564  27.963  -14.773  -5.256   0.019  -1.356  C1*  AKM  26  
AKM  "O4'"  O4*  O  0  1  N  N  N  18.749  26.532  -14.804  -3.985   0.328  -0.761  O4*  AKM  27  
AKM  N11    N11  N  0  1  N  N  N  18.688  28.433  -13.387  -5.953  -0.986  -0.550  N11  AKM  28  
AKM  C21    C21  C  0  1  N  N  N  17.620  28.957  -12.796  -6.126  -0.780   0.768  C21  AKM  29  
AKM  O21    O21  O  0  1  N  N  N  16.473  29.112  -13.502  -5.702   0.241   1.276  O21  AKM  30  
AKM  N31    N31  N  0  1  N  N  N  17.628  29.398  -11.527  -6.762  -1.686   1.533  N31  AKM  31  
AKM  C41    C41  C  0  1  N  N  N  18.760  29.262  -10.813  -7.239  -2.823   0.986  C41  AKM  32  
AKM  O41    O41  O  0  1  N  N  N  18.831  29.666   -9.523  -7.815  -3.643   1.677  O41  AKM  33  
AKM  C51    C51  C  0  1  N  N  N  19.957  28.644  -11.411  -7.063  -3.053  -0.400  C51  AKM  34  
AKM  C5A    C5A  C  0  1  N  N  N  21.207  28.485  -10.592  -7.585  -4.315  -1.037  C5A  AKM  35  
AKM  C61    C61  C  0  1  N  N  N  19.853  28.250  -12.734  -6.426  -2.124  -1.145  C61  AKM  36  
AKM  H1     H1   H  0  1  N  N  N  18.510  20.809  -15.182  -0.549   0.596   2.272  H1   AKM  37  
AKM  H2     H2   H  0  1  N  N  N  16.349  20.840  -17.518   5.373   0.784  -0.203  H2   AKM  38  
AKM  H3     H3   H  0  1  N  N  N  17.015  18.663  -19.555   4.779  -1.957  -1.418  H3   AKM  39  
AKM  H4     H4   H  0  1  N  N  N  17.199  18.621  -17.769   5.149  -0.475  -2.325  H4   AKM  40  
AKM  H5     H5   H  0  1  N  N  N  15.718  17.988  -16.417   7.371   0.730  -0.851  H5   AKM  41  
AKM  H6     H6   H  0  1  N  N  N  14.893  19.564  -16.661   8.706  -0.272  -1.469  H6   AKM  42  
AKM  H7     H7   H  0  1  N  N  N  13.948  18.038  -16.720   7.431   0.292  -2.575  H7   AKM  43  
AKM  H8     H8   H  0  1  N  N  N  15.789  16.474  -18.303   6.986  -1.982  -3.223  H8   AKM  44  
AKM  H9     H9   H  0  1  N  N  N  14.218  16.625  -18.724   8.151  -2.600  -2.210  H9   AKM  45  
AKM  H11    H11  H  0  1  N  N  N  13.993  17.561  -20.638   7.099  -3.734   0.933  H11  AKM  46  
AKM  H12    H12  H  0  1  N  N  N  12.710  19.168  -18.037   8.916  -2.098   1.142  H12  AKM  47  
AKM  H13    H13  H  0  1  N  N  N  14.710  20.281  -20.934   6.476  -1.929   2.109  H13  AKM  48  
AKM  H14    H14  H  0  1  N  N  N  12.409  20.968  -20.457   6.778   0.411   2.647  H14  AKM  49  
AKM  H15    H15  H  0  1  N  N  N  13.083  22.001  -19.151   8.274  -0.241   1.937  H15  AKM  50  
AKM  H16    H16  H  0  1  N  N  N  13.615  22.240  -20.850   7.204   0.794   0.961  H16  AKM  51  
AKM  H17    H17  H  0  1  N  N  N  16.911  24.109  -18.990   3.085   2.637  -1.506  H17  AKM  52  
AKM  H18    H18  H  0  1  N  N  N  20.657  24.614  -16.809  -3.054   2.066   1.004  H18  AKM  53  
AKM  H19    H19  H  0  1  N  N  N  20.800  24.936  -15.047  -2.624   3.358  -0.143  H19  AKM  54  
AKM  H20    H20  H  0  1  N  N  N  18.507  25.977  -16.802  -3.380   1.875  -2.034  H20  AKM  55  
AKM  H21    H21  H  0  1  N  N  N  21.205  27.198  -16.201  -5.317   2.553   0.252  H21  AKM  56  
AKM  H22    H22  H  0  1  N  N  N  20.516  28.235  -18.193  -6.060   4.066  -1.440  H22  AKM  57  
AKM  H23    H23  H  0  1  N  N  N  20.334  29.121  -15.278  -6.967   1.230  -0.770  H23  AKM  58  
AKM  H24    H24  H  0  1  N  N  N  19.028  29.188  -16.509  -6.348   1.575  -2.416  H24  AKM  59  
AKM  H25    H25  H  0  1  N  N  N  17.549  28.195  -15.127  -5.111  -0.355  -2.370  H25  AKM  60  
AKM  H26    H26  H  0  1  N  N  N  16.814  29.816  -11.124  -6.879  -1.521   2.482  H26  AKM  61  
AKM  H27    H27  H  0  1  N  N  N  21.033  28.873   -9.578  -8.069  -4.931  -0.278  H27  AKM  62  
AKM  H28    H28  H  0  1  N  N  N  21.475  27.420  -10.536  -8.308  -4.059  -1.812  H28  AKM  63  
AKM  H29    H29  H  0  1  N  N  N  22.028  29.045  -11.063  -6.757  -4.868  -1.480  H29  AKM  64  
AKM  H30    H30  H  0  1  N  N  N  20.696  27.801  -13.238  -6.286  -2.280  -2.204  H30  AKM  65  
#   #
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
AKM  O4A    C4     SING  N  N   1  
AKM  C6     C5     SING  N  N   2  
AKM  O3P    P2     DOUB  N  N   3  
AKM  C5     O5     SING  N  N   4  
AKM  C5     C4     SING  N  N   5  
AKM  O5     C1     SING  N  N   6  
AKM  C4     O4B    SING  N  N   7  
AKM  C4     C3     SING  N  N   8  
AKM  O1     P2     SING  N  N   9  
AKM  O1     C1     SING  N  N  10  
AKM  N3     C3     SING  N  N  11  
AKM  P2     O4P    SING  N  N  12  
AKM  P2     OPP    SING  N  N  13  
AKM  C2     C1     SING  N  N  14  
AKM  C2     C3     SING  N  N  15  
AKM  C3     C3M    SING  N  N  16  
AKM  "O3'"  "C3'"  SING  N  N  17  
AKM  OPP    P      SING  N  N  18  
AKM  "C3'"  "C4'"  SING  N  N  19  
AKM  "C3'"  "C2'"  SING  N  N  20  
AKM  P      O1P    DOUB  N  N  21  
AKM  P      O2P    SING  N  N  22  
AKM  P      "O5'"  SING  N  N  23  
AKM  "C4'"  "C5'"  SING  N  N  24  
AKM  "C4'"  "O4'"  SING  N  N  25  
AKM  "C5'"  "O5'"  SING  N  N  26  
AKM  "C2'"  "C1'"  SING  N  N  27  
AKM  "O4'"  "C1'"  SING  N  N  28  
AKM  "C1'"  N11    SING  N  N  29  
AKM  O21    C21    DOUB  N  N  30  
AKM  N11    C21    SING  N  N  31  
AKM  N11    C61    SING  N  N  32  
AKM  C21    N31    SING  N  N  33  
AKM  C61    C51    DOUB  N  N  34  
AKM  N31    C41    SING  N  N  35  
AKM  C51    C41    SING  N  N  36  
AKM  C51    C5A    SING  N  N  37  
AKM  C41    O41    DOUB  N  N  38  
AKM  O2P    H1     SING  N  N  39  
AKM  C1     H2     SING  N  N  40  
AKM  C2     H3     SING  N  N  41  
AKM  C2     H4     SING  N  N  42  
AKM  C3M    H5     SING  N  N  43  
AKM  C3M    H6     SING  N  N  44  
AKM  C3M    H7     SING  N  N  45  
AKM  N3     H8     SING  N  N  46  
AKM  N3     H9     SING  N  N  47  
AKM  O4A    H11    SING  N  N  48  
AKM  O4B    H12    SING  N  N  49  
AKM  C5     H13    SING  N  N  50  
AKM  C6     H14    SING  N  N  51  
AKM  C6     H15    SING  N  N  52  
AKM  C6     H16    SING  N  N  53  
AKM  O4P    H17    SING  N  N  54  
AKM  "C5'"  H18    SING  N  N  55  
AKM  "C5'"  H19    SING  N  N  56  
AKM  "C4'"  H20    SING  N  N  57  
AKM  "C3'"  H21    SING  N  N  58  
AKM  "O3'"  H22    SING  N  N  59  
AKM  "C2'"  H23    SING  N  N  60  
AKM  "C2'"  H24    SING  N  N  61  
AKM  "C1'"  H25    SING  N  N  62  
AKM  N31    H26    SING  N  N  63  
AKM  C5A    H27    SING  N  N  64  
AKM  C5A    H28    SING  N  N  65  
AKM  C5A    H29    SING  N  N  66  
AKM  C61    H30    SING  N  N  67  
#   #
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
AKM  SMILES            ACDLabs               12.01  "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)(O)C(N)(C3)C)C)O)O)C"  
AKM  InChI             InChI                 1.03   "InChI=1S/C17H29N3O14P2/c1-8-6-20(15(23)19-14(8)22)12-4-10(21)11(32-12)7-30-35(26,27)34-36(28,29)33-13-5-16(3,18)17(24,25)9(2)31-13/h6,9-13,21,24-25H,4-5,7,18H2,1-3H3,(H,26,27)(H,28,29)(H,19,22,23)/t9-,10+,11-,12-,13-,16+/m1/s1"  
AKM  InChIKey          InChI                 1.03   GACNZVKWDHTCBB-HHMBNNFFSA-N  
AKM  SMILES_CANONICAL  CACTVS                3.370  "C[C@H]1O[C@@H](C[C@](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O"  
AKM  SMILES            CACTVS                3.370  "C[CH]1O[CH](C[C](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O"  
AKM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@@H]1C([C@@](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(O)O"  
AKM  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(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
AKM  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,4S,6R)-4-amino-5,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
AKM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen 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
AKM  "Create component"    2013-04-29  RCSB  
AKM  "Other modification"  2013-05-23  RCSB  
AKM  "Modify synonyms"     2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     AKM
_pdbx_chem_comp_synonyms.name        "dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
