data_L6M
#

_chem_comp.id                                   L6M
_chem_comp.name                                 "5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C30 H37 N5 O10"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-02-07
_chem_comp.pdbx_modified_date                   2020-02-07
_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                       627.642
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    L6M
_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       6NWN
_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
L6M  C13  C1   C  0  1  N  N  N   -5.079  -37.163  24.327   2.051  -3.096   0.306  C13  L6M   1  
L6M  C17  C2   C  0  1  N  N  R   -9.516  -37.642  25.064   6.393  -0.885  -0.273  C17  L6M   2  
L6M  C21  C3   C  0  1  N  N  N  -10.836  -38.116  23.292   8.149   0.803  -0.215  C21  L6M   3  
L6M  C22  C4   C  0  1  N  N  R  -11.748  -37.984  24.621   6.875   1.250  -0.966  C22  L6M   4  
L6M  C24  C5   C  0  1  N  N  N  -12.645  -35.635  24.595   6.669   3.563  -1.737  C24  L6M   5  
L6M  C26  C6   C  0  1  N  N  N  -14.222  -37.606  24.276   6.294   3.078   0.531  C26  L6M   6  
L6M  C28  C7   C  0  1  N  N  N  -15.173  -35.242  24.262   6.094   5.268  -0.177  C28  L6M   7  
L6M  C02  C8   C  0  1  N  N  N    1.623  -33.410  21.923  -5.748  -0.758  -0.867  C02  L6M   8  
L6M  C03  C9   C  0  1  N  N  R    1.613  -34.689  22.733  -4.606  -0.691  -1.849  C03  L6M   9  
L6M  C04  C10  C  0  1  N  N  S    0.254  -35.588  22.247  -3.693  -1.933  -1.703  C04  L6M  10  
L6M  C05  C11  C  0  1  N  N  N   -0.889  -34.866  22.948  -2.656  -1.717  -0.599  C05  L6M  11  
L6M  C06  C12  C  0  1  N  N  N   -1.438  -35.499  24.231  -1.865  -2.984  -0.398  C06  L6M  12  
L6M  C08  C13  C  0  1  N  N  S   -2.788  -37.161  25.436  -0.120  -4.260   0.726  C08  L6M  13  
L6M  C09  C14  C  0  1  N  N  N   -1.628  -37.947  26.029  -0.861  -5.172   1.669  C09  L6M  14  
L6M  C12  C15  C  0  1  N  N  N   -4.084  -37.993  25.247   1.249  -3.918   1.317  C12  L6M  15  
L6M  C14  C16  C  0  1  N  N  N   -6.465  -36.902  25.031   3.399  -2.759   0.889  C14  L6M  16  
L6M  C16  C17  C  0  1  N  N  N   -8.943  -36.365  24.812   5.592  -1.707   0.738  C16  L6M  17  
L6M  C19  C18  C  0  1  N  N  S   -9.651  -38.455  23.765   7.825  -0.634   0.251  C19  L6M  18  
L6M  C25  C19  C  0  1  N  N  N  -13.801  -34.706  24.481   6.417   4.871  -1.490  C25  L6M  19  
L6M  C33  C20  C  0  1  N  N  N    0.451  -36.803  22.693  -3.007  -2.018  -3.090  C33  L6M  20  
L6M  C34  C21  C  0  1  N  N  N    2.061  -36.914  22.848  -4.117  -1.620  -4.085  C34  L6M  21  
L6M  C35  C22  C  0  1  N  N  N    2.648  -35.481  22.479  -5.134  -0.777  -3.296  C35  L6M  22  
L6M  C36  C23  C  0  1  Y  N  N    2.413  -32.190  22.446  -6.462   0.471  -0.484  C36  L6M  23  
L6M  C37  C24  C  0  1  Y  N  N    3.123  -32.260  23.644  -7.521   0.413   0.427  C37  L6M  24  
L6M  C38  C25  C  0  1  Y  N  N    3.849  -31.162  24.102  -8.185   1.569   0.781  C38  L6M  25  
L6M  C39  C26  C  0  1  Y  N  N    3.854  -29.994  23.338  -7.806   2.783   0.236  C39  L6M  26  
L6M  C40  C27  C  0  1  N  N  N    4.672  -28.735  23.777  -8.537   4.042   0.629  C40  L6M  27  
L6M  C41  C28  C  0  1  N  N  N    4.338  -28.205  25.160  -7.869   4.657   1.831  C41  L6M  28  
L6M  C44  C29  C  0  1  Y  N  N    3.155  -29.942  22.142  -6.758   2.849  -0.666  C44  L6M  29  
L6M  C45  C30  C  0  1  Y  N  N    2.423  -31.035  21.688  -6.080   1.703  -1.025  C45  L6M  30  
L6M  N07  N1   N  0  1  N  N  N   -2.353  -36.684  24.165  -0.889  -3.029   0.531  N07  L6M  31  
L6M  N15  N2   N  0  1  N  N  N   -7.625  -36.599  24.184   4.281  -2.035   0.171  N15  L6M  32  
L6M  N23  N3   N  0  1  N  N  N  -12.857  -37.082  24.481   6.605   2.668  -0.712  N23  L6M  33  
L6M  N27  N4   N  0  1  N  N  N  -15.379  -36.670  24.160   6.043   4.360   0.789  N27  L6M  34  
L6M  N29  N5   N  0  1  N  N  N  -16.291  -34.352  24.152   5.833   6.590   0.102  N29  L6M  35  
L6M  O01  O1   O  0  1  N  N  N    1.053  -33.335  20.879  -6.078  -1.824  -0.393  O01  L6M  36  
L6M  O10  O2   O  0  1  N  N  N   -1.314  -37.762  27.244  -1.923  -4.828   2.132  O10  L6M  37  
L6M  O11  O3   O  0  1  N  N  N   -0.978  -38.734  25.283  -0.342  -6.365   1.997  O11  L6M  38  
L6M  O18  O4   O  0  1  N  N  N  -10.974  -37.502  25.567   5.818   0.431  -0.420  O18  L6M  39  
L6M  O20  O5   O  0  1  N  N  N   -9.607  -39.908  24.103   8.740  -1.567  -0.327  O20  L6M  40  
L6M  O30  O6   O  0  1  N  N  N  -14.399  -38.761  24.199   6.240   2.262   1.436  O30  L6M  41  
L6M  O31  O7   O  0  1  N  N  N   -6.555  -36.947  26.223   3.690  -3.139   2.003  O31  L6M  42  
L6M  O32  O8   O  0  1  N  N  N   -1.167  -35.060  25.306  -2.106  -3.963  -1.072  O32  L6M  43  
L6M  O42  O9   O  0  1  N  N  N    3.451  -27.331  25.238  -6.898   4.128   2.320  O42  L6M  44  
L6M  O43  O10  O  0  1  N  N  N    4.946  -28.632  26.164  -8.351   5.792   2.360  O43  L6M  45  
L6M  H1   H1   H  0  1  N  N  N   -4.615  -36.195  24.088   2.184  -3.674  -0.608  H1   L6M  46  
L6M  H2   H2   H  0  1  N  N  N   -5.254  -37.725  23.398   1.513  -2.175   0.078  H2   L6M  47  
L6M  H3   H3   H  0  1  N  N  N   -8.925  -38.210  25.798   6.426  -1.396  -1.236  H3   L6M  48  
L6M  H4   H4   H  0  1  N  N  N  -11.229  -38.894  22.621   9.007   0.802  -0.886  H4   L6M  49  
L6M  H5   H5   H  0  1  N  N  N  -10.785  -37.158  22.753   8.333   1.450   0.643  H5   L6M  50  
L6M  H6   H6   H  0  1  N  N  N  -12.116  -38.990  24.870   6.982   1.070  -2.036  H6   L6M  51  
L6M  H7   H7   H  0  1  N  N  N  -11.652  -35.245  24.761   6.915   3.234  -2.736  H7   L6M  52  
L6M  H8   H8   H  0  1  N  N  N    1.499  -34.458  23.802  -4.034   0.225  -1.706  H8   L6M  53  
L6M  H10  H10  H  0  1  N  N  N    0.155  -35.513  21.154  -4.284  -2.827  -1.507  H10  L6M  54  
L6M  H12  H12  H  0  1  N  N  N   -0.535  -33.856  23.203  -1.983  -0.910  -0.885  H12  L6M  55  
L6M  H13  H13  H  0  1  N  N  N   -1.722  -34.793  22.233  -3.164  -1.455   0.329  H13  L6M  56  
L6M  H14  H14  H  0  1  N  N  N   -3.015  -36.313  26.099   0.014  -4.761  -0.233  H14  L6M  57  
L6M  H15  H15  H  0  1  N  N  N   -4.551  -38.181  26.225   1.787  -4.838   1.545  H15  L6M  58  
L6M  H16  H16  H  0  1  N  N  N   -3.844  -38.952  24.765   1.115  -3.339   2.231  H16  L6M  59  
L6M  H17  H17  H  0  1  N  N  N   -9.588  -35.789  24.133   6.130  -2.628   0.966  H17  L6M  60  
L6M  H18  H18  H  0  1  N  N  N   -8.819  -35.814  25.756   5.458  -1.129   1.652  H18  L6M  61  
L6M  H19  H19  H  0  1  N  N  N   -8.827  -38.199  23.083   7.849  -0.698   1.339  H19  L6M  62  
L6M  H20  H20  H  0  1  N  N  N  -13.645  -33.640  24.557   6.463   5.598  -2.288  H20  L6M  63  
L6M  H21  H21  H  0  1  N  N  N   -0.045  -36.947  23.664  -2.175  -1.317  -3.147  H21  L6M  64  
L6M  H22  H22  H  0  1  N  N  N    0.076  -37.548  21.975  -2.666  -3.034  -3.285  H22  L6M  65  
L6M  H23  H23  H  0  1  N  N  N    2.326  -37.179  23.882  -3.695  -1.031  -4.899  H23  L6M  66  
L6M  H24  H24  H  0  1  N  N  N    2.458  -37.676  22.161  -4.600  -2.513  -4.482  H24  L6M  67  
L6M  H25  H25  H  0  1  N  N  N    2.941  -35.429  21.420  -6.110  -1.260  -3.310  H25  L6M  68  
L6M  H26  H26  H  0  1  N  N  N    3.511  -35.227  23.112  -5.205   0.222  -3.728  H26  L6M  69  
L6M  H27  H27  H  0  1  N  N  N    3.110  -33.172  24.222  -7.819  -0.534   0.852  H27  L6M  70  
L6M  H28  H28  H  0  1  N  N  N    4.398  -31.214  25.031  -9.003   1.526   1.484  H28  L6M  71  
L6M  H29  H29  H  0  1  N  N  N    5.740  -28.999  23.761  -8.514   4.749  -0.201  H29  L6M  72  
L6M  H30  H30  H  0  1  N  N  N    4.482  -27.933  23.049  -9.571   3.800   0.872  H30  L6M  73  
L6M  H31  H31  H  0  1  N  N  N    3.179  -29.038  21.552  -6.468   3.800  -1.086  H31  L6M  74  
L6M  H32  H32  H  0  1  N  N  N    1.873  -30.981  20.760  -5.260   1.756  -1.725  H32  L6M  75  
L6M  H33  H33  H  0  1  N  N  N   -2.635  -37.104  23.302  -0.696  -2.246   1.070  H33  L6M  76  
L6M  H34  H34  H  0  1  N  N  N   -7.525  -36.551  23.190   4.048  -1.731  -0.720  H34  L6M  77  
L6M  H35  H35  H  0  1  N  N  N  -17.210  -34.719  24.005   5.871   7.251  -0.607  H35  L6M  78  
L6M  H36  H36  H  0  1  N  N  N  -16.152  -33.364  24.222   5.611   6.860   1.007  H36  L6M  79  
L6M  H37  H37  H  0  1  N  N  N   -0.267  -39.125  25.777  -0.854  -6.915   2.605  H37  L6M  80  
L6M  H38  H38  H  0  1  N  N  N   -9.690  -40.421  23.308   9.654  -1.454  -0.032  H38  L6M  81  
L6M  H39  H39  H  0  1  N  N  N    4.623  -28.192  26.941  -7.890   6.149   3.131  H39  L6M  82  
#   #
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
L6M  C13  C12  SING  N  N   1  
L6M  C13  C14  SING  N  N   2  
L6M  C17  C16  SING  N  N   3  
L6M  C17  C19  SING  N  N   4  
L6M  C17  O18  SING  N  N   5  
L6M  C21  C22  SING  N  N   6  
L6M  C21  C19  SING  N  N   7  
L6M  C22  N23  SING  N  N   8  
L6M  C22  O18  SING  N  N   9  
L6M  C24  C25  DOUB  N  N  10  
L6M  C24  N23  SING  N  N  11  
L6M  C26  N23  SING  N  N  12  
L6M  C26  N27  SING  N  N  13  
L6M  C26  O30  DOUB  N  N  14  
L6M  C28  C25  SING  N  N  15  
L6M  C28  N27  DOUB  N  N  16  
L6M  C28  N29  SING  N  N  17  
L6M  C02  C03  SING  N  N  18  
L6M  C02  C36  SING  N  N  19  
L6M  C02  O01  DOUB  N  N  20  
L6M  C03  C35  SING  N  N  21  
L6M  C04  C05  SING  N  N  22  
L6M  C04  C33  SING  N  N  23  
L6M  C05  C06  SING  N  N  24  
L6M  C06  N07  SING  N  N  25  
L6M  C06  O32  DOUB  N  N  26  
L6M  C08  C09  SING  N  N  27  
L6M  C08  C12  SING  N  N  28  
L6M  C08  N07  SING  N  N  29  
L6M  C09  O10  DOUB  N  N  30  
L6M  C09  O11  SING  N  N  31  
L6M  C14  N15  SING  N  N  32  
L6M  C14  O31  DOUB  N  N  33  
L6M  C16  N15  SING  N  N  34  
L6M  C19  O20  SING  N  N  35  
L6M  C33  C34  SING  N  N  36  
L6M  C34  C35  SING  N  N  37  
L6M  C36  C37  DOUB  Y  N  38  
L6M  C36  C45  SING  Y  N  39  
L6M  C37  C38  SING  Y  N  40  
L6M  C38  C39  DOUB  Y  N  41  
L6M  C39  C40  SING  N  N  42  
L6M  C39  C44  SING  Y  N  43  
L6M  C40  C41  SING  N  N  44  
L6M  C41  O42  DOUB  N  N  45  
L6M  C41  O43  SING  N  N  46  
L6M  C44  C45  DOUB  Y  N  47  
L6M  C13  H1   SING  N  N  48  
L6M  C13  H2   SING  N  N  49  
L6M  C17  H3   SING  N  N  50  
L6M  C21  H4   SING  N  N  51  
L6M  C21  H5   SING  N  N  52  
L6M  C22  H6   SING  N  N  53  
L6M  C24  H7   SING  N  N  54  
L6M  C03  H8   SING  N  N  55  
L6M  C04  H10  SING  N  N  56  
L6M  C05  H12  SING  N  N  57  
L6M  C05  H13  SING  N  N  58  
L6M  C08  H14  SING  N  N  59  
L6M  C12  H15  SING  N  N  60  
L6M  C12  H16  SING  N  N  61  
L6M  C16  H17  SING  N  N  62  
L6M  C16  H18  SING  N  N  63  
L6M  C19  H19  SING  N  N  64  
L6M  C25  H20  SING  N  N  65  
L6M  C33  H21  SING  N  N  66  
L6M  C33  H22  SING  N  N  67  
L6M  C34  H23  SING  N  N  68  
L6M  C34  H24  SING  N  N  69  
L6M  C35  H25  SING  N  N  70  
L6M  C35  H26  SING  N  N  71  
L6M  C37  H27  SING  N  N  72  
L6M  C38  H28  SING  N  N  73  
L6M  C40  H29  SING  N  N  74  
L6M  C40  H30  SING  N  N  75  
L6M  C44  H31  SING  N  N  76  
L6M  C45  H32  SING  N  N  77  
L6M  N07  H33  SING  N  N  78  
L6M  N15  H34  SING  N  N  79  
L6M  N29  H35  SING  N  N  80  
L6M  N29  H36  SING  N  N  81  
L6M  O11  H37  SING  N  N  82  
L6M  O20  H38  SING  N  N  83  
L6M  O43  H39  SING  N  N  84  
L6M  C03  C04  SING  N  N  85  
#   #
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
L6M  SMILES            ACDLabs               12.01  "C(CC(C(=O)O)NC(CC2C(C(c1ccc(CC(=O)O)cc1)=O)CCC2)=O)C(NCC4C(CC(N3C=CC(=NC3=O)N)O4)O)=O"  
L6M  InChI             InChI                 1.03   "InChI=1S/C30H37N5O10/c31-23-10-11-35(30(44)34-23)26-14-21(36)22(45-26)15-32-24(37)9-8-20(29(42)43)33-25(38)13-18-2-1-3-19(18)28(41)17-6-4-16(5-7-17)12-27(39)40/h4-7,10-11,18-22,26,36H,1-3,8-9,12-15H2,(H,32,37)(H,33,38)(H,39,40)(H,42,43)(H2,31,34,44)/t18-,19+,20-,21-,22+,26+/m0/s1"  
L6M  InChIKey          InChI                 1.03   JVRVDICAIPFWFZ-BONAQRLYSA-N  
L6M  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CNC(=O)CC[C@H](NC(=O)C[C@@H]3CCC[C@H]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2"  
L6M  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CNC(=O)CC[CH](NC(=O)C[CH]3CCC[CH]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2"  
L6M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)N[C@@H](CCC(=O)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=NC4=O)N)O)C(=O)O"  
L6M  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)NC(CCC(=O)NCC3C(CC(O3)N4C=CC(=NC4=O)N)O)C(=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
L6M  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine"  
L6M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-5-[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methylamino]-2-[2-[2-[4-(2-hydroxy-2-oxoethyl)phenyl]carbonylcyclopentyl]ethanoylamino]-5-oxidanylidene-pentanoic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L6M  "Create component"     2019-02-07  RCSB  
L6M  "Modify linking type"  2019-02-08  RCSB  
L6M  "Initial release"      2020-02-12  RCSB  
##
