data_YQP
#

_chem_comp.id                                   YQP
_chem_comp.name                                 "(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]butanoic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H21 N3 O7 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-23
_chem_comp.pdbx_modified_date                   2022-02-25
_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                       375.397
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YQP
_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       7LNH
_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
YQP  N    N1   N  0  1  N  N  N  8.133  -58.580  29.945   6.213   0.667   0.997  N    YQP   1  
YQP  CA   C1   C  0  1  N  N  S  6.709  -58.335  30.082   5.650  -0.647   0.658  CA   YQP   2  
YQP  C    C2   C  0  1  N  N  N  5.953  -59.652  30.171   6.685  -1.462  -0.075  C    YQP   3  
YQP  O    O1   O  0  1  N  N  N  4.882  -59.720  30.825   6.568  -2.798  -0.135  O    YQP   4  
YQP  CB   C3   C  0  1  N  N  N  6.183  -57.501  28.884   4.421  -0.461  -0.233  CB   YQP   5  
YQP  CG   C4   C  0  1  N  N  N  7.389  -56.846  28.109   3.324   0.257   0.554  CG   YQP   6  
YQP  SD   S1   S  0  1  N  N  N  6.878  -56.558  26.389   1.866   0.477  -0.502  SD   YQP   7  
YQP  CE   C5   C  0  1  N  N  N  8.285  -56.799  25.312   2.311   1.598  -1.482  CE   YQP   8  
YQP  OXT  O2   O  0  1  N  N  N  6.395  -60.667  29.586   7.619  -0.912  -0.610  OXT  YQP   9  
YQP  CAH  C6   C  0  1  N  N  N  6.257  -54.833  26.210   0.696   1.332   0.589  CAH  YQP  10  
YQP  CAK  C7   C  0  1  N  N  S  5.711  -54.648  24.842  -0.608   1.595  -0.167  CAK  YQP  11  
YQP  CAM  C8   C  0  1  N  N  R  4.410  -55.666  23.155  -2.681   0.734  -0.651  CAM  YQP  12  
YQP  CAN  C9   C  0  1  N  N  R  3.753  -54.455  23.659  -2.969   1.852   0.376  CAN  YQP  13  
YQP  CAO  C10  C  0  1  N  N  S  4.343  -54.127  24.911  -1.574   2.431   0.701  CAO  YQP  14  
YQP  CAS  C11  C  0  1  N  N  N  3.449  -57.425  21.801  -4.493  -0.745  -1.380  CAS  YQP  15  
YQP  CAT  C12  C  0  1  N  N  N  2.732  -57.216  24.117  -3.478  -1.112   0.716  CAT  YQP  16  
YQP  CAV  C13  C  0  1  N  N  N  2.589  -58.523  21.629  -5.311  -1.800  -1.175  CAV  YQP  17  
YQP  CAW  C14  C  0  1  N  N  N  1.778  -58.983  22.720  -5.197  -2.537   0.028  CAW  YQP  18  
YQP  NAR  N2   N  0  1  N  N  N  3.526  -56.762  23.046  -3.572  -0.407  -0.426  NAR  YQP  19  
YQP  NAU  N3   N  0  1  N  N  N  1.844  -58.352  23.928  -4.276  -2.171   0.943  NAU  YQP  20  
YQP  OAL  O3   O  0  1  N  N  N  5.620  -56.005  24.093  -1.308   0.355  -0.408  OAL  YQP  21  
YQP  OAP  O4   O  0  1  N  N  N  4.360  -52.666  25.095  -1.507   3.811   0.337  OAP  YQP  22  
YQP  OAQ  O5   O  0  1  N  N  N  3.991  -53.340  22.699  -3.806   2.857  -0.200  OAQ  YQP  23  
YQP  OAX  O6   O  0  1  N  N  N  0.922  -60.083  22.532  -5.923  -3.492   0.235  OAX  YQP  24  
YQP  OAY  O7   O  0  1  N  N  N  2.771  -56.596  25.373  -2.652  -0.794   1.550  OAY  YQP  25  
YQP  H1   H1   H  0  1  N  N  N  8.456  -59.118  30.724   6.489   1.168   0.166  H1   YQP  26  
YQP  H2   H2   H  0  1  N  N  N  8.305  -59.084  29.098   5.561   1.208   1.546  H2   YQP  27  
YQP  H4   H4   H  0  1  N  N  N  6.524  -57.764  31.004   5.361  -1.166   1.572  H4   YQP  28  
YQP  H5   H5   H  0  1  N  N  N  4.536  -60.603  30.776   7.256  -3.277  -0.617  H5   YQP  29  
YQP  H6   H6   H  0  1  N  N  N  5.517  -56.709  29.257   4.691   0.134  -1.105  H6   YQP  30  
YQP  H7   H7   H  0  1  N  N  N  5.625  -58.158  28.200   4.057  -1.436  -0.557  H7   YQP  31  
YQP  H8   H8   H  0  1  N  N  N  8.256  -57.523  28.131   3.053  -0.338   1.427  H8   YQP  32  
YQP  H9   H9   H  0  1  N  N  N  7.659  -55.890  28.581   3.688   1.232   0.879  H9   YQP  33  
YQP  H10  H10  H  0  1  N  N  N  9.243  -57.072  25.728   1.633   1.948  -2.246  H10  YQP  34  
YQP  H11  H11  H  0  1  N  N  N  8.177  -56.671  24.245   3.299   2.026  -1.400  H11  YQP  35  
YQP  H13  H13  H  0  1  N  N  N  7.083  -54.126  26.375   0.491   0.709   1.461  H13  YQP  36  
YQP  H14  H14  H  0  1  N  N  N  5.464  -54.649  26.950   1.126   2.279   0.912  H14  YQP  37  
YQP  H15  H15  H  0  1  N  N  N  6.353  -53.962  24.269  -0.404   2.106  -1.108  H15  YQP  38  
YQP  H16  H16  H  0  1  N  N  N  4.826  -55.443  22.161  -2.796   1.112  -1.666  H16  YQP  39  
YQP  H17  H17  H  0  1  N  N  N  2.672  -54.628  23.769  -3.429   1.438   1.273  H17  YQP  40  
YQP  H18  H18  H  0  1  N  N  N  3.797  -54.605  25.737  -1.344   2.303   1.759  H18  YQP  41  
YQP  H19  H19  H  0  1  N  N  N  4.056  -57.085  20.975  -4.563  -0.174  -2.294  H19  YQP  42  
YQP  H20  H20  H  0  1  N  N  N  2.538  -59.022  20.673  -6.043  -2.078  -1.920  H20  YQP  43  
YQP  H21  H21  H  0  1  N  N  N  1.278  -58.673  24.688  -4.192  -2.671   1.770  H21  YQP  44  
YQP  H22  H22  H  0  1  N  N  N  4.755  -52.456  25.933  -2.094   4.383   0.851  H22  YQP  45  
YQP  H23  H23  H  0  1  N  N  N  3.569  -52.551  23.018  -4.019   3.583   0.401  H23  YQP  46  
#   #
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
YQP  CAV  CAS  DOUB  N  N   1  
YQP  CAV  CAW  SING  N  N   2  
YQP  CAS  NAR  SING  N  N   3  
YQP  OAX  CAW  DOUB  N  N   4  
YQP  OAQ  CAN  SING  N  N   5  
YQP  CAW  NAU  SING  N  N   6  
YQP  NAR  CAM  SING  N  N   7  
YQP  NAR  CAT  SING  N  N   8  
YQP  CAM  CAN  SING  N  N   9  
YQP  CAM  OAL  SING  N  N  10  
YQP  CAN  CAO  SING  N  N  11  
YQP  NAU  CAT  SING  N  N  12  
YQP  OAL  CAK  SING  N  N  13  
YQP  CAT  OAY  DOUB  N  N  14  
YQP  CAK  CAO  SING  N  N  15  
YQP  CAK  CAH  SING  N  N  16  
YQP  CAO  OAP  SING  N  N  17  
YQP  CE   SD   DOUB  N  N  18  
YQP  CAH  SD   SING  N  N  19  
YQP  SD   CG   SING  N  N  20  
YQP  CG   CB   SING  N  N  21  
YQP  CB   CA   SING  N  N  22  
YQP  OXT  C    DOUB  N  N  23  
YQP  N    CA   SING  N  N  24  
YQP  CA   C    SING  N  N  25  
YQP  C    O    SING  N  N  26  
YQP  N    H1   SING  N  N  27  
YQP  N    H2   SING  N  N  28  
YQP  CA   H4   SING  N  N  29  
YQP  O    H5   SING  N  N  30  
YQP  CB   H6   SING  N  N  31  
YQP  CB   H7   SING  N  N  32  
YQP  CG   H8   SING  N  N  33  
YQP  CG   H9   SING  N  N  34  
YQP  CE   H10  SING  N  N  35  
YQP  CE   H11  SING  N  N  36  
YQP  CAH  H13  SING  N  N  37  
YQP  CAH  H14  SING  N  N  38  
YQP  CAK  H15  SING  N  N  39  
YQP  CAM  H16  SING  N  N  40  
YQP  CAN  H17  SING  N  N  41  
YQP  CAO  H18  SING  N  N  42  
YQP  CAS  H19  SING  N  N  43  
YQP  CAV  H20  SING  N  N  44  
YQP  NAU  H21  SING  N  N  45  
YQP  OAP  H22  SING  N  N  46  
YQP  OAQ  H23  SING  N  N  47  
#   #
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
YQP  SMILES            ACDLabs               12.01  "O=C(O)C(N)CCS(=C)CC1OC(N2C=CC(=O)NC2=O)C(O)C1O"  
YQP  InChI             InChI                 1.03   "InChI=1S/C14H21N3O7S/c1-25(5-3-7(15)13(21)22)6-8-10(19)11(20)12(24-8)17-4-2-9(18)16-14(17)23/h2,4,7-8,10-12,19-20H,1,3,5-6,15H2,(H,21,22)(H,16,18,23)/t7-,8+,10+,11+,12+,25-/m0/s1"  
YQP  InChIKey          InChI                 1.03   HBPDMWXHIXRRKQ-GGUSWIIGSA-N  
YQP  SMILES_CANONICAL  CACTVS                3.385  "N[C@@H](CC[S](=C)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C(O)=O"  
YQP  SMILES            CACTVS                3.385  "N[CH](CC[S](=C)C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O)C(O)=O"  
YQP  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C=S(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O"  
YQP  SMILES            "OpenEye OEToolkits"  2.0.7  "C=S(CCC(C(=O)O)N)CC1C(C(C(O1)N2C=CC(=O)NC2=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
YQP  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-{[(3S)-3-amino-3-carboxypropyl](methylidene)-lambda~4~-sulfanyl}-5'-deoxyuridine"  
YQP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methylidene-$l^{4}-sulfanyl]butanoic 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
YQP  "Create component"  2021-03-23  RCSB  
YQP  "Initial release"   2022-03-02  RCSB  
##
