data_V2S
#

_chem_comp.id                                   V2S
_chem_comp.name                                 "(2~{S})-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]amino]-3-phenyl-propanoic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H23 N6 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-06-19
_chem_comp.pdbx_modified_date                   2021-03-12
_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                       494.395
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    V2S
_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       6XHF
_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
V2S  C      C1   C  0  1  N  N  N   5.739   -6.670  32.181  -1.279   1.092   0.662  C      V2S   1  
V2S  O      O1   O  0  1  N  N  N   6.807   -5.799  31.821  -0.623   2.178   0.223  O      V2S   2  
V2S  CA     C2   C  0  1  N  N  S   5.653   -7.244  33.595  -2.715   0.868   0.264  CA     V2S   3  
V2S  CB     C3   C  0  1  N  N  N   4.482   -6.572  34.311  -3.570   2.039   0.753  CB     V2S   4  
V2S  CG     C4   C  0  1  Y  N  N   4.183   -7.292  35.603  -4.981   1.875   0.250  CG     V2S   5  
V2S  C6     C5   C  0  1  Y  N  N   9.754   -9.634  42.433   5.772   2.671  -0.029  C6     V2S   6  
V2S  C5     C6   C  0  1  Y  N  N   8.943   -9.923  41.216   4.567   1.957   0.086  C5     V2S   7  
V2S  C4     C7   C  0  1  Y  N  N   9.684  -10.438  40.049   4.535   0.631  -0.377  C4     V2S   8  
V2S  C2     C8   C  0  1  Y  N  N  11.703  -10.281  41.312   6.745   0.809  -0.985  C2     V2S   9  
V2S  OXT    O2   O  0  1  N  N  N   4.756   -7.021  31.207  -0.717   0.293   1.372  OXT    V2S  10  
V2S  OP1    O3   O  0  1  N  N  N   8.291   -7.928  32.347  -3.547  -2.906   0.439  OP1    V2S  11  
V2S  P      P1   P  0  1  N  N  N   8.363   -7.454  33.786  -3.049  -1.669  -0.203  P      V2S  12  
V2S  OP2    O4   O  0  1  N  N  N   9.401   -6.388  34.000  -3.910  -1.368  -1.530  OP2    V2S  13  
V2S  N10    N1   N  0  1  N  N  N   6.898   -6.876  34.269  -3.201  -0.380   0.868  N10    V2S  14  
V2S  CD1    C9   C  0  1  Y  N  N   4.307   -8.682  35.631  -5.909   1.183   1.007  CD1    V2S  15  
V2S  CE1    C10  C  0  1  Y  N  N   4.077   -9.369  36.823  -7.203   1.033   0.545  CE1    V2S  16  
V2S  CZ     C11  C  0  1  Y  N  N   3.669   -8.656  37.953  -7.570   1.576  -0.672  CZ     V2S  17  
V2S  CE2    C12  C  0  1  Y  N  N   3.560   -7.262  37.917  -6.643   2.269  -1.428  CE2    V2S  18  
V2S  CD2    C13  C  0  1  Y  N  N   3.819   -6.560  36.740  -5.349   2.422  -0.964  CD2    V2S  19  
V2S  "O5'"  O5   O  0  1  N  N  N   8.690   -8.665  34.790  -1.500  -1.857  -0.600  "O5'"  V2S  20  
V2S  "C5'"  C14  C  0  1  N  N  N   9.910   -9.395  34.674  -0.535  -2.433   0.283  "C5'"  V2S  21  
V2S  "C4'"  C15  C  0  1  N  N  R   9.729  -10.645  35.527   0.832  -2.462  -0.404  "C4'"  V2S  22  
V2S  "O4'"  O6   O  0  1  N  N  N  10.013  -10.393  36.914   1.306  -1.120  -0.606  "O4'"  V2S  23  
V2S  "C1'"  C16  C  0  1  N  N  R   9.085  -11.160  37.711   2.742  -1.153  -0.462  "C1'"  V2S  24  
V2S  "C2'"  C17  C  0  1  N  N  R   7.813  -11.328  36.883   2.964  -2.121   0.728  "C2'"  V2S  25  
V2S  "O2'"  O7   O  0  1  N  N  N   7.247  -12.627  37.106   4.260  -2.718   0.665  "O2'"  V2S  26  
V2S  "C3'"  C18  C  0  1  N  N  S   8.278  -11.127  35.443   1.856  -3.178   0.497  "C3'"  V2S  27  
V2S  "O3'"  O8   O  0  1  N  N  N   8.233  -12.353  34.707   2.391  -4.325  -0.167  "O3'"  V2S  28  
V2S  N9     N2   N  0  1  Y  N  N   8.776  -10.636  39.077   3.260   0.180  -0.147  N9     V2S  29  
V2S  C8     C19  C  0  1  Y  N  N   7.555  -10.326  39.565   2.564   1.200   0.431  C8     V2S  30  
V2S  N7     N3   N  0  1  Y  N  N   7.647   -9.868  40.844   3.333   2.242   0.566  N7     V2S  31  
V2S  N6     N4   N  0  1  N  N  N   9.123   -9.174  43.541   5.863   3.981   0.410  N6     V2S  32  
V2S  N1     N5   N  0  1  Y  N  N  11.106   -9.847  42.418   6.823   2.058  -0.563  N1     V2S  33  
V2S  N3     N6   N  0  1  Y  N  N  11.031  -10.574  40.173   5.636   0.104  -0.903  N3     V2S  34  
V2S  H1     H1   H  0  1  N  N  N   6.717   -5.547  30.909   0.296   2.280   0.505  H1     V2S  35  
V2S  H2     H2   H  0  1  N  N  N   5.515   -8.335  33.564  -2.784   0.796  -0.822  H2     V2S  36  
V2S  H3     H3   H  0  1  N  N  N   4.741   -5.525  34.529  -3.572   2.056   1.843  H3     V2S  37  
V2S  H4     H4   H  0  1  N  N  N   3.593   -6.603  33.663  -3.155   2.973   0.376  H4     V2S  38  
V2S  H5     H5   H  0  1  N  N  N  12.776  -10.406  41.322   7.623   0.350  -1.413  H5     V2S  39  
V2S  H6     H6   H  0  1  N  N  N   9.835   -6.198  33.177  -3.637  -0.570  -2.003  H6     V2S  40  
V2S  H7     H7   H  0  1  N  N  N   6.960   -5.879  34.215  -2.723  -0.572   1.735  H7     V2S  41  
V2S  H8     H8   H  0  1  N  N  N   4.579   -9.222  34.736  -5.622   0.759   1.957  H8     V2S  42  
V2S  H9     H9   H  0  1  N  N  N   4.213  -10.439  36.872  -7.927   0.492   1.135  H9     V2S  43  
V2S  H10    H10  H  0  1  N  N  N   3.435   -9.187  38.864  -8.581   1.459  -1.033  H10    V2S  44  
V2S  H11    H11  H  0  1  N  N  N   3.273   -6.724  38.809  -6.929   2.692  -2.379  H11    V2S  45  
V2S  H12    H12  H  0  1  N  N  N   3.741   -5.483  36.706  -4.626   2.967  -1.553  H12    V2S  46  
V2S  H13    H13  H  0  1  N  N  N  10.093   -9.670  33.625  -0.472  -1.836   1.193  H13    V2S  47  
V2S  H14    H14  H  0  1  N  N  N  10.753   -8.795  35.048  -0.836  -3.450   0.536  H14    V2S  48  
V2S  H15    H15  H  0  1  N  N  N  10.389  -11.437  35.144   0.754  -2.975  -1.362  H15    V2S  49  
V2S  H16    H16  H  0  1  N  N  N   9.511  -12.166  37.841   3.209  -1.541  -1.367  H16    V2S  50  
V2S  H17    H17  H  0  1  N  N  N   7.095  -10.539  37.150   2.819  -1.608   1.679  H17    V2S  51  
V2S  H18    H18  H  0  1  N  N  N   6.974  -12.703  38.013   4.446  -3.332   1.389  H18    V2S  52  
V2S  H19    H19  H  0  1  N  N  N   7.661  -10.355  34.960   1.398  -3.464   1.444  H19    V2S  53  
V2S  H20    H20  H  0  1  N  N  N   7.335  -12.657  34.652   3.041  -4.814   0.355  H20    V2S  54  
V2S  H21    H21  H  0  1  N  N  N   6.631  -10.428  39.015   1.528   1.151   0.732  H21    V2S  55  
V2S  H22    H22  H  0  1  N  N  N   9.791   -9.037  44.273   5.090   4.416   0.802  H22    V2S  56  
V2S  H23    H23  H  0  1  N  N  N   8.674   -8.305  43.332   6.700   4.463   0.325  H23    V2S  57  
#   #
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
V2S  OXT    C      DOUB  N  N   1  
V2S  O      C      SING  N  N   2  
V2S  C      CA     SING  N  N   3  
V2S  OP1    P      DOUB  N  N   4  
V2S  CA     N10    SING  N  N   5  
V2S  CA     CB     SING  N  N   6  
V2S  P      OP2    SING  N  N   7  
V2S  P      N10    SING  N  N   8  
V2S  P      "O5'"  SING  N  N   9  
V2S  CB     CG     SING  N  N  10  
V2S  "C5'"  "O5'"  SING  N  N  11  
V2S  "C5'"  "C4'"  SING  N  N  12  
V2S  "O3'"  "C3'"  SING  N  N  13  
V2S  "C3'"  "C4'"  SING  N  N  14  
V2S  "C3'"  "C2'"  SING  N  N  15  
V2S  "C4'"  "O4'"  SING  N  N  16  
V2S  CG     CD1    DOUB  Y  N  17  
V2S  CG     CD2    SING  Y  N  18  
V2S  CD1    CE1    SING  Y  N  19  
V2S  CD2    CE2    DOUB  Y  N  20  
V2S  CE1    CZ     DOUB  Y  N  21  
V2S  "C2'"  "O2'"  SING  N  N  22  
V2S  "C2'"  "C1'"  SING  N  N  23  
V2S  "O4'"  "C1'"  SING  N  N  24  
V2S  "C1'"  N9     SING  N  N  25  
V2S  CE2    CZ     SING  Y  N  26  
V2S  N9     C8     SING  Y  N  27  
V2S  N9     C4     SING  Y  N  28  
V2S  C8     N7     DOUB  Y  N  29  
V2S  C4     N3     DOUB  Y  N  30  
V2S  C4     C5     SING  Y  N  31  
V2S  N3     C2     SING  Y  N  32  
V2S  N7     C5     SING  Y  N  33  
V2S  C5     C6     DOUB  Y  N  34  
V2S  C2     N1     DOUB  Y  N  35  
V2S  N1     C6     SING  Y  N  36  
V2S  C6     N6     SING  N  N  37  
V2S  O      H1     SING  N  N  38  
V2S  CA     H2     SING  N  N  39  
V2S  CB     H3     SING  N  N  40  
V2S  CB     H4     SING  N  N  41  
V2S  C2     H5     SING  N  N  42  
V2S  OP2    H6     SING  N  N  43  
V2S  N10    H7     SING  N  N  44  
V2S  CD1    H8     SING  N  N  45  
V2S  CE1    H9     SING  N  N  46  
V2S  CZ     H10    SING  N  N  47  
V2S  CE2    H11    SING  N  N  48  
V2S  CD2    H12    SING  N  N  49  
V2S  "C5'"  H13    SING  N  N  50  
V2S  "C5'"  H14    SING  N  N  51  
V2S  "C4'"  H15    SING  N  N  52  
V2S  "C1'"  H16    SING  N  N  53  
V2S  "C2'"  H17    SING  N  N  54  
V2S  "O2'"  H18    SING  N  N  55  
V2S  "C3'"  H19    SING  N  N  56  
V2S  "O3'"  H20    SING  N  N  57  
V2S  C8     H21    SING  N  N  58  
V2S  N6     H22    SING  N  N  59  
V2S  N6     H23    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
V2S  SMILES            ACDLabs               12.01  "C(C(NP(=O)(O)OCC3OC(n2c1c(c(N)ncn1)nc2)C(O)C3O)Cc4ccccc4)(O)=O"  
V2S  InChI             InChI                 1.03   "InChI=1S/C19H23N6O8P/c20-16-13-17(22-8-21-16)25(9-23-13)18-15(27)14(26)12(33-18)7-32-34(30,31)24-11(19(28)29)6-10-4-2-1-3-5-10/h1-5,8-9,11-12,14-15,18,26-27H,6-7H2,(H,28,29)(H2,20,21,22)(H2,24,30,31)/t11-,12+,14+,15+,18+/m0/s1"  
V2S  InChIKey          InChI                 1.03   OXCQKAQOLIIWJO-URQYDQELSA-N  
V2S  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N[C@@H](Cc4ccccc4)C(O)=O)[C@@H](O)[C@H]3O"  
V2S  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N[CH](Cc4ccccc4)C(O)=O)[CH](O)[CH]3O"  
V2S  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)C[C@@H](C(=O)O)NP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O"  
V2S  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CC(C(=O)O)NP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)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
V2S  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}-3-phenylpropanoic acid (non-preferred name)"  
V2S  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]amino]-3-phenyl-propanoic 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
V2S  "Create component"  2020-06-19  RCSB  
V2S  "Initial release"   2021-03-17  RCSB  
##
