data_A3S
#

_chem_comp.id                                   A3S
_chem_comp.name                                 "SERINE-3'-AMINOADENOSINE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H19 N7 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2004-06-24
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       353.334
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A3S
_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       1TKY
_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
A3S  "O5'"   "O5'"   O  0  1  N  N  N  13.784  12.887  43.539   1.900  -3.657  -1.249  "O5'"   A3S   1  
A3S  "C5'"   "C5'"   C  0  1  N  N  N  14.145  12.035  42.455   1.987  -2.739  -0.158  "C5'"   A3S   2  
A3S  "C4'"   "C4'"   C  0  1  N  N  S  15.118  10.977  42.924   1.261  -1.442  -0.522  "C4'"   A3S   3  
A3S  "O4'"   "O4'"   O  0  1  N  N  N  16.321  11.628  43.420  -0.159  -1.681  -0.657  "O4'"   A3S   4  
A3S  "C1'"   "C1'"   C  0  1  N  N  R  16.542  11.258  44.767  -0.781  -0.387  -0.504  "C1'"   A3S   5  
A3S  N9      N9      N  0  1  Y  N  N  17.046  12.427  45.486  -2.191  -0.536  -0.133  N9      A3S   6  
A3S  C4      C4      C  0  1  Y  N  N  18.133  12.463  46.326  -3.173   0.411  -0.277  C4      A3S   7  
A3S  N3      N3      N  0  1  Y  N  N  18.950  11.446  46.647  -3.219   1.650  -0.755  N3      A3S   8  
A3S  C2      C2      C  0  1  Y  N  N  19.893  11.850  47.497  -4.350   2.323  -0.765  C2      A3S   9  
A3S  N1      N1      N  0  1  Y  N  N  20.096  13.066  48.024  -5.482   1.814  -0.315  N1      A3S  10  
A3S  C6      C6      C  0  1  Y  N  N  19.255  14.067  47.681  -5.535   0.581   0.177  C6      A3S  11  
A3S  N6      N6      N  0  1  N  N  N  19.452  15.277  48.209  -6.726   0.056   0.647  N6      A3S  12  
A3S  C5      C5      C  0  1  Y  N  N  18.214  13.767  46.783  -4.353  -0.178   0.209  C5      A3S  13  
A3S  N7      N7      N  0  1  Y  N  N  17.200  14.542  46.235  -4.034  -1.427   0.624  N7      A3S  14  
A3S  C8      C8      C  0  1  Y  N  N  16.539  13.704  45.474  -2.765  -1.640   0.425  C8      A3S  15  
A3S  "C2'"   "C2'"   C  0  1  N  N  R  15.196  10.770  45.297   0.005   0.297   0.636  "C2'"   A3S  16  
A3S  "O2'"   "O2'"   O  0  1  N  N  N  15.386   9.880  46.380   0.160   1.694   0.373  "O2'"   A3S  17  
A3S  "C3'"   "C3'"   C  0  1  N  N  S  14.616  10.092  44.061   1.378  -0.411   0.622  "C3'"   A3S  18  
A3S  N8      N8      N  0  1  N  N  N  15.140   8.769  44.021   2.449   0.548   0.341  N8      A3S  19  
A3S  N       N       N  0  1  N  N  N  16.067   6.257  44.132   5.949   1.012   1.334  N       A3S  20  
A3S  CA      CA      C  0  1  N  N  S  15.373   6.557  42.884   4.813   1.268   0.438  CA      A3S  21  
A3S  CB      CB      C  0  1  N  N  N  14.294   5.502  42.624   5.266   1.116  -1.015  CB      A3S  22  
A3S  OG      OG      O  0  1  N  N  N  13.540   5.246  43.796   6.227   2.127  -1.324  OG      A3S  23  
A3S  C       C       C  0  1  N  N  N  14.751   7.950  42.925   3.712   0.281   0.727  C       A3S  24  
A3S  O       O       O  0  1  N  N  N  13.968   8.321  42.049   3.963  -0.754   1.308  O       A3S  25  
A3S  "H5'"   "H5'"   H  0  1  N  N  N  13.173  13.552  43.244   2.369  -4.458  -0.979  "H5'"   A3S  26  
A3S  "H5'1"  "1H5'"  H  0  0  N  N  N  14.543  12.611  41.587   3.034  -2.522   0.052  "H5'1"  A3S  27  
A3S  "H5'2"  "2H5'"  H  0  0  N  N  N  13.251  11.589  41.960   1.523  -3.179   0.725  "H5'2"  A3S  28  
A3S  "H4'"   "H4'"   H  0  1  N  N  N  15.285  10.327  42.034   1.665  -1.029  -1.446  "H4'"   A3S  29  
A3S  "H1'"   "H1'"   H  0  1  N  N  N  17.299  10.449  44.891  -0.691   0.188  -1.426  "H1'"   A3S  30  
A3S  H2      H2      H  0  1  N  N  N  20.606  11.068  47.808  -4.352   3.330  -1.157  H2      A3S  31  
A3S  HN61    1HN6    H  0  0  N  N  N  20.410  15.570  48.017  -6.752  -0.846   1.004  HN61    A3S  32  
A3S  HN62    2HN6    H  0  0  N  N  N  18.817  16.032  47.950  -7.536   0.590   0.619  HN62    A3S  33  
A3S  H8      H8      H  0  1  N  N  N  15.661  14.034  44.893  -2.245  -2.555   0.665  H8      A3S  34  
A3S  "H2'"   "H2'"   H  0  1  N  N  N  14.529  11.562  45.709  -0.495   0.143   1.592  "H2'"   A3S  35  
A3S  H1      H1      H  0  1  N  N  N  14.548   9.576  46.710  -0.725   2.082   0.394  H1      A3S  36  
A3S  "H3'"   "H3'"   H  0  1  N  N  N  13.506   9.994  44.022   1.558  -0.915   1.573  "H3'"   A3S  37  
A3S  HN8     HN8     H  0  1  N  N  N  15.768   8.423  44.747   2.248   1.376  -0.123  HN8     A3S  38  
A3S  HN1     1HN     H  0  1  N  N  N  16.446   5.310  44.142   5.584   1.020   2.275  HN1     A3S  39  
A3S  HN2     2HN     H  0  1  N  N  N  16.786   6.960  44.305   6.255   0.068   1.151  HN2     A3S  40  
A3S  HA      HA      H  0  1  N  N  N  16.116   6.536  42.053   4.445   2.281   0.599  HA      A3S  41  
A3S  HB1     1HB     H  0  1  N  N  N  14.728   4.566  42.202   5.716   0.133  -1.155  HB1     A3S  42  
A3S  HB2     2HB     H  0  1  N  N  N  13.639   5.787  41.768   4.406   1.218  -1.677  HB2     A3S  43  
A3S  HOG     HOG     H  0  1  N  N  N  12.871   4.592  43.635   6.486   1.996  -2.246  HOG     A3S  44  
#   #
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
A3S  "O5'"  "C5'"   SING  N  N   1  
A3S  "O5'"  "H5'"   SING  N  N   2  
A3S  "C5'"  "C4'"   SING  N  N   3  
A3S  "C5'"  "H5'1"  SING  N  N   4  
A3S  "C5'"  "H5'2"  SING  N  N   5  
A3S  "C4'"  "O4'"   SING  N  N   6  
A3S  "C4'"  "C3'"   SING  N  N   7  
A3S  "C4'"  "H4'"   SING  N  N   8  
A3S  "O4'"  "C1'"   SING  N  N   9  
A3S  "C1'"  N9      SING  N  N  10  
A3S  "C1'"  "C2'"   SING  N  N  11  
A3S  "C1'"  "H1'"   SING  N  N  12  
A3S  N9     C4      SING  Y  N  13  
A3S  N9     C8      SING  Y  N  14  
A3S  C4     N3      SING  Y  N  15  
A3S  C4     C5      DOUB  Y  N  16  
A3S  N3     C2      DOUB  Y  N  17  
A3S  C2     N1      SING  Y  N  18  
A3S  C2     H2      SING  N  N  19  
A3S  N1     C6      DOUB  Y  N  20  
A3S  C6     N6      SING  N  N  21  
A3S  C6     C5      SING  Y  N  22  
A3S  N6     HN61    SING  N  N  23  
A3S  N6     HN62    SING  N  N  24  
A3S  C5     N7      SING  Y  N  25  
A3S  N7     C8      DOUB  Y  N  26  
A3S  C8     H8      SING  N  N  27  
A3S  "C2'"  "O2'"   SING  N  N  28  
A3S  "C2'"  "C3'"   SING  N  N  29  
A3S  "C2'"  "H2'"   SING  N  N  30  
A3S  "O2'"  H1      SING  N  N  31  
A3S  "C3'"  N8      SING  N  N  32  
A3S  "C3'"  "H3'"   SING  N  N  33  
A3S  N8     C       SING  N  N  34  
A3S  N8     HN8     SING  N  N  35  
A3S  N      CA      SING  N  N  36  
A3S  N      HN1     SING  N  N  37  
A3S  N      HN2     SING  N  N  38  
A3S  CA     CB      SING  N  N  39  
A3S  CA     C       SING  N  N  40  
A3S  CA     HA      SING  N  N  41  
A3S  CB     OG      SING  N  N  42  
A3S  CB     HB1     SING  N  N  43  
A3S  CB     HB2     SING  N  N  44  
A3S  OG     HOG     SING  N  N  45  
A3S  C      O       DOUB  N  N  46  
#   #
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
A3S  SMILES            ACDLabs               10.04  "O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)CO"  
A3S  SMILES_CANONICAL  CACTVS                3.341  "N[C@@H](CO)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23"  
A3S  SMILES            CACTVS                3.341  "N[CH](CO)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO)n2cnc3c(N)ncnc23"  
A3S  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)[C@H](CO)N)O)N"  
A3S  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)NC(=O)C(CO)N)O)N"  
A3S  InChI             InChI                 1.03   "InChI=1S/C13H19N7O5/c14-5(1-21)12(24)19-7-6(2-22)25-13(9(7)23)20-4-18-8-10(15)16-3-17-11(8)20/h3-7,9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,7+,9+,13+/m0/s1"  
A3S  InChIKey          InChI                 1.03   ITDKSTILAWHDJI-AYEBZEFBSA-N  
#   #
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
A3S  "SYSTEMATIC NAME"  ACDLabs               10.04  "3'-deoxy-3'-(L-serylamino)adenosine"  
A3S  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2S)-2-amino-N-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-hydroxy-propanamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A3S  "Create component"   2004-06-24  RCSB  
A3S  "Modify descriptor"  2011-06-04  RCSB  
A3S  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     A3S
_pdbx_chem_comp_synonyms.name        "N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
