data_5ID
#

_chem_comp.id                                   5ID
_chem_comp.name                                 "(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H13 I N4 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        5-IODOTUBERCIDIN
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-10-16
_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                       392.150
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5ID
_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       2C47
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
5ID  "O5'"   "O5'"   O  0  1  N  N  N  2.406  33.277  20.148  -4.584  -2.905   1.532  "O5'"   5ID   1  
5ID  "C5'"   "C5'"   C  0  1  N  N  N  3.690  32.661  20.403  -4.586  -2.277   0.248  "C5'"   5ID   2  
5ID  "C4'"   "C4'"   C  0  1  N  N  R  4.766  33.737  20.752  -4.115  -0.829   0.388  "C4'"   5ID   3  
5ID  "O4'"   "O4'"   O  0  1  N  N  N  5.031  34.425  19.544  -2.727  -0.788   0.786  "O4'"   5ID   4  
5ID  "C1'"   "C1'"   C  0  1  N  N  R  5.305  35.846  19.837  -2.263   0.529   0.415  "C1'"   5ID   5  
5ID  N9      N9      N  0  1  Y  N  N  4.405  36.771  19.001  -0.802   0.543   0.307  N9      5ID   6  
5ID  C8      C8      C  0  1  Y  N  N  3.190  36.428  18.577  -0.018  -0.563   0.098  C8      5ID   7  
5ID  C7      C7      C  0  1  Y  N  N  2.665  37.452  17.887   1.275  -0.202   0.050  C7      5ID   8  
5ID  C5      C5      C  0  1  Y  N  N  3.569  38.516  17.875   1.316   1.247   0.237  C5      5ID   9  
5ID  C6      C6      C  0  1  Y  N  N  3.602  39.816  17.346   2.331   2.213   0.297  C6      5ID  10  
5ID  N1      N1      N  0  1  Y  N  N  4.699  40.556  17.569   1.985   3.482   0.494  N1      5ID  11  
5ID  C2      C2      C  0  1  Y  N  N  5.731  40.065  18.244   0.718   3.827   0.636  C2      5ID  12  
5ID  N3      N3      N  0  1  Y  N  N  5.732  38.838  18.735  -0.266   2.955   0.592  N3      5ID  13  
5ID  C4      C4      C  0  1  Y  N  N  4.663  38.040  18.588  -0.020   1.661   0.399  C4      5ID  14  
5ID  N6      N6      N  0  1  N  N  N  2.595  40.348  16.630   3.659   1.856   0.148  N6      5ID  15  
5ID  "C2'"   "C2'"   C  0  1  N  N  R  4.980  36.098  21.336  -2.907   0.803  -0.962  "C2'"   5ID  16  
5ID  "O2'"   "O2'"   O  0  1  N  N  N  6.189  36.353  22.116  -3.292   2.174  -1.078  "O2'"   5ID  17  
5ID  "C3'"   "C3'"   C  0  1  N  N  S  4.228  34.810  21.729  -4.153  -0.113  -0.981  "C3'"   5ID  18  
5ID  "O3'"   "O3'"   O  0  1  N  N  N  4.423  34.427  23.114  -5.346   0.664  -1.106  "O3'"   5ID  19  
5ID  IAE     IAE     I  0  1  N  N  N  0.724  37.383  17.000   2.916  -1.470  -0.245  IAE     5ID  20  
5ID  "H5'"   "H5'"   H  0  1  N  N  N  1.751  32.622  19.936  -4.886  -3.814   1.399  "H5'"   5ID  21  
5ID  "H5'1"  "1H5'"  H  0  0  N  N  N  4.013  32.016  19.553  -5.596  -2.293  -0.162  "H5'1"  5ID  22  
5ID  "H5'2"  "2H5'"  H  0  0  N  N  N  3.621  31.877  21.193  -3.914  -2.815  -0.421  "H5'2"  5ID  23  
5ID  "H4'"   "H4'"   H  0  1  N  N  N  5.692  33.261  21.152  -4.733  -0.297   1.111  "H4'"   5ID  24  
5ID  "H1'"   "H1'"   H  0  1  N  N  N  6.378  36.076  19.636  -2.596   1.268   1.144  "H1'"   5ID  25  
5ID  H8      H8      H  0  1  N  N  N  2.696  35.460  18.763  -0.385  -1.573  -0.010  H8      5ID  26  
5ID  H2      H2      H  0  1  N  N  N  6.617  40.702  18.400   0.480   4.869   0.795  H2      5ID  27  
5ID  H6N1    1H6N    H  0  0  N  N  N  2.619  41.292  16.246   4.351   2.535   0.188  H6N1    5ID  28  
5ID  H6N2    2H6N    H  0  0  N  N  N  1.761  39.785  16.461   3.899   0.927   0.009  H6N2    5ID  29  
5ID  "H2'"   "H2'"   H  0  1  N  N  N  4.291  36.971  21.424  -2.221   0.531  -1.764  "H2'"   5ID  30  
5ID  HA      HA      H  0  1  N  N  N  6.652  37.146  21.874  -3.741   2.268  -1.929  HA      5ID  31  
5ID  "H3'"   "H3'"   H  0  1  N  N  N  3.138  34.956  21.543  -4.084  -0.838  -1.793  "H3'"   5ID  32  
5ID  HB      HB      H  0  1  N  N  N  4.093  35.086  23.714  -6.088   0.048  -1.050  HB      5ID  33  
#   #
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
5ID  "O5'"  "C5'"   SING  N  N   1  
5ID  "O5'"  "H5'"   SING  N  N   2  
5ID  "C5'"  "C4'"   SING  N  N   3  
5ID  "C5'"  "H5'1"  SING  N  N   4  
5ID  "C5'"  "H5'2"  SING  N  N   5  
5ID  "C4'"  "O4'"   SING  N  N   6  
5ID  "C4'"  "C3'"   SING  N  N   7  
5ID  "C4'"  "H4'"   SING  N  N   8  
5ID  "O4'"  "C1'"   SING  N  N   9  
5ID  "C1'"  N9      SING  N  N  10  
5ID  "C1'"  "C2'"   SING  N  N  11  
5ID  "C1'"  "H1'"   SING  N  N  12  
5ID  N9     C8      SING  Y  N  13  
5ID  N9     C4      SING  Y  N  14  
5ID  C8     C7      DOUB  Y  N  15  
5ID  C8     H8      SING  N  N  16  
5ID  C7     C5      SING  Y  N  17  
5ID  C7     IAE     SING  N  N  18  
5ID  C5     C6      DOUB  Y  N  19  
5ID  C5     C4      SING  Y  N  20  
5ID  C6     N1      SING  Y  N  21  
5ID  C6     N6      SING  N  N  22  
5ID  N1     C2      DOUB  Y  N  23  
5ID  C2     N3      SING  Y  N  24  
5ID  C2     H2      SING  N  N  25  
5ID  N3     C4      DOUB  Y  N  26  
5ID  N6     H6N1    SING  N  N  27  
5ID  N6     H6N2    SING  N  N  28  
5ID  "C2'"  "O2'"   SING  N  N  29  
5ID  "C2'"  "C3'"   SING  N  N  30  
5ID  "C2'"  "H2'"   SING  N  N  31  
5ID  "O2'"  HA      SING  N  N  32  
5ID  "C3'"  "O3'"   SING  N  N  33  
5ID  "C3'"  "H3'"   SING  N  N  34  
5ID  "O3'"  HB      SING  N  N  35  
#   #
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
5ID  SMILES            ACDLabs               10.04  "Ic2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N"  
5ID  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cc(I)c12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O"  
5ID  SMILES            CACTVS                3.341  "Nc1ncnc2n(cc(I)c12)[CH]3O[CH](CO)[CH](O)[CH]3O"  
5ID  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)I"  
5ID  SMILES            "OpenEye OEToolkits"  1.5.0  "c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)I"  
5ID  InChI             InChI                 1.03   "InChI=1S/C11H13IN4O4/c12-4-1-16(10-6(4)9(13)14-3-15-10)11-8(19)7(18)5(2-17)20-11/h1,3,5,7-8,11,17-19H,2H2,(H2,13,14,15)/t5-,7-,8-,11-/m1/s1"  
5ID  InChIKey          InChI                 1.03   WHSIXKUPQCKWBY-IOSLPCCCSA-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
5ID  "SYSTEMATIC NAME"  ACDLabs               10.04  "5-iodo-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine"  
5ID  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R,3R,4S,5R)-2-(4-amino-5-iodo-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)oxolane-3,4-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5ID  "Create component"   2005-10-16  EBI   
5ID  "Modify descriptor"  2011-06-04  RCSB  
5ID  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5ID
_pdbx_chem_comp_synonyms.name        5-IODOTUBERCIDIN
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
