data_P6D
#

_chem_comp.id                                   P6D
_chem_comp.name                                 "2'-azidocytidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H13 N6 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-07-31
_chem_comp.pdbx_modified_date                   2020-07-24
_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                       269.237
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    P6D
_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  Y
_chem_comp.pdbx_model_coordinates_db_code       6PWZ
_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
P6D  C02  C1   C   0  1  N  N  S  -12.023  22.795  23.875  ?  ?  ?  C02  P6D   1  
P6D  C03  C2   C   0  1  N  N  R  -11.466  22.761  22.419  ?  ?  ?  C03  P6D   2  
P6D  C04  C3   C   0  1  N  N  N  -12.322  22.038  21.657  ?  ?  ?  C04  P6D   3  
P6D  C11  C4   C   0  1  N  N  R  -10.824  24.828  23.108  ?  ?  ?  C11  P6D   4  
P6D  C12  C5   C   0  1  N  N  R  -11.753  24.039  24.220  ?  ?  ?  C12  P6D   5  
P6D  C17  C6   C   0  1  N  N  N  -11.927  27.173  23.532  ?  ?  ?  C17  P6D   6  
P6D  C18  C7   C   0  1  N  N  N  -11.755  28.662  23.679  ?  ?  ?  C18  P6D   7  
P6D  C19  C8   C   0  1  N  N  N  -10.392  29.245  23.526  ?  ?  ?  C19  P6D   8  
P6D  C21  C9   C   0  1  N  N  N   -9.422  26.927  23.111  ?  ?  ?  C21  P6D   9  
P6D  N13  N1   N   0  1  N  N  N  -11.931  24.431  25.641  ?  ?  ?  N13  P6D  10  
P6D  N14  N2   N   1  1  N  N  N  -11.641  25.553  26.091  ?  ?  ?  N14  P6D  11  
P6D  N15  N3   N  -1  1  N  N  N  -11.994  25.771  27.253  ?  ?  ?  N15  P6D  12  
P6D  N16  N4   N   0  1  N  N  N  -10.769  26.295  23.246  ?  ?  ?  N16  P6D  13  
P6D  N20  N5   N   0  1  N  N  N   -9.233  28.400  23.245  ?  ?  ?  N20  P6D  14  
P6D  N23  N6   N   0  1  N  N  N  -10.217  30.680  23.660  ?  ?  ?  N23  P6D  15  
P6D  O01  O1   O   0  1  N  N  N  -11.352  21.817  24.766  ?  ?  ?  O01  P6D  16  
P6D  O05  O2   O   0  1  N  N  N  -13.003  21.188  22.560  ?  ?  ?  O05  P6D  17  
P6D  O10  O3   O   0  1  N  N  N  -11.354  24.351  22.008  ?  ?  ?  O10  P6D  18  
P6D  O22  O4   O   0  1  N  N  N   -8.506  26.222  22.889  ?  ?  ?  O22  P6D  19  
P6D  H1   H1   H   0  1  N  N  N  -13.104  22.593  23.846  ?  ?  ?  H1   P6D  20  
P6D  H2   H2   H   0  1  N  N  N  -10.452  22.335  22.428  ?  ?  ?  H2   P6D  21  
P6D  H3   H3   H   0  1  N  N  N  -13.033  22.701  21.142  ?  ?  ?  H3   P6D  22  
P6D  H4   H4   H   0  1  N  N  N  -11.769  21.445  20.913  ?  ?  ?  H4   P6D  23  
P6D  H5   H5   H   0  1  N  N  N   -9.803  24.439  23.237  ?  ?  ?  H5   P6D  24  
P6D  H6   H6   H   0  1  N  N  N  -12.704  24.468  23.872  ?  ?  ?  H6   P6D  25  
P6D  H7   H7   H   0  1  N  N  N  -12.910  26.739  23.637  ?  ?  ?  H7   P6D  26  
P6D  H8   H8   H   0  1  N  N  N  -12.604  29.295  23.891  ?  ?  ?  H8   P6D  27  
P6D  H10  H10  H   0  1  N  N  N  -11.796  26.640  27.672  ?  ?  ?  H10  P6D  28  
P6D  H11  H11  H   0  1  N  N  N   -9.308  31.084  23.560  ?  ?  ?  H11  P6D  29  
P6D  H12  H12  H   0  1  N  N  N  -11.006  31.264  23.852  ?  ?  ?  H12  P6D  30  
P6D  H13  H13  H   0  1  N  N  N  -11.724  21.875  25.638  ?  ?  ?  H13  P6D  31  
P6D  H14  H14  H   0  1  N  N  N  -13.624  20.650  22.082  ?  ?  ?  H14  P6D  32  
#   #
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
P6D  C04  C03  SING  N  N   1  
P6D  C04  O05  SING  N  N   2  
P6D  O10  C03  SING  N  N   3  
P6D  O10  C11  SING  N  N   4  
P6D  C03  C02  SING  N  N   5  
P6D  O22  C21  DOUB  N  N   6  
P6D  C11  N16  SING  N  N   7  
P6D  C11  C12  SING  N  N   8  
P6D  C21  N20  SING  N  N   9  
P6D  C21  N16  SING  N  N  10  
P6D  N20  C19  DOUB  N  N  11  
P6D  N16  C17  SING  N  N  12  
P6D  C19  N23  SING  N  N  13  
P6D  C19  C18  SING  N  N  14  
P6D  C17  C18  DOUB  N  N  15  
P6D  C02  C12  SING  N  N  16  
P6D  C02  O01  SING  N  N  17  
P6D  C12  N13  SING  N  N  18  
P6D  N13  N14  DOUB  N  N  19  
P6D  N14  N15  DOUB  N  N  20  
P6D  C02  H1   SING  N  N  21  
P6D  C03  H2   SING  N  N  22  
P6D  C04  H3   SING  N  N  23  
P6D  C04  H4   SING  N  N  24  
P6D  C11  H5   SING  N  N  25  
P6D  C12  H6   SING  N  N  26  
P6D  C17  H7   SING  N  N  27  
P6D  C18  H8   SING  N  N  28  
P6D  N15  H10  SING  N  N  29  
P6D  N23  H11  SING  N  N  30  
P6D  N23  H12  SING  N  N  31  
P6D  O01  H13  SING  N  N  32  
P6D  O05  H14  SING  N  N  33  
#   #
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
P6D  InChI             InChI                 1.03   "InChI=1S/C9H13N6O4/c10-5-1-2-15(9(18)12-5)8-6(13-14-11)7(17)4(3-16)19-8/h1-2,4,6-8,11,16-17H,3H2,(H2,10,12,18)/t4-,6-,7-,8-/m1/s1"  
P6D  InChIKey          InChI                 1.03   SXKUZFQHWHCRFO-XVFCMESISA-N  
P6D  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N=[N+]=[NH-]"  
P6D  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2N=[N+]=[NH-]"  
P6D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)N=[N+]=[NH-]"  
P6D  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)N=[N+]=[NH-]"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P6D  "Create component"  2019-07-31  RCSB  
P6D  "Initial release"   2020-07-29  RCSB  
##
