data_3D1
#

_chem_comp.id                                   3D1
_chem_comp.name                                 "(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H13 N5 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-DEOXYADENOSINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2004-02-16
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       251.242
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3D1
_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       1S2G
_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
3D1  "O5'"   "O5'"   O  0  1  N  N  N  -1.376  -10.273  -22.038   4.569   1.772   1.047  "O5'"   3D1   1  
3D1  "C5'"   "C5'"   C  0  1  N  N  N  -2.028   -9.017  -22.262   4.217   0.988  -0.094  "C5'"   3D1   2  
3D1  "C4'"   "C4'"   C  0  1  N  N  R  -2.338   -8.253  -20.946   3.184  -0.067   0.310  "C4'"   3D1   3  
3D1  "O4'"   "O4'"   O  0  1  N  N  N  -1.147   -7.957  -20.184   1.940   0.560   0.689  "O4'"   3D1   4  
3D1  "C1'"   "C1'"   C  0  1  N  N  R  -0.721   -6.618  -20.530   0.912  -0.437   0.559  "C1'"   3D1   5  
3D1  N9      N9      N  0  1  Y  N  N   0.371   -6.662  -21.829  -0.339   0.191   0.126  N9      3D1   6  
3D1  C4      C4      C  0  1  Y  N  N   0.788   -5.643  -22.680  -1.604  -0.302   0.319  C4      3D1   7  
3D1  N3      N3      N  0  1  Y  N  N   0.397   -4.324  -22.647  -2.110  -1.388   0.893  N3      3D1   8  
3D1  C2      C2      C  0  1  Y  N  N   0.994   -3.586  -23.634  -3.411  -1.589   0.920  C2      3D1   9  
3D1  N1      N1      N  0  1  Y  N  N   1.887   -4.047  -24.579  -4.271  -0.738   0.389  N1      3D1  10  
3D1  C6      C6      C  0  1  Y  N  N   2.255   -5.410  -24.567  -3.858   0.376  -0.206  C6      3D1  11  
3D1  N6      N6      N  0  1  N  N  N   3.102   -5.949  -25.431  -4.766   1.261  -0.761  N6      3D1  12  
3D1  C5      C5      C  0  1  Y  N  N   1.698   -6.248  -23.590  -2.477   0.634  -0.261  C5      3D1  13  
3D1  N7      N7      N  0  1  Y  N  N   1.898   -7.611  -23.368  -1.714   1.631  -0.768  N7      3D1  14  
3D1  C8      C8      C  0  1  Y  N  N   1.121   -7.799  -22.352  -0.459   1.377  -0.537  C8      3D1  15  
3D1  "C2'"   "C2'"   C  0  1  N  N  N  -1.945   -5.876  -21.032   1.386  -1.447  -0.503  "C2'"   3D1  16  
3D1  "C3'"   "C3'"   C  0  1  N  N  S  -3.006   -6.915  -21.302   2.793  -0.943  -0.907  "C3'"   3D1  17  
3D1  "O3'"   "O3'"   O  0  1  N  N  N  -4.146   -6.607  -20.480   3.701  -2.035  -1.062  "O3'"   3D1  18  
3D1  "H5'"   "H5'"   H  0  1  N  N  N  -1.232  -10.708  -22.870   5.221   2.462   0.863  "H5'"   3D1  19  
3D1  "H5'1"  "H5'1"  H  0  0  N  N  N  -1.368   -8.390  -22.879   3.793   1.634  -0.863  "H5'1"  3D1  20  
3D1  "H5'2"  "H5'2"  H  0  0  N  N  N  -2.987   -9.225  -22.759   5.107   0.494  -0.485  "H5'2"  3D1  21  
3D1  "H4'"   "H4'"   H  0  1  N  N  N  -2.989   -8.897  -20.337   3.567  -0.684   1.123  "H4'"   3D1  22  
3D1  "H1'"   "H1'"   H  0  1  N  N  N  -0.253   -6.146  -19.654   0.762  -0.942   1.513  "H1'"   3D1  23  
3D1  H2      H2      H  0  1  N  N  N   0.740   -2.537  -23.677  -3.790  -2.482   1.395  H2      3D1  24  
3D1  HN61    HN61    H  0  0  N  N  N   2.642   -6.085  -26.309  -5.716   1.071  -0.717  HN61    3D1  25  
3D1  HN62    HN62    H  0  0  N  N  N   3.884   -5.339  -25.556  -4.452   2.070  -1.193  HN62    3D1  26  
3D1  H8      H8      H  0  1  N  N  N   1.029   -8.776  -21.900   0.366   2.009  -0.829  H8      3D1  27  
3D1  "H2'1"  "H2'1"  H  0  0  N  N  N  -2.295   -5.159  -20.275   1.447  -2.449  -0.077  "H2'1"  3D1  28  
3D1  "H2'2"  "H2'2"  H  0  0  N  N  N  -1.712   -5.306  -21.943   0.716  -1.439  -1.364  "H2'2"  3D1  29  
3D1  "H3'"   "H3'"   H  0  1  N  N  N  -3.371   -6.949  -22.339   2.745  -0.345  -1.817  "H3'"   3D1  30  
3D1  H1      H1      H  0  1  N  N  N  -3.874   -6.539  -19.572   3.497  -2.612  -1.811  H1      3D1  31  
#   #
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
3D1  "O5'"  "C5'"   SING  N  N   1  
3D1  "O5'"  "H5'"   SING  N  N   2  
3D1  "C5'"  "C4'"   SING  N  N   3  
3D1  "C5'"  "H5'1"  SING  N  N   4  
3D1  "C5'"  "H5'2"  SING  N  N   5  
3D1  "C4'"  "O4'"   SING  N  N   6  
3D1  "C4'"  "C3'"   SING  N  N   7  
3D1  "C4'"  "H4'"   SING  N  N   8  
3D1  "O4'"  "C1'"   SING  N  N   9  
3D1  "C1'"  N9      SING  N  N  10  
3D1  "C1'"  "C2'"   SING  N  N  11  
3D1  "C1'"  "H1'"   SING  N  N  12  
3D1  N9     C4      SING  Y  N  13  
3D1  N9     C8      SING  Y  N  14  
3D1  C4     N3      DOUB  Y  N  15  
3D1  C4     C5      SING  Y  N  16  
3D1  N3     C2      SING  Y  N  17  
3D1  C2     N1      DOUB  Y  N  18  
3D1  C2     H2      SING  N  N  19  
3D1  N1     C6      SING  Y  N  20  
3D1  C6     N6      SING  N  N  21  
3D1  C6     C5      DOUB  Y  N  22  
3D1  N6     HN61    SING  N  N  23  
3D1  N6     HN62    SING  N  N  24  
3D1  C5     N7      SING  Y  N  25  
3D1  N7     C8      DOUB  Y  N  26  
3D1  C8     H8      SING  N  N  27  
3D1  "C2'"  "C3'"   SING  N  N  28  
3D1  "C2'"  "H2'1"  SING  N  N  29  
3D1  "C2'"  "H2'2"  SING  N  N  30  
3D1  "C3'"  "O3'"   SING  N  N  31  
3D1  "C3'"  "H3'"   SING  N  N  32  
3D1  "O3'"  H1      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
3D1  SMILES            ACDLabs               10.04  "n2c1c(ncnc1n(c2)C3OC(C(O)C3)CO)N"  
3D1  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3"  
3D1  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO)O3"  
3D1  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O)N"  
3D1  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3CC(C(O3)CO)O)N"  
3D1  InChI             InChI                 1.03   "InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1"  
3D1  InChIKey          InChI                 1.03   OLXZPDWKRNYJJZ-RRKCRQDMSA-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
3D1  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxyadenosine"  
3D1  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3D1  "Create component"   2004-02-16  RCSB  
3D1  "Modify descriptor"  2011-06-04  RCSB  
3D1  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3D1
_pdbx_chem_comp_synonyms.name        "2'-DEOXYADENOSINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
