data_6D6
#

_chem_comp.id                                   6D6
_chem_comp.name                                 "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H28 N8 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-03-16
_chem_comp.pdbx_modified_date                   2021-08-26
_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                       424.455
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    6D6
_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       5ISG
_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
6D6  C1   C4    C  0  1  N  N  N  52.620  31.191  129.501  -3.817   3.851   2.064  C1   6D6   1  
6D6  C2   C5    C  0  1  N  N  N  52.397  32.715  129.578  -3.534   2.403   1.659  C2   6D6   2  
6D6  C3   C6    C  0  1  N  N  N  51.508  33.036  130.784  -3.012   2.368   0.222  C3   6D6   3  
6D6  C4   C8    C  0  1  N  N  N  52.494  34.867  132.028  -3.798   0.139  -0.302  C4   6D6   4  
6D6  C5   C10   C  0  1  N  N  S  52.985  36.027  134.295  -4.599  -2.222  -0.465  C5   6D6   5  
6D6  C6   C15   C  0  1  N  N  N  51.281  35.266  129.952  -1.767   0.976  -1.320  C6   6D6   6  
6D6  C7   C21   C  0  1  N  N  S  49.157  36.673  130.184   0.412   1.766  -2.293  C7   6D6   7  
6D6  C8   C24   C  0  1  Y  N  N  50.255  37.895  126.388   2.018  -1.264   0.560  C8   6D6   8  
6D6  C9   C26   C  0  1  Y  N  N  50.472  39.941  125.622   4.157  -1.314   0.913  C9   6D6   9  
6D6  N1   N2    N  0  1  N  Y  N  53.525  30.883  128.447  -4.319   3.885   3.444  N1   6D6  10  
6D6  N2   N7    N  0  1  N  N  N  51.393  34.451  131.132  -2.618   0.995  -0.123  N2   6D6  11  
6D6  C10  C9    C  0  1  N  N  N  51.925  35.607  133.299  -3.374  -1.330  -0.253  C10  6D6  12  
6D6  N3   N11   N  0  1  N  N  N  54.048  36.746  133.627  -5.532  -2.049   0.656  N3   6D6  13  
6D6  C11  C12   C  0  1  N  N  N  53.605  34.824  135.071  -4.165  -3.663  -0.539  C11  6D6  14  
6D6  O1   O13   O  0  1  N  N  N  54.835  34.527  134.899  -4.278  -4.378   0.428  O1   6D6  15  
6D6  O2   O14   O  0  1  N  N  N  52.877  34.148  135.879  -3.653  -4.152  -1.679  O2   6D6  16  
6D6  C12  C16   C  0  1  N  N  R  50.629  36.673  130.335  -0.438   1.669  -1.011  C12  6D6  17  
6D6  O3   O17   O  0  1  N  N  N  51.158  37.700  129.434   0.309   0.892  -0.060  O3   6D6  18  
6D6  C13  C18   C  0  1  N  N  R  49.980  38.393  128.818   1.706   1.053  -0.390  C13  6D6  19  
6D6  C14  C19   C  0  1  N  N  R  48.839  37.396  128.952   1.719   1.015  -1.939  C14  6D6  20  
6D6  O4   O20   O  0  1  N  N  N  47.579  38.063  129.029   2.859   1.703  -2.457  O4   6D6  21  
6D6  O5   O22   O  0  1  N  N  N  48.596  37.355  131.331   0.690   3.132  -2.607  O5   6D6  22  
6D6  N4   N23   N  0  1  Y  N  N  50.139  38.729  127.425   2.496  -0.052   0.160  N4   6D6  23  
6D6  N5   N25   N  0  1  Y  N  N  50.439  38.623  125.271   2.994  -2.003   1.002  N5   6D6  24  
6D6  C15  C27   C  0  1  Y  N  N  50.643  41.140  124.897   5.498  -1.594   1.227  C15  6D6  25  
6D6  N6   N28   N  0  1  N  N  N  50.828  41.074  123.484   5.859  -2.816   1.767  N6   6D6  26  
6D6  N7   N29   N  0  1  Y  N  N  50.627  42.313  125.549   6.411  -0.657   0.994  N7   6D6  27  
6D6  C16  C30   C  0  1  Y  N  N  50.453  42.351  126.877   6.076   0.512   0.479  C16  6D6  28  
6D6  N8   N31   N  0  1  Y  N  N  50.290  41.219  127.608   4.833   0.821   0.177  N8   6D6  29  
6D6  C17  C32   C  0  1  Y  N  N  50.294  40.011  126.974   3.852  -0.056   0.367  C17  6D6  30  
6D6  H1   H1    H  0  1  N  N  N  51.658  30.691  129.313  -2.898   4.433   1.997  H1   6D6  31  
6D6  H2   H33   H  0  1  N  N  N  53.037  30.836  130.455  -4.565   4.276   1.395  H2   6D6  32  
6D6  H3   H2    H  0  1  N  N  N  53.366  33.223  129.690  -2.786   1.979   2.329  H3   6D6  33  
6D6  H4   H34   H  0  1  N  N  N  51.906  33.062  128.657  -4.454   1.821   1.726  H4   6D6  34  
6D6  H5   H3    H  0  1  N  N  N  50.498  32.659  130.568  -3.795   2.703  -0.458  H5   6D6  35  
6D6  H6   H4    H  0  1  N  N  N  51.919  32.506  131.656  -2.148   3.027   0.133  H6   6D6  36  
6D6  H7   H5    H  0  1  N  N  N  53.055  33.977  132.349  -4.516   0.337   0.494  H7   6D6  37  
6D6  H8   H6    H  0  1  N  N  N  53.166  35.547  131.484  -4.258   0.352  -1.267  H8   6D6  38  
6D6  H9   H7    H  0  1  N  N  N  52.514  36.691  135.035  -5.094  -1.944  -1.396  H9   6D6  39  
6D6  H10  H8    H  0  1  N  N  N  50.645  34.756  129.214  -1.578  -0.056  -1.615  H10  6D6  40  
6D6  H11  H9    H  0  1  N  N  N  52.281  35.430  129.524  -2.270   1.501  -2.132  H11  6D6  41  
6D6  H12  H10   H  0  1  N  N  N  48.783  35.640  130.128  -0.096   1.280  -3.126  H12  6D6  42  
6D6  H13  H11   H  0  1  N  N  N  50.209  36.817  126.438   0.981  -1.566   0.521  H13  6D6  43  
6D6  H14  HE*1  H  0  1  N  Y  N  53.664  29.894  128.404  -3.671   3.439   4.076  H14  6D6  44  
6D6  H15  HE*2  H  0  1  N  Y  N  53.147  31.204  127.579  -4.514   4.832   3.735  H15  6D6  45  
6D6  H18  H19   H  0  1  N  N  N  51.390  36.508  132.964  -2.643  -1.524  -1.037  H18  6D6  46  
6D6  H19  H20   H  0  1  N  N  N  51.222  34.930  133.807  -2.931  -1.548   0.719  H19  6D6  47  
6D6  H20  H21   H  0  1  N  N  N  54.740  37.017  134.296  -5.096  -2.300   1.531  H20  6D6  48  
6D6  H21  H22   H  0  1  N  N  N  54.466  36.156  132.936  -5.888  -1.105   0.688  H21  6D6  49  
6D6  H23  H15   H  0  1  N  N  N  53.398  33.458  136.274  -3.388  -5.082  -1.678  H23  6D6  50  
6D6  H24  H25   H  0  1  N  N  N  50.898  36.908  131.375  -0.624   2.667  -0.614  H24  6D6  51  
6D6  H25  H26   H  0  1  N  N  N  49.741  39.294  129.401   2.078   2.010  -0.026  H25  6D6  52  
6D6  H26  H27   H  0  1  N  N  N  48.859  36.706  128.095   1.688  -0.012  -2.303  H26  6D6  53  
6D6  H27  H28   H  0  1  N  N  N  46.884  37.420  129.112   2.911   1.706  -3.422  H27  6D6  54  
6D6  H28  H29   H  0  1  N  N  N  48.811  36.874  132.122   1.223   3.252  -3.405  H28  6D6  55  
6D6  H29  H31   H  0  1  N  N  N  50.933  41.998  123.118   6.787  -2.997   1.980  H29  6D6  56  
6D6  H30  H30   H  0  1  N  N  N  51.648  40.539  123.280   5.182  -3.491   1.933  H30  6D6  57  
6D6  H31  H32   H  0  1  N  N  N  50.442  43.307  127.379   6.850   1.245   0.306  H31  6D6  58  
#   #
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
6D6  N6   C15  SING  N  N   1  
6D6  C15  N7   DOUB  Y  N   2  
6D6  C15  C9   SING  Y  N   3  
6D6  N5   C9   SING  Y  N   4  
6D6  N5   C8   DOUB  Y  N   5  
6D6  N7   C16  SING  Y  N   6  
6D6  C9   C17  DOUB  Y  N   7  
6D6  C8   N4   SING  Y  N   8  
6D6  C16  N8   DOUB  Y  N   9  
6D6  C17  N4   SING  Y  N  10  
6D6  C17  N8   SING  Y  N  11  
6D6  N4   C13  SING  N  N  12  
6D6  N1   C1   SING  N  N  13  
6D6  C13  C14  SING  N  N  14  
6D6  C13  O3   SING  N  N  15  
6D6  C14  O4   SING  N  N  16  
6D6  C14  C7   SING  N  N  17  
6D6  O3   C12  SING  N  N  18  
6D6  C1   C2   SING  N  N  19  
6D6  C2   C3   SING  N  N  20  
6D6  C6   C12  SING  N  N  21  
6D6  C6   N2   SING  N  N  22  
6D6  C7   C12  SING  N  N  23  
6D6  C7   O5   SING  N  N  24  
6D6  C3   N2   SING  N  N  25  
6D6  N2   C4   SING  N  N  26  
6D6  C4   C10  SING  N  N  27  
6D6  C10  C5   SING  N  N  28  
6D6  N3   C5   SING  N  N  29  
6D6  C5   C11  SING  N  N  30  
6D6  O1   C11  DOUB  N  N  31  
6D6  C11  O2   SING  N  N  32  
6D6  C1   H1   SING  N  N  33  
6D6  C1   H2   SING  N  N  34  
6D6  C2   H3   SING  N  N  35  
6D6  C2   H4   SING  N  N  36  
6D6  C3   H5   SING  N  N  37  
6D6  C3   H6   SING  N  N  38  
6D6  C4   H7   SING  N  N  39  
6D6  C4   H8   SING  N  N  40  
6D6  C5   H9   SING  N  N  41  
6D6  C6   H10  SING  N  N  42  
6D6  C6   H11  SING  N  N  43  
6D6  C7   H12  SING  N  N  44  
6D6  C8   H13  SING  N  N  45  
6D6  N1   H14  SING  N  N  46  
6D6  N1   H15  SING  N  N  47  
6D6  C10  H18  SING  N  N  48  
6D6  C10  H19  SING  N  N  49  
6D6  N3   H20  SING  N  N  50  
6D6  N3   H21  SING  N  N  51  
6D6  O2   H23  SING  N  N  52  
6D6  C12  H24  SING  N  N  53  
6D6  C13  H25  SING  N  N  54  
6D6  C14  H26  SING  N  N  55  
6D6  O4   H27  SING  N  N  56  
6D6  O5   H28  SING  N  N  57  
6D6  N6   H29  SING  N  N  58  
6D6  N6   H30  SING  N  N  59  
6D6  C16  H31  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
6D6  SMILES            ACDLabs               12.01  "C(CCN(CCC(C(O)=O)N)CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O)N"  
6D6  InChI             InChI                 1.03   "InChI=1S/C17H28N8O5/c18-3-1-4-24(5-2-9(19)17(28)29)6-10-12(26)13(27)16(30-10)25-8-23-11-14(20)21-7-22-15(11)25/h7-10,12-13,16,26-27H,1-6,18-19H2,(H,28,29)(H2,20,21,22)/t9-,10+,12+,13+,16+/m0/s1"  
6D6  InChIKey          InChI                 1.03   NHAKJKNYYCYZBR-UOYPZJKHSA-N  
6D6  SMILES_CANONICAL  CACTVS                3.385  "NCCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"  
6D6  SMILES            CACTVS                3.385  "NCCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"  
6D6  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCCN)CC[C@@H](C(=O)O)N)O)O)N"  
6D6  SMILES            "OpenEye OEToolkits"  2.0.4  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCN)CCC(C(=O)O)N)O)O)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
6D6  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine"  
6D6  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.4  "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]-2-azanyl-butanoic 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
6D6  "Create component"          2016-03-16  EBI   
6D6  "Initial release"           2017-03-15  RCSB  
6D6  "Modify leaving atom flag"  2021-08-26  PDBE  
##
