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                    2024-09-27 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 Y N Y 52.620 31.191 129.501 -3.817 3.851  2.064  C1  6D6 1  
6D6 C2  C5   C 0 1 N N N 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 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 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 N N N 52.985 36.027 134.295 -4.599 -2.222 -0.465 C5  6D6 5  
6D6 C6  C15  C 0 1 N N N 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 N N N 49.157 36.673 130.184 0.412  1.766  -2.293 C7  6D6 7  
6D6 C8  C24  C 0 1 Y N N N 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 N 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 Y N Y 53.525 30.883 128.447 -4.319 3.885  3.444  N1  6D6 10 
6D6 N2  N7   N 0 1 N N N 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 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 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 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 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 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 N N N 50.629 36.673 130.335 -0.438 1.669  -1.011 C12 6D6 17 
6D6 O3  O17  O 0 1 N N N 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 N N N 49.980 38.393 128.818 1.706  1.053  -0.390 C13 6D6 19 
6D6 C14 C19  C 0 1 N N R N N N 48.839 37.396 128.952 1.719  1.015  -1.939 C14 6D6 20 
6D6 O4  O20  O 0 1 N N N 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 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 N 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 N 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 N 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 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 N 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 N 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 N 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 N 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 Y N Y 51.658 30.691 129.313 -2.898 4.433  1.997  H1  6D6 31 
6D6 H2  H33  H 0 1 N N N Y N Y 53.037 30.836 130.455 -4.565 4.276  1.395  H2  6D6 32 
6D6 H3  H2   H 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 Y N Y 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 Y N Y 53.147 31.204 127.579 -4.514 4.832  3.735  H15 6D6 45 
6D6 H18 H19  H 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 
6D6 "Modify backbone"          2023-11-03 PDBE 
6D6 "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            6D6 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain and backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               N-terminal 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
