data_6D4
# 
_chem_comp.id                                    6D4 
_chem_comp.name                                  "5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H28 N10 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                    2017-03-10 
_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                        440.458 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6D4 
_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        5ISF 
_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 
6D4 C16 C1  C 0 1 N N N 52.453 32.824 130.326 3.617  2.228  -0.923 C16 6D4 1  
6D4 C15 C2  C 0 1 N N N 51.730 33.065 131.670 3.028  1.951  0.462  C15 6D4 2  
6D4 C14 C3  C 0 1 N N N 53.560 34.689 136.234 3.747  -4.181 0.049  C14 6D4 3  
6D4 N10 N1  N 0 1 N N N 52.354 29.889 131.694 3.851  5.041  -2.959 N10 6D4 4  
6D4 C11 C4  C 0 1 N N N 52.593 34.924 132.981 3.642  -0.390 0.559  C11 6D4 5  
6D4 C12 C5  C 0 1 N N N 51.924 35.220 134.380 3.125  -1.786 0.205  C12 6D4 6  
6D4 C01 C6  C 0 1 Y N N 50.312 39.923 127.971 -3.968 0.125  -0.386 C01 6D4 7  
6D4 C02 C7  C 0 1 Y N N 50.511 39.881 126.556 -4.332 -0.976 -1.180 C02 6D4 8  
6D4 C03 C8  C 0 1 Y N N 50.693 41.079 125.938 -5.672 -1.087 -1.586 C03 6D4 9  
6D4 N01 N2  N 0 1 Y N N 50.680 42.211 126.639 -6.530 -0.147 -1.202 N01 6D4 10 
6D4 C04 C9  C 0 1 Y N N 50.483 42.136 127.980 -6.141 0.870  -0.455 C04 6D4 11 
6D4 N02 N3  N 0 1 Y N N 50.289 41.011 128.726 -4.895 1.017  -0.055 N02 6D4 12 
6D4 N03 N4  N 0 1 Y N N 50.165 38.650 128.241 -2.625 -0.015 -0.139 N03 6D4 13 
6D4 C05 C10 C 0 1 Y N N 50.245 37.786 127.307 -2.213 -1.157 -0.757 C05 6D4 14 
6D4 N04 N5  N 0 1 Y N N 50.463 38.426 126.110 -3.214 -1.717 -1.372 N04 6D4 15 
6D4 N05 N6  N 0 1 N N N 50.904 41.111 124.483 -6.089 -2.149 -2.369 N05 6D4 16 
6D4 C06 C11 C 0 1 N N R 49.958 38.248 129.590 -1.789 0.897  0.646  C06 6D4 17 
6D4 C07 C12 C 0 1 N N R 48.910 37.231 129.811 -1.877 0.555  2.155  C07 6D4 18 
6D4 C08 C13 C 0 1 N N S 49.341 36.462 130.983 -0.541 1.122  2.694  C08 6D4 19 
6D4 C09 C14 C 0 1 N N R 50.791 36.629 131.129 0.360  1.215  1.447  C09 6D4 20 
6D4 O01 O1  O 0 1 N N N 51.258 37.638 130.091 -0.393 0.700  0.337  O01 6D4 21 
6D4 O02 O2  O 0 1 N N N 47.639 37.876 130.073 -2.991 1.213  2.763  O02 6D4 22 
6D4 O03 O3  O 0 1 N N N 48.683 36.973 132.187 -0.740 2.416  3.265  O03 6D4 23 
6D4 C10 C15 C 0 1 N N N 51.516 35.349 130.865 1.625  0.380  1.655  C10 6D4 24 
6D4 N06 N7  N 0 1 N N N 51.548 34.492 132.041 2.530  0.570  0.514  N06 6D4 25 
6D4 C13 C16 C 0 1 N N S 52.914 35.808 135.433 4.278  -2.789 0.277  C13 6D4 26 
6D4 O04 O4  O 0 1 N N N 52.898 34.044 137.084 3.151  -4.845 1.052  O04 6D4 27 
6D4 O05 O5  O 0 1 N N N 54.773 34.410 136.039 3.857  -4.700 -1.037 O05 6D4 28 
6D4 N07 N8  N 0 1 N N N 53.963 36.578 134.819 5.271  -2.469 -0.757 N07 6D4 29 
6D4 N08 N9  N 0 1 N N N 52.996 31.698 130.188 3.998  3.644  -1.018 N08 6D4 30 
6D4 N09 N10 N 0 1 N N N 52.678 30.790 130.935 4.563  3.945  -2.323 N09 6D4 31 
6D4 H23 H1  H 0 1 N N N 53.235 33.590 130.222 4.498  1.604  -1.074 H23 6D4 32 
6D4 H24 H2  H 0 1 N N N 51.714 32.943 129.520 2.874  2.000  -1.686 H24 6D4 33 
6D4 H22 H3  H 0 1 N N N 50.735 32.599 131.610 3.800  2.087  1.219  H22 6D4 34 
6D4 H21 H4  H 0 1 N N N 52.316 32.579 132.464 2.207  2.641  0.652  H21 6D4 35 
6D4 H25 H5  H 0 1 N N N 52.586 29.007 131.283 4.243  5.250  -3.865 H25 6D4 36 
6D4 H1  H6  H 0 1 N N N 52.842 29.992 132.561 2.865  4.839  -3.030 H1  6D4 37 
6D4 H14 H7  H 0 1 N N N 53.344 34.128 133.091 4.069  -0.404 1.561  H14 6D4 38 
6D4 H13 H8  H 0 1 N N N 53.078 35.836 132.602 4.407  -0.093 -0.158 H13 6D4 39 
6D4 H15 H9  H 0 1 N N N 51.107 35.941 134.229 2.347  -2.075 0.912  H15 6D4 40 
6D4 H16 H10 H 0 1 N N N 51.514 34.279 134.776 2.714  -1.776 -0.804 H16 6D4 41 
6D4 H01 H11 H 0 1 N N N 50.480 43.073 128.517 -6.871 1.611  -0.166 H01 6D4 42 
6D4 H02 H12 H 0 1 N N N 50.155 36.717 127.436 -1.202 -1.538 -0.745 H02 6D4 43 
6D4 H03 H13 H 0 1 N N N 51.020 42.058 124.183 -5.454 -2.828 -2.644 H03 6D4 44 
6D4 H04 H14 H 0 1 N N N 51.724 40.586 124.254 -7.018 -2.214 -2.644 H04 6D4 45 
6D4 H26 H15 H 0 1 N N N 49.732 39.130 130.206 -2.082 1.932  0.469  H26 6D4 46 
6D4 H05 H16 H 0 1 N N N 48.833 36.573 128.933 -1.933 -0.522 2.308  H05 6D4 47 
6D4 H06 H17 H 0 1 N N N 49.098 35.398 130.844 -0.107 0.442  3.428  H06 6D4 48 
6D4 H07 H18 H 0 1 N N N 51.034 36.997 132.137 0.629  2.255  1.262  H07 6D4 49 
6D4 H08 H19 H 0 1 N N N 46.971 37.215 130.214 -3.088 1.030  3.707  H08 6D4 50 
6D4 H09 H20 H 0 1 N N N 48.967 36.470 132.941 -1.346 2.425  4.019  H09 6D4 51 
6D4 H10 H21 H 0 1 N N N 51.008 34.814 130.049 2.123  0.697  2.571  H10 6D4 52 
6D4 H11 H22 H 0 1 N N N 52.549 35.580 130.565 1.355  -0.674 1.734  H11 6D4 53 
6D4 H17 H24 H 0 1 N N N 52.341 36.446 136.122 4.746  -2.735 1.260  H17 6D4 54 
6D4 H2  H25 H 0 1 N N N 53.454 33.388 137.487 2.827  -5.735 0.858  H2  6D4 55 
6D4 H20 H26 H 0 1 N N N 54.573 36.935 135.527 4.861  -2.512 -1.678 H20 6D4 56 
6D4 H19 H27 H 0 1 N N N 54.483 35.995 134.195 5.689  -1.566 -0.590 H19 6D4 57 
6D4 H3  H29 H 0 1 N N N 52.801 31.392 129.256 3.212  4.244  -0.817 H3  6D4 58 
6D4 H4  H30 H 0 1 N N N 52.138 30.373 130.204 4.567  3.126  -2.913 H4  6D4 59 
# 
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 
6D4 N05 C03 SING N N 1  
6D4 C03 C02 DOUB Y N 2  
6D4 C03 N01 SING Y N 3  
6D4 N04 C02 SING Y N 4  
6D4 N04 C05 DOUB Y N 5  
6D4 C02 C01 SING Y N 6  
6D4 N01 C04 DOUB Y N 7  
6D4 C05 N03 SING Y N 8  
6D4 C01 N03 SING Y N 9  
6D4 C01 N02 DOUB Y N 10 
6D4 C04 N02 SING Y N 11 
6D4 N03 C06 SING N N 12 
6D4 C06 C07 SING N N 13 
6D4 C06 O01 SING N N 14 
6D4 C07 O02 SING N N 15 
6D4 C07 C08 SING N N 16 
6D4 O01 C09 SING N N 17 
6D4 N08 C16 SING N N 18 
6D4 N08 N09 SING N N 19 
6D4 C16 C15 SING N N 20 
6D4 C10 C09 SING N N 21 
6D4 C10 N06 SING N N 22 
6D4 N09 N10 SING N N 23 
6D4 C08 C09 SING N N 24 
6D4 C08 O03 SING N N 25 
6D4 C15 N06 SING N N 26 
6D4 N06 C11 SING N N 27 
6D4 C11 C12 SING N N 28 
6D4 C12 C13 SING N N 29 
6D4 N07 C13 SING N N 30 
6D4 C13 C14 SING N N 31 
6D4 O05 C14 DOUB N N 32 
6D4 C14 O04 SING N N 33 
6D4 C16 H23 SING N N 34 
6D4 C16 H24 SING N N 35 
6D4 C15 H22 SING N N 36 
6D4 C15 H21 SING N N 37 
6D4 N10 H25 SING N N 38 
6D4 N10 H1  SING N N 39 
6D4 C11 H14 SING N N 40 
6D4 C11 H13 SING N N 41 
6D4 C12 H15 SING N N 42 
6D4 C12 H16 SING N N 43 
6D4 C04 H01 SING N N 44 
6D4 C05 H02 SING N N 45 
6D4 N05 H03 SING N N 46 
6D4 N05 H04 SING N N 47 
6D4 C06 H26 SING N N 48 
6D4 C07 H05 SING N N 49 
6D4 C08 H06 SING N N 50 
6D4 C09 H07 SING N N 51 
6D4 O02 H08 SING N N 52 
6D4 O03 H09 SING N N 53 
6D4 C10 H10 SING N N 54 
6D4 C10 H11 SING N N 55 
6D4 C13 H17 SING N N 56 
6D4 O04 H2  SING N N 57 
6D4 N07 H20 SING N N 58 
6D4 N07 H19 SING N N 59 
6D4 N08 H3  SING N N 60 
6D4 N09 H4  SING N N 61 
# 
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 
6D4 SMILES           ACDLabs              12.01 "C(CN(CCC(C(O)=O)N)CC3C(C(C(n2c1ncnc(c1nc2)N)O3)O)O)NNN"                                                                                                                                                   
6D4 InChI            InChI                1.03  "InChI=1S/C16H28N10O5/c17-8(16(29)30)1-3-25(4-2-23-24-19)5-9-11(27)12(28)15(31-9)26-7-22-10-13(18)20-6-21-14(10)26/h6-9,11-12,15,23-24,27-28H,1-5,17,19H2,(H,29,30)(H2,18,20,21)/t8-,9+,11+,12+,15+/m0/s1" 
6D4 InChIKey         InChI                1.03  VMVULOLZRIEVIA-OPYVMVOTSA-N                                                                                                                                                                                
6D4 SMILES_CANONICAL CACTVS               3.385 "NNNCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                                                  
6D4 SMILES           CACTVS               3.385 "NNNCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                                        
6D4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)O)N)CCNNN)O)O)N"                                                                                                                          
6D4 SMILES           "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCNNN)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 
6D4 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine"                                                                          
6D4 "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-[2-(2-azanylhydrazinyl)ethyl]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 
6D4 "Create component" 2016-03-16 EBI  
6D4 "Initial release"  2017-03-15 RCSB 
# 
