data_6D2
# 
_chem_comp.id                                    6D2 
_chem_comp.name                                  "5'-{[(3S)-3-amino-3-carboxypropyl](3-carbamimidamidopropyl)amino}-5'-deoxyadenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H30 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                        466.495 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6D2 
_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        5ISE 
_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 
6D2 C11    C1  C 0 1 N N N 52.559 32.412 131.120 3.806  -0.985 0.347  C11    6D2 1  
6D2 C10    C2  C 0 1 N N N 51.272 33.270 131.264 2.970  -0.841 -0.926 C10    6D2 2  
6D2 C2     C3  C 0 1 Y N N 50.478 42.393 127.611 -5.981 -2.417 0.947  C2     6D2 3  
6D2 C6     C4  C 0 1 Y N N 50.723 41.251 125.590 -6.193 -0.295 1.830  C6     6D2 4  
6D2 C5     C5  C 0 1 Y N N 50.539 40.025 126.234 -4.937 0.032  1.291  C5     6D2 5  
6D2 C4     C6  C 0 1 Y N N 50.327 40.057 127.581 -4.249 -0.956 0.565  C4     6D2 6  
6D2 C14    C7  C 0 1 N N N 52.405 29.585 129.909 6.425  -3.371 1.558  C14    6D2 7  
6D2 C12    C8  C 0 1 N N N 52.917 32.081 129.676 4.723  -2.203 0.221  C12    6D2 8  
6D2 C8     C9  C 0 1 Y N N 50.303 37.965 126.927 -3.065 0.903  0.629  C8     6D2 9  
6D2 N6     N1  N 0 1 N N N 50.917 41.249 124.213 -6.917 0.636  2.554  N6     6D2 10 
6D2 N1     N2  N 0 1 Y N N 50.690 42.403 126.312 -6.667 -1.521 1.633  N1     6D2 11 
6D2 N3     N3  N 0 1 Y N N 50.300 41.231 128.267 -4.802 -2.156 0.424  N3     6D2 12 
6D2 ND     N4  N 0 1 N N N 51.443 34.577 131.841 2.090  0.329  -0.805 ND     6D2 13 
6D2 CG     C10 C 0 1 N N N 52.469 34.699 132.903 2.870  1.572  -0.757 CG     6D2 14 
6D2 CB     C11 C 0 1 N N N 51.997 35.692 133.982 1.990  2.707  -0.231 CB     6D2 15 
6D2 CA     C12 C 0 1 N N S 53.088 36.139 134.991 2.790  4.011  -0.219 CA     6D2 16 
6D2 C      C13 C 0 1 N N N 53.781 35.004 135.676 1.890  5.150  0.186  C      6D2 17 
6D2 O      O1  O 0 1 N N N 55.024 34.710 135.402 1.929  5.579  1.315  O      6D2 18 
6D2 N      N5  N 0 1 N N N 54.130 36.878 134.400 3.897  3.897  0.740  N      6D2 19 
6D2 "C5'"  C14 C 0 1 N N N 51.641 35.551 130.756 1.109  0.365  -1.897 "C5'"  6D2 20 
6D2 "C4'"  C15 C 0 1 N N R 50.710 36.821 130.904 0.016  -0.674 -1.636 "C4'"  6D2 21 
6D2 "C3'"  C16 C 0 1 N N S 49.248 36.621 130.756 -0.984 -0.710 -2.813 "C3'"  6D2 22 
6D2 "C2'"  C17 C 0 1 N N R 48.773 37.362 129.559 -2.353 -0.941 -2.135 "C2'"  6D2 23 
6D2 "O2'"  O2  O 0 1 N N N 47.511 37.968 129.799 -2.932 -2.169 -2.582 "O2'"  6D2 24 
6D2 "C1'"  C18 C 0 1 N N R 49.952 38.359 129.349 -2.018 -1.017 -0.629 "C1'"  6D2 25 
6D2 N9     N6  N 0 1 Y N N 50.131 38.756 127.977 -3.073 -0.377 0.161  N9     6D2 26 
6D2 N7     N7  N 0 1 Y N N 50.510 38.713 125.824 -4.161 1.142  1.288  N7     6D2 27 
6D2 "O4'"  O3  O 0 1 N N N 51.122 37.605 129.773 -0.774 -0.295 -0.488 "O4'"  6D2 28 
6D2 "O3'"  O4  O 0 1 N N N 48.711 37.178 131.963 -0.676 -1.788 -3.699 "O3'"  6D2 29 
6D2 N10    N8  N 0 1 N N N 52.845 29.402 131.301 6.569  -4.226 0.584  N10    6D2 30 
6D2 N11    N9  N 0 1 N N N 51.930 28.487 129.277 7.176  -3.500 2.702  N11    6D2 31 
6D2 N12    N10 N 0 1 N N N 52.442 30.806 129.189 5.523  -2.340 1.441  N12    6D2 32 
6D2 OXT    O5  O 0 1 N N N 53.128 34.378 136.533 1.046  5.688  -0.708 OXT    6D2 33 
6D2 H112   H1  H 0 0 N N N 52.410 31.469 131.666 4.410  -0.088 0.489  H112   6D2 34 
6D2 H111   H2  H 0 0 N N N 53.397 32.966 131.567 3.144  -1.115 1.204  H111   6D2 35 
6D2 H102   H3  H 0 0 N N N 50.841 33.400 130.260 3.632  -0.710 -1.782 H102   6D2 36 
6D2 H101   H4  H 0 0 N N N 50.566 32.713 131.897 2.366  -1.737 -1.067 H101   6D2 37 
6D2 H21    H5  H 0 1 N N N 50.447 43.325 128.155 -6.402 -3.403 0.814  H21    6D2 38 
6D2 H122   H6  H 0 0 N N N 54.014 32.089 129.589 4.119  -3.099 0.080  H122   6D2 39 
6D2 H121   H7  H 0 0 N N N 52.493 32.867 129.034 5.385  -2.072 -0.635 H121   6D2 40 
6D2 H81    H8  H 0 1 N N N 50.281 36.886 126.951 -2.268 1.615  0.473  H81    6D2 41 
6D2 H61    H9  H 0 1 N N N 51.019 42.190 123.889 -6.558 1.526  2.694  H61    6D2 42 
6D2 H62    H10 H 0 1 N N N 51.743 40.730 123.994 -7.783 0.398  2.921  H62    6D2 43 
6D2 HG3    H12 H 0 1 N N N 52.636 33.714 133.363 3.726  1.439  -0.094 HG3    6D2 44 
6D2 HG2    H13 H 0 1 N N N 53.409 35.061 132.461 3.222  1.819  -1.758 HG2    6D2 45 
6D2 HB2    H14 H 0 1 N N N 51.615 36.590 133.474 1.119  2.821  -0.877 HB2    6D2 46 
6D2 HB3    H15 H 0 1 N N N 51.183 35.217 134.549 1.662  2.473  0.782  HB3    6D2 47 
6D2 HA     H16 H 0 1 N N N 52.596 36.754 135.759 3.191  4.200  -1.215 HA     6D2 48 
6D2 H      H17 H 0 1 N N N 54.796 37.134 135.100 3.552  3.721  1.672  H      6D2 49 
6D2 H2     H18 H 0 1 N N N 54.579 36.321 133.701 4.550  3.182  0.456  H2     6D2 50 
6D2 "H5'1" H20 H 0 0 N N N 51.419 35.061 129.797 0.661  1.357  -1.951 "H5'1" 6D2 51 
6D2 "H5'2" H21 H 0 0 N N N 52.691 35.880 130.765 1.607  0.139  -2.840 "H5'2" 6D2 52 
6D2 "H4'1" H22 H 0 0 N N N 50.938 37.332 131.851 0.459  -1.659 -1.484 "H4'1" 6D2 53 
6D2 "H3'1" H23 H 0 0 N N N 49.010 35.551 130.668 -0.976 0.238  -3.350 "H3'1" 6D2 54 
6D2 "H2'1" H24 H 0 0 N N N 48.722 36.683 128.695 -3.025 -0.107 -2.338 "H2'1" 6D2 55 
6D2 "H2'2" H25 H 0 0 N N N 46.852 37.293 129.915 -3.107 -2.198 -3.533 "H2'2" 6D2 56 
6D2 "H1'1" H26 H 0 0 N N N 49.802 39.237 129.994 -1.889 -2.055 -0.321 "H1'1" 6D2 57 
6D2 "H3'2" H27 H 0 0 N N N 49.031 36.685 132.709 -1.273 -1.858 -4.457 "H3'2" 6D2 58 
6D2 H104   H28 H 0 0 N N N 52.732 28.457 131.609 7.206  -4.953 0.667  H104   6D2 59 
6D2 H113   H29 H 0 0 N N N 51.892 27.611 129.757 7.813  -4.227 2.785  H113   6D2 60 
6D2 H4     H30 H 0 1 N N N 51.617 28.552 128.330 7.070  -2.864 3.427  H4     6D2 61 
6D2 H123   H31 H 0 0 N N N 52.105 30.782 128.248 5.416  -1.704 2.165  H123   6D2 62 
6D2 H5     H32 H 0 1 N N N 53.673 33.700 136.914 0.543  6.464  -0.425 H5     6D2 63 
# 
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 
6D2 N6    C6     SING N N 1  
6D2 C6    C5     DOUB Y N 2  
6D2 C6    N1     SING Y N 3  
6D2 N7    C5     SING Y N 4  
6D2 N7    C8     DOUB Y N 5  
6D2 C5    C4     SING Y N 6  
6D2 N1    C2     DOUB Y N 7  
6D2 C8    N9     SING Y N 8  
6D2 C4    N9     SING Y N 9  
6D2 C4    N3     DOUB Y N 10 
6D2 C2    N3     SING Y N 11 
6D2 N9    "C1'"  SING N N 12 
6D2 N12   C12    SING N N 13 
6D2 N12   C14    SING N N 14 
6D2 N11   C14    SING N N 15 
6D2 "C1'" "C2'"  SING N N 16 
6D2 "C1'" "O4'"  SING N N 17 
6D2 "C2'" "O2'"  SING N N 18 
6D2 "C2'" "C3'"  SING N N 19 
6D2 C12   C11    SING N N 20 
6D2 "O4'" "C4'"  SING N N 21 
6D2 C14   N10    DOUB N N 22 
6D2 "C3'" "C4'"  SING N N 23 
6D2 "C3'" "O3'"  SING N N 24 
6D2 "C5'" "C4'"  SING N N 25 
6D2 "C5'" ND     SING N N 26 
6D2 C11   C10    SING N N 27 
6D2 C10   ND     SING N N 28 
6D2 ND    CG     SING N N 29 
6D2 CG    CB     SING N N 30 
6D2 CB    CA     SING N N 31 
6D2 N     CA     SING N N 32 
6D2 CA    C      SING N N 33 
6D2 O     C      DOUB N N 34 
6D2 C     OXT    SING N N 35 
6D2 C11   H112   SING N N 36 
6D2 C11   H111   SING N N 37 
6D2 C10   H102   SING N N 38 
6D2 C10   H101   SING N N 39 
6D2 C2    H21    SING N N 40 
6D2 C12   H122   SING N N 41 
6D2 C12   H121   SING N N 42 
6D2 C8    H81    SING N N 43 
6D2 N6    H61    SING N N 44 
6D2 N6    H62    SING N N 45 
6D2 CG    HG3    SING N N 46 
6D2 CG    HG2    SING N N 47 
6D2 CB    HB2    SING N N 48 
6D2 CB    HB3    SING N N 49 
6D2 CA    HA     SING N N 50 
6D2 N     H      SING N N 51 
6D2 N     H2     SING N N 52 
6D2 "C5'" "H5'1" SING N N 53 
6D2 "C5'" "H5'2" SING N N 54 
6D2 "C4'" "H4'1" SING N N 55 
6D2 "C3'" "H3'1" SING N N 56 
6D2 "C2'" "H2'1" SING N N 57 
6D2 "O2'" "H2'2" SING N N 58 
6D2 "C1'" "H1'1" SING N N 59 
6D2 "O3'" "H3'2" SING N N 60 
6D2 N10   H104   SING N N 61 
6D2 N11   H113   SING N N 62 
6D2 N11   H4     SING N N 63 
6D2 N12   H123   SING N N 64 
6D2 OXT   H5     SING N N 65 
# 
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 
6D2 SMILES           ACDLabs              12.01 "C(CN(CCC(C(O)=O)N)CC1C(O)C(O)C(O1)n3c2c(c(ncn2)N)nc3)CNC(=N)\N" 
6D2 InChI            InChI                1.03  
"InChI=1S/C18H30N10O5/c19-9(17(31)32)2-5-27(4-1-3-23-18(21)22)6-10-12(29)13(30)16(33-10)28-8-26-11-14(20)24-7-25-15(11)28/h7-10,12-13,16,29-30H,1-6,19H2,(H,31,32)(H2,20,24,25)(H4,21,22,23)/t9-,10+,12+,13+,16+/m0/s1" 
6D2 InChIKey         InChI                1.03  XBMZCXWGTKEJNB-UOYPZJKHSA-N 
6D2 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCN(CCCNC(N)=N)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O" 
6D2 SMILES           CACTVS               3.385 "N[CH](CCN(CCCNC(N)=N)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O" 
6D2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C(/N)\NCCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 
6D2 SMILES           "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCNC(=N)N)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 
6D2 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-{[(3S)-3-amino-3-carboxypropyl](3-carbamimidamidopropyl)amino}-5'-deoxyadenosine"                                                                    
6D2 "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-carbamimidamidopropyl)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 
6D2 "Create component" 2016-03-16 EBI  
6D2 "Initial release"  2017-03-15 RCSB 
# 
