data_3VN
#

_chem_comp.id                                   3VN
_chem_comp.name                                 "(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H30 N4 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        bis-Lysine
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-11-14
_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                       318.412
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3VN
_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       4RT9
_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
3VN  N01  N01  N  0  1  N  N  N  19.394   6.467  49.507   1.896   1.145  -1.474  N01  3VN   1  
3VN  C02  C02  C  0  1  N  N  R  19.222   7.890  49.592   1.894   0.303  -0.270  C02  3VN   2  
3VN  C03  C03  C  0  1  N  N  N  17.910   8.257  48.966   2.003   1.176   0.954  C03  3VN   3  
3VN  O04  O04  O  0  1  N  N  N  17.164   7.350  48.511   1.424   0.869   1.969  O04  3VN   4  
3VN  O05  O05  O  0  1  N  N  N  17.535   9.460  48.875   2.742   2.296   0.915  O05  3VN   5  
3VN  C06  C06  C  0  1  N  N  N  20.337   8.554  48.852   3.083  -0.659  -0.317  C06  3VN   6  
3VN  C07  C07  C  0  1  N  N  N  20.174   8.774  47.385   4.385   0.143  -0.377  C07  3VN   7  
3VN  C08  C08  C  0  1  N  N  N  21.391   9.082  46.587   5.574  -0.819  -0.424  C08  3VN   8  
3VN  C09  C09  C  0  1  N  N  N  21.215   9.976  45.411   6.876  -0.018  -0.483  C09  3VN   9  
3VN  N10  N10  N  0  1  N  N  N  20.578   9.409  44.259   8.017  -0.941  -0.529  N10  3VN  10  
3VN  C11  C11  C  0  1  N  N  N  19.264   8.301  51.033   0.592  -0.498  -0.211  C11  3VN  11  
3VN  C12  C12  C  0  1  N  N  N  19.152   9.749  51.389  -0.600   0.459  -0.289  C12  3VN  12  
3VN  C13  C13  C  0  1  N  N  R  19.190  10.183  52.818  -1.902  -0.343  -0.229  C13  3VN  13  
3VN  N14  N14  N  0  1  N  N  N  18.623  11.493  52.923  -1.898  -1.362  -1.287  N14  3VN  14  
3VN  C15  C15  C  0  1  N  N  N  20.613  10.212  53.262  -3.090   0.600  -0.433  C15  3VN  15  
3VN  C16  C16  C  0  1  N  N  N  20.881  10.341  54.723  -4.392  -0.202  -0.373  C16  3VN  16  
3VN  C17  C17  C  0  1  N  N  N  22.135   9.736  55.253  -5.581   0.740  -0.577  C17  3VN  17  
3VN  C18  C18  C  0  1  N  N  N  22.404   9.933  56.704  -6.883  -0.061  -0.517  C18  3VN  18  
3VN  N19  N19  N  0  1  N  N  N  21.423   9.407  57.612  -8.023   0.844  -0.713  N19  3VN  19  
3VN  C20  C20  C  0  1  N  N  N  18.413   9.258  53.695  -2.017  -1.014   1.115  C20  3VN  20  
3VN  O21  O21  O  0  1  N  N  N  18.871   8.123  53.996  -1.445  -0.552   2.072  O21  3VN  21  
3VN  O22  O22  O  0  1  N  N  N  17.293   9.619  54.146  -2.757  -2.126   1.248  O22  3VN  22  
3VN  H1   H1   H  0  1  N  N  N  18.653   6.011  49.999   2.717   1.732  -1.503  H1   3VN  23  
3VN  H2   H2   H  0  1  N  N  N  19.379   6.186  48.547   1.824   0.582  -2.308  H2   3VN  24  
3VN  H4   H4   H  0  1  N  N  N  16.688   9.497  48.447   2.781   2.824   1.725  H4   3VN  25  
3VN  H5   H5   H  0  1  N  N  N  21.236   7.935  48.992   3.081  -1.283   0.576  H5   3VN  26  
3VN  H6   H6   H  0  1  N  N  N  19.476   9.614  47.256   4.387   0.767  -1.270  H6   3VN  27  
3VN  H7   H7   H  0  1  N  N  N  21.799   8.128  46.221   5.572  -1.444   0.470  H7   3VN  28  
3VN  H8   H8   H  0  1  N  N  N  22.119   9.558  47.261   5.495  -1.451  -1.309  H8   3VN  29  
3VN  H9   H9   H  0  1  N  N  N  22.213  10.322  45.103   6.878   0.607  -1.377  H9   3VN  30  
3VN  H10  H10  H  0  1  N  N  N  20.612  10.837  45.735   6.955   0.614   0.402  H10  3VN  31  
3VN  H11  H11  H  0  1  N  N  N  20.516  10.099  43.538   7.934  -1.581  -1.305  H11  3VN  32  
3VN  H12  H12  H  0  1  N  N  N  21.114   8.632  43.931   8.890  -0.436  -0.568  H12  3VN  33  
3VN  H14  H14  H  0  1  N  N  N  18.436   7.782  51.538   0.555  -1.194  -1.049  H14  3VN  34  
3VN  H15  H15  H  0  1  N  N  N  19.981  10.264  50.881  -0.563   1.155   0.549  H15  3VN  35  
3VN  H16  H16  H  0  1  N  N  N  18.645  11.791  53.877  -1.822  -0.936  -2.199  H16  3VN  36  
3VN  H17  H17  H  0  1  N  N  N  19.152  12.131  52.363  -1.161  -2.034  -1.139  H17  3VN  37  
3VN  H19  H19  H  0  1  N  N  N  21.082   9.276  52.923  -3.093   1.356   0.352  H19  3VN  38  
3VN  H20  H20  H  0  1  N  N  N  21.095  11.065  52.763  -3.006   1.085  -1.405  H20  3VN  39  
3VN  H21  H21  H  0  1  N  N  N  20.910  11.415  54.958  -4.390  -0.958  -1.158  H21  3VN  40  
3VN  H22  H22  H  0  1  N  N  N  22.089   8.653  55.065  -5.583   1.497   0.208  H22  3VN  41  
3VN  H23  H23  H  0  1  N  N  N  23.366   9.452  56.935  -6.880  -0.817  -1.302  H23  3VN  42  
3VN  H24  H24  H  0  1  N  N  N  22.483  11.015  56.886  -6.966  -0.547   0.455  H24  3VN  43  
3VN  H25  H25  H  0  1  N  N  N  21.704   9.595  58.553  -8.896   0.338  -0.678  H25  3VN  44  
3VN  H26  H26  H  0  1  N  N  N  20.539   9.840  57.435  -8.012   1.592  -0.036  H26  3VN  45  
3VN  H28  H28  H  0  1  N  N  N  16.932   8.928  54.688  -2.801  -2.522   2.129  H28  3VN  46  
3VN  H3   H3   H  0  1  N  N  N  20.495   9.539  49.315   3.004  -1.290  -1.202  H3   3VN  47  
3VN  H29  H29  H  0  1  N  N  N  19.729   7.860  46.964   4.463   0.774   0.508  H29  3VN  48  
3VN  H13  H13  H  0  1  N  N  N  20.222   7.945  51.440   0.550  -1.054   0.726  H13  3VN  49  
3VN  H30  H30  H  0  1  N  N  N  18.195  10.102  50.978  -0.558   1.015  -1.225  H30  3VN  50  
3VN  H18  H18  H  0  1  N  N  N  20.040   9.872  55.254  -4.476  -0.688   0.599  H18  3VN  51  
3VN  H31  H31  H  0  1  N  N  N  22.978  10.170  54.695  -5.497   1.226  -1.549  H31  3VN  52  
#   #
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
3VN  N10  C09  SING  N  N   1  
3VN  C09  C08  SING  N  N   2  
3VN  C08  C07  SING  N  N   3  
3VN  C07  C06  SING  N  N   4  
3VN  O04  C03  DOUB  N  N   5  
3VN  C06  C02  SING  N  N   6  
3VN  O05  C03  SING  N  N   7  
3VN  C03  C02  SING  N  N   8  
3VN  N01  C02  SING  N  N   9  
3VN  C02  C11  SING  N  N  10  
3VN  C11  C12  SING  N  N  11  
3VN  C12  C13  SING  N  N  12  
3VN  C13  N14  SING  N  N  13  
3VN  C13  C15  SING  N  N  14  
3VN  C13  C20  SING  N  N  15  
3VN  C15  C16  SING  N  N  16  
3VN  C20  O21  DOUB  N  N  17  
3VN  C20  O22  SING  N  N  18  
3VN  C16  C17  SING  N  N  19  
3VN  C17  C18  SING  N  N  20  
3VN  C18  N19  SING  N  N  21  
3VN  N01  H1   SING  N  N  22  
3VN  N01  H2   SING  N  N  23  
3VN  O05  H4   SING  N  N  24  
3VN  C06  H5   SING  N  N  25  
3VN  C07  H6   SING  N  N  26  
3VN  C08  H7   SING  N  N  27  
3VN  C08  H8   SING  N  N  28  
3VN  C09  H9   SING  N  N  29  
3VN  C09  H10  SING  N  N  30  
3VN  N10  H11  SING  N  N  31  
3VN  N10  H12  SING  N  N  32  
3VN  C11  H14  SING  N  N  33  
3VN  C12  H15  SING  N  N  34  
3VN  N14  H16  SING  N  N  35  
3VN  N14  H17  SING  N  N  36  
3VN  C15  H19  SING  N  N  37  
3VN  C15  H20  SING  N  N  38  
3VN  C16  H21  SING  N  N  39  
3VN  C17  H22  SING  N  N  40  
3VN  C18  H23  SING  N  N  41  
3VN  C18  H24  SING  N  N  42  
3VN  N19  H25  SING  N  N  43  
3VN  N19  H26  SING  N  N  44  
3VN  O22  H28  SING  N  N  45  
3VN  C06  H3   SING  N  N  46  
3VN  C07  H29  SING  N  N  47  
3VN  C11  H13  SING  N  N  48  
3VN  C12  H30  SING  N  N  49  
3VN  C16  H18  SING  N  N  50  
3VN  C17  H31  SING  N  N  51  
#   #
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
3VN  SMILES            ACDLabs               12.01  "O=C(O)C(N)(CCC(N)(C(=O)O)CCCCN)CCCCN"  
3VN  InChI             InChI                 1.03   "InChI=1S/C14H30N4O4/c15-9-3-1-5-13(17,11(19)20)7-8-14(18,12(21)22)6-2-4-10-16/h1-10,15-18H2,(H,19,20)(H,21,22)/t13-,14-/m1/s1"  
3VN  InChIKey          InChI                 1.03   XYUHPPVEDOOPDE-ZIAGYGMSSA-N  
3VN  SMILES_CANONICAL  CACTVS                3.385  "NCCCC[C@@](N)(CC[C@](N)(CCCCN)C(O)=O)C(O)=O"  
3VN  SMILES            CACTVS                3.385  "NCCCC[C](N)(CC[C](N)(CCCCN)C(O)=O)C(O)=O"  
3VN  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C(CCN)C[C@@](CC[C@](CCCCN)(C(=O)O)N)(C(=O)O)N"  
3VN  SMILES            "OpenEye OEToolkits"  1.7.6  "C(CCN)CC(CCC(CCCCN)(C(=O)O)N)(C(=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
3VN  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid (non-preferred name)"  
3VN  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "(2R,5R)-2,5-bis(azanyl)-2,5-bis(4-azanylbutyl)hexanedioic 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
3VN  "Create component"  2014-11-14  RCSB  
3VN  "Initial release"   2016-02-17  RCSB  
3VN  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3VN
_pdbx_chem_comp_synonyms.name        bis-Lysine
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
