data_5DK
#

_chem_comp.id                                   5DK
_chem_comp.name                                 "(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H22 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        PLP-DArg
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-09-09
_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                       403.328
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5DK
_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       5DJ3
_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
5DK  C2   C1   C  0  1  Y  N  N  67.802   8.239  -25.278   1.313  -2.439   2.644  C2   5DK   1  
5DK  C3   C2   C  0  1  Y  N  N  67.309   8.601  -26.523   0.446  -2.183   1.591  C3   5DK   2  
5DK  C4   C3   C  0  1  Y  N  N  66.002   8.278  -26.884   0.832  -1.261   0.605  C4   5DK   3  
5DK  C5   C4   C  0  1  Y  N  N  65.252   7.597  -25.924   2.080  -0.642   0.734  C5   5DK   4  
5DK  C6   C5   C  0  1  Y  N  N  65.811   7.260  -24.698   2.876  -0.958   1.816  C6   5DK   5  
5DK  CB   C6   C  0  1  N  N  N  64.523   8.685  -30.818  -3.405  -0.666  -1.250  CB   5DK   6  
5DK  O3   O1   O  0  1  N  N  N  68.166   9.299  -27.371  -0.754  -2.814   1.515  O3   5DK   7  
5DK  O1P  O2   O  0  1  N  N  N  62.740   4.089  -28.318   5.016   1.288  -2.243  O1P  5DK   8  
5DK  O2P  O3   O  0  1  N  N  N  61.552   5.261  -26.461   6.009   2.328  -0.042  O2P  5DK   9  
5DK  O3P  O4   O  0  1  N  N  N  61.832   6.391  -28.604   3.814   3.126  -0.999  O3P  5DK  10  
5DK  O4P  O5   O  0  1  N  N  N  63.912   6.123  -27.134   3.845   0.838   0.068  O4P  5DK  11  
5DK  N    N1   N  0  1  N  N  N  66.145   9.143  -29.083  -1.203  -1.538  -0.637  N    5DK  12  
5DK  P    P1   P  0  1  N  N  N  62.515   5.442  -27.649   4.652   1.922  -0.808  P    5DK  13  
5DK  C2A  C7   C  0  1  N  N  N  69.242   8.656  -24.946   0.916  -3.426   3.712  C2A  5DK  14  
5DK  C4A  C8   C  0  1  N  N  N  65.346   8.632  -28.253  -0.054  -0.954  -0.535  C4A  5DK  15  
5DK  C5A  C9   C  0  1  N  N  N  63.809   7.195  -26.244   2.549   0.356  -0.293  C5A  5DK  16  
5DK  N1   N2   N  0  1  Y  N  N  67.051   7.580  -24.403   2.480  -1.835   2.719  N1   5DK  17  
5DK  CA   C10  C  0  1  N  N  R  65.372   9.774  -30.152  -2.082  -1.233  -1.769  CA   5DK  18  
5DK  C    C11  C  0  1  N  N  N  66.287  10.414  -31.202  -2.348  -2.493  -2.552  C    5DK  19  
5DK  O    O6   O  0  1  N  N  N  67.494  10.624  -30.998  -3.133  -2.454  -3.640  O    5DK  20  
5DK  CG   C12  C  0  1  N  N  N  63.101   9.177  -31.189  -3.149   0.677  -0.562  CG   5DK  21  
5DK  CD   C13  C  0  1  N  N  N  62.103   7.996  -31.146  -4.472   1.243  -0.043  CD   5DK  22  
5DK  NE   N3   N  0  1  N  N  N  62.084   7.326  -32.454  -4.228   2.529   0.615  NE   5DK  23  
5DK  CZ   C14  C  0  1  N  N  N  60.979   6.424  -32.811  -5.276   3.231   1.164  CZ   5DK  24  
5DK  NH1  N4   N  0  1  N  N  N  60.154   5.792  -31.771  -6.552   2.726   1.095  NH1  5DK  25  
5DK  NH2  N5   N  0  1  N  N  N  60.757   6.177  -34.023  -5.058   4.375   1.750  NH2  5DK  26  
5DK  OXT  O7   O  0  1  N  N  N  65.875  10.782  -32.330  -1.854  -3.538  -2.200  OXT  5DK  27  
5DK  H1   H1   H  0  1  N  N  N  65.215   6.725  -23.973   3.841  -0.485   1.922  H1   5DK  28  
5DK  H2   H2   H  0  1  N  N  N  64.432   7.837  -30.124  -4.091  -0.522  -2.084  H2   5DK  29  
5DK  H3   H3   H  0  1  N  N  N  65.032   8.355  -31.736  -3.843  -1.363  -0.535  H3   5DK  30  
5DK  H4   H4   H  0  1  N  N  N  69.006   9.419  -26.944  -1.474  -2.344   1.959  H4   5DK  31  
5DK  H5   H5   H  0  1  N  N  N  62.404   4.115  -29.206   5.565   0.494  -2.194  H5   5DK  32  
5DK  H6   H6   H  0  1  N  N  N  60.769   5.779  -26.606   6.547   2.979  -0.513  H6   5DK  33  
5DK  H9   H9   H  0  1  N  N  N  69.495   8.325  -23.928   0.392  -2.904   4.512  H9   5DK  34  
5DK  H10  H10  H  0  1  N  N  N  69.933   8.191  -25.665   0.260  -4.183   3.282  H10  5DK  35  
5DK  H11  H11  H  0  1  N  N  N  69.330   9.751  -25.008   1.809  -3.905   4.114  H11  5DK  36  
5DK  H12  H12  H  0  1  N  N  N  64.303   8.456  -28.470   0.259  -0.242  -1.285  H12  5DK  37  
5DK  H14  H14  H  0  1  N  N  N  63.271   8.033  -26.711   2.599  -0.124  -1.270  H14  5DK  38  
5DK  H15  H15  H  0  1  N  N  N  63.283   6.886  -25.328   1.849   1.191  -0.334  H15  5DK  39  
5DK  H16  H16  H  0  1  N  N  N  64.708  10.545  -29.734  -1.601  -0.498  -2.415  H16  5DK  40  
5DK  H17  H17  H  0  1  N  N  N  67.878  11.036  -31.763  -3.275  -3.287  -4.109  H17  5DK  41  
5DK  H18  H18  H  0  1  N  N  N  63.116   9.604  -32.203  -2.463   0.533   0.272  H18  5DK  42  
5DK  H19  H19  H  0  1  N  N  N  62.784   9.948  -30.471  -2.712   1.373  -1.277  H19  5DK  43  
5DK  H20  H20  H  0  1  N  N  N  61.097   8.374  -30.912  -5.159   1.387  -0.877  H20  5DK  44  
5DK  H21  H21  H  0  1  N  N  N  62.415   7.280  -30.371  -4.910   0.547   0.672  H21  5DK  45  
5DK  H22  H22  H  0  1  N  N  N  62.827   7.484  -33.105  -3.327   2.886   0.664  H22  5DK  46  
5DK  H23  H23  H  0  1  N  N  N  60.341   5.973  -30.806  -6.714   1.874   0.659  H23  5DK  47  
5DK  H24  H24  H  0  1  N  N  N  59.406   5.181  -32.029  -7.291   3.221   1.482  H24  5DK  48  
5DK  H25  H25  H  0  1  N  N  N  59.996   5.539  -34.142  -5.797   4.870   2.136  H25  5DK  49  
#   #
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
5DK  NH2  CZ   DOUB  N  N   1  
5DK  CZ   NE   SING  N  N   2  
5DK  CZ   NH1  SING  N  N   3  
5DK  NE   CD   SING  N  N   4  
5DK  OXT  C    DOUB  N  N   5  
5DK  C    O    SING  N  N   6  
5DK  C    CA   SING  N  N   7  
5DK  CG   CD   SING  N  N   8  
5DK  CG   CB   SING  N  N   9  
5DK  CB   CA   SING  N  N  10  
5DK  CA   N    SING  N  N  11  
5DK  N    C4A  DOUB  N  N  12  
5DK  O3P  P    DOUB  N  N  13  
5DK  O1P  P    SING  N  N  14  
5DK  C4A  C4   SING  N  N  15  
5DK  P    O4P  SING  N  N  16  
5DK  P    O2P  SING  N  N  17  
5DK  O3   C3   SING  N  N  18  
5DK  O4P  C5A  SING  N  N  19  
5DK  C4   C3   DOUB  Y  N  20  
5DK  C4   C5   SING  Y  N  21  
5DK  C3   C2   SING  Y  N  22  
5DK  C5A  C5   SING  N  N  23  
5DK  C5   C6   DOUB  Y  N  24  
5DK  C2   C2A  SING  N  N  25  
5DK  C2   N1   DOUB  Y  N  26  
5DK  C6   N1   SING  Y  N  27  
5DK  C6   H1   SING  N  N  28  
5DK  CB   H2   SING  N  N  29  
5DK  CB   H3   SING  N  N  30  
5DK  O3   H4   SING  N  N  31  
5DK  O1P  H5   SING  N  N  32  
5DK  O2P  H6   SING  N  N  33  
5DK  C2A  H9   SING  N  N  34  
5DK  C2A  H10  SING  N  N  35  
5DK  C2A  H11  SING  N  N  36  
5DK  C4A  H12  SING  N  N  37  
5DK  C5A  H14  SING  N  N  38  
5DK  C5A  H15  SING  N  N  39  
5DK  CA   H16  SING  N  N  40  
5DK  O    H17  SING  N  N  41  
5DK  CG   H18  SING  N  N  42  
5DK  CG   H19  SING  N  N  43  
5DK  CD   H20  SING  N  N  44  
5DK  CD   H21  SING  N  N  45  
5DK  NE   H22  SING  N  N  46  
5DK  NH1  H23  SING  N  N  47  
5DK  NH1  H24  SING  N  N  48  
5DK  NH2  H25  SING  N  N  49  
#   #
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
5DK  SMILES            ACDLabs               12.01  "c1(C)ncc(c(c1O)/C=N/C(CCCN/C(N)=N)C(O)=O)COP(O)(O)=O"  
5DK  InChI             InChI                 1.03   "InChI=1S/C14H22N5O7P/c1-8-12(20)10(9(5-18-8)7-26-27(23,24)25)6-19-11(13(21)22)3-2-4-17-14(15)16/h5-6,11,20H,2-4,7H2,1H3,(H,21,22)(H4,15,16,17)(H2,23,24,25)/b19-6+/t11-/m1/s1"  
5DK  InChIKey          InChI                 1.03   PFHOMURYEGODJI-WZZUDYRYSA-N  
5DK  SMILES_CANONICAL  CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](CCCNC(N)=N)C(O)=O)c1O"  
5DK  SMILES            CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](CCCNC(N)=N)C(O)=O)c1O"  
5DK  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "[H]/N=C(\N)/NCCC[C@H](C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O"  
5DK  SMILES            "OpenEye OEToolkits"  1.9.2  "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(CCCNC(=N)N)C(=O)O)O"  
#   #
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
5DK  "SYSTEMATIC NAME"  ACDLabs               12.01  "(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine"  
5DK  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "(2R)-5-carbamimidamido-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]pentanoic 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
5DK  "Create component"    2015-09-09  RCSB  
5DK  "Modify value order"  2015-09-25  RCSB  
5DK  "Initial release"     2015-11-25  RCSB  
5DK  "Modify synonyms"     2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5DK
_pdbx_chem_comp_synonyms.name        PLP-DArg
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
