data_5YB
#

_chem_comp.id                                   5YB
_chem_comp.name                                 "N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C24 H27 N5 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        Ro-435054
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-01-05
_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                       497.500
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5YB
_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       5HDB
_chem_comp.pdbx_subcomponent_list               "65K BAL ASP PHE"
_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
5YB  C26   C1   C  0  1  N  N  N  53.619  105.381  73.684   -4.350   0.863   0.652  C26   65K   1  
5YB  O27   O1   O  0  1  N  N  N  54.647  105.180  73.118   -4.009   1.847   1.280  O27   65K   2  
5YB  C28   C2   C  0  1  Y  N  N  52.707  104.196  74.039   -5.767   0.686   0.267  C28   65K   3  
5YB  C29   C3   C  0  1  Y  N  N  51.360  104.383  74.305   -6.713   1.647   0.626  C29   65K   4  
5YB  C30   C4   C  0  1  Y  N  N  50.565  103.291  74.622   -8.033   1.481   0.267  C30   65K   5  
5YB  C31   C5   C  0  1  Y  N  N  51.119  102.021  74.666   -8.424   0.353  -0.455  C31   65K   6  
5YB  C32   C6   C  0  1  Y  N  N  52.466  101.838  74.400   -7.478  -0.608  -0.813  C32   65K   7  
5YB  C33   C7   C  0  1  Y  N  N  53.259  102.924  74.086   -6.157  -0.440  -0.460  C33   65K   8  
5YB  C34   C8   C  0  1  N  N  N  50.254  100.817  75.008   -9.843   0.175  -0.841  C34   65K   9  
5YB  N35   N1   N  0  1  N  N  N  50.682   99.939  75.855  -10.726   1.072  -0.506  N35   65K  10  
5YB  N36   N2   N  0  1  N  N  N  48.978  100.664  74.389  -10.229  -0.939  -1.554  N36   65K  11  
5YB  N25   N3   N  0  1  N  N  N  53.248  106.734  74.028   -3.435  -0.062   0.301  N     BAL  12  
5YB  C24   C9   C  0  1  N  N  N  54.181  107.836  73.667   -2.031   0.114   0.682  CB    BAL  13  
5YB  C23   C10  C  0  1  N  N  N  53.497  108.904  72.784   -1.210  -1.068   0.164  CA    BAL  14  
5YB  C21   C11  C  0  1  N  N  N  54.474  110.152  72.582    0.234  -0.887   0.556  C     BAL  15  
5YB  O22   O2   O  0  1  N  N  N  55.535  110.161  73.112    0.573   0.091   1.188  O     BAL  16  
5YB  N20   N4   N  0  1  N  N  N  54.083  111.286  71.744    1.149  -1.813   0.205  N     ASP  17  
5YB  C15   C12  C  0  1  N  N  S  55.020  112.386  71.599    2.567  -1.586   0.492  CA    ASP  18  
5YB  C13   C13  C  0  1  N  N  N  54.876  113.348  72.796    3.160  -0.701  -0.575  C     ASP  19  
5YB  O14   O3   O  0  1  N  N  N  54.217  114.343  72.682    2.466  -0.300  -1.484  O     ASP  20  
5YB  C16   C14  C  0  1  N  N  N  54.753  113.169  70.331    3.305  -2.927   0.510  CB    ASP  21  
5YB  C17   C15  C  0  1  N  N  N  55.810  114.296  70.178    2.806  -3.758   1.664  CG    ASP  22  
5YB  O18   O5   O  0  1  N  N  N  55.476  115.431  69.705    2.023  -3.287   2.455  OD1   ASP  23  
5YB  O19   O4   O  0  1  N  N  N  57.004  114.084  70.532    3.231  -5.022   1.814  OD2   ASP  24  
5YB  N12   N5   N  0  1  N  N  N  55.563  113.039  74.093    4.462  -0.356  -0.517  N     PHE  25  
5YB  C08   C16  C  0  1  N  N  S  55.432  113.962  75.220    5.038   0.503  -1.554  CA    PHE  26  
5YB  C09   C17  C  0  1  N  N  N  56.303  113.476  76.366    5.463  -0.341  -2.728  C     PHE  27  
5YB  O10   O7   O  0  1  N  N  N  56.847  112.334  76.304    5.300  -1.538  -2.701  O     PHE  28  
5YB  C07   C18  C  0  1  N  N  N  53.946  114.058  75.668    6.255   1.239  -0.988  CB    PHE  29  
5YB  C04   C19  C  0  1  Y  N  N  53.242  112.666  75.887    5.811   2.176   0.106  CG    PHE  30  
5YB  C03   C20  C  0  1  Y  N  N  53.582  111.876  76.972    5.451   3.475  -0.200  CD1   PHE  31  
5YB  C05   C21  C  0  1  Y  N  N  52.266  112.234  74.995    5.759   1.734   1.415  CD2   PHE  32  
5YB  C02   C22  C  0  1  Y  N  N  52.948  110.636  77.168    5.044   4.334   0.803  CE1   PHE  33  
5YB  C06   C23  C  0  1  Y  N  N  51.637  111.008  75.188    5.352   2.594   2.419  CE2   PHE  34  
5YB  C01   C24  C  0  1  Y  N  N  51.986  110.210  76.283    4.997   3.894   2.113  CZ    PHE  35  
5YB  O11   O6   O  0  1  N  N  N  56.488  114.213  77.378    6.021   0.237  -3.803  OXT   PHE  36  
5YB  H291  H1   H  0  0  N  N  N  50.931  105.373  74.266   -6.411   2.520   1.185  H291  65K  37  
5YB  H301  H2   H  0  0  N  N  N  49.515  103.430  74.834   -8.766   2.225   0.544  H301  65K  38  
5YB  H321  H3   H  0  0  N  N  N  52.895  100.848  74.438   -7.781  -1.482  -1.371  H321  65K  39  
5YB  H331  H4   H  0  0  N  N  N  54.309  102.783  73.877   -5.424  -1.183  -0.741  H331  65K  40  
5YB  H351  H5   H  0  0  N  N  N  50.024   99.198  75.991  -11.655   0.955  -0.759  H351  65K  41  
5YB  H362  H6   H  0  0  N  N  N  48.407   99.873  74.609   -9.571  -1.607  -1.803  H362  65K  42  
5YB  H361  H7   H  0  0  N  N  N  48.654  101.348  73.735  -11.158  -1.056  -1.806  H361  65K  43  
5YB  H251  H8   H  0  0  N  N  N  52.386  106.925  74.497   -3.706  -0.845  -0.204  H     BAL  44  
5YB  H242  H10  H  0  0  N  N  N  55.035  107.413  73.117   -1.650   1.039   0.248  HB3   BAL  45  
5YB  H241  H9   H  0  0  N  N  N  54.540  108.315  74.590   -1.953   0.163   1.768  HB2   BAL  46  
5YB  H231  H12  H  0  0  N  N  N  52.571  109.242  73.272   -1.591  -1.993   0.598  HA1   BAL  47  
5YB  H232  H11  H  0  0  N  N  N  53.257  108.467  71.804   -1.288  -1.117  -0.922  HA2   BAL  48  
5YB  H201  H13  H  0  0  N  N  N  53.195  111.303  71.284    0.868  -2.629  -0.237  H2    ASP  49  
5YB  H151  H14  H  0  0  N  N  N  56.050  112.002  71.575    2.669  -1.102   1.463  HA    ASP  50  
5YB  H161  H15  H  0  0  N  N  N  54.811  112.493  69.465    3.120  -3.455  -0.425  HB2   ASP  51  
5YB  H162  H16  H  0  0  N  N  N  53.749  113.614  70.381    4.374  -2.751   0.624  HB3   ASP  52  
5YB  H2    H17  H  0  1  N  N  N  57.523  114.866  70.382    2.884  -5.516   2.569  HD2   ASP  53  
5YB  H121  H18  H  0  0  N  N  N  56.108  112.206  74.187    5.017  -0.678   0.211  H     PHE  54  
5YB  H081  H19  H  0  0  N  N  N  55.769  114.964  74.918    4.293   1.230  -1.879  HA    PHE  55  
5YB  H071  H21  H  0  0  N  N  N  53.907  114.616  76.615    6.961   0.515  -0.582  HB2   PHE  56  
5YB  H072  H22  H  0  0  N  N  N  53.388  114.608  74.896    6.736   1.810  -1.782  HB3   PHE  57  
5YB  H031  H23  H  0  0  N  N  N  54.335  112.213  77.669    5.488   3.818  -1.223  HD1   PHE  58  
5YB  H051  H24  H  0  0  N  N  N  51.996  112.851  74.151    6.036   0.718   1.654  HD2   PHE  59  
5YB  H021  H25  H  0  0  N  N  N  53.217  110.019  78.013    4.764   5.349   0.564  HE1   PHE  60  
5YB  H061  H26  H  0  0  N  N  N  50.881  110.673  74.494    5.312   2.249   3.441  HE2   PHE  61  
5YB  H011  H27  H  0  0  N  N  N  51.499  109.258  76.433    4.680   4.566   2.897  HZ    PHE  62  
5YB  H3    H20  H  0  1  N  N  N  57.055  113.767  77.996    6.277  -0.345  -4.531  HXT   PHE  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
5YB  C26  C28   SING  N  N   1  
5YB  C26  O27   DOUB  N  N   2  
5YB  C26  N25   SING  N  N   3  
5YB  C28  C29   DOUB  Y  N   4  
5YB  C28  C33   SING  Y  N   5  
5YB  C29  C30   SING  Y  N   6  
5YB  C30  C31   DOUB  Y  N   7  
5YB  C31  C34   SING  N  N   8  
5YB  C31  C32   SING  Y  N   9  
5YB  C32  C33   DOUB  Y  N  10  
5YB  C34  N36   SING  N  N  11  
5YB  C34  N35   DOUB  N  N  12  
5YB  N25  C24   SING  N  N  13  
5YB  C24  C23   SING  N  N  14  
5YB  C23  C21   SING  N  N  15  
5YB  C21  O22   DOUB  N  N  16  
5YB  C21  N20   SING  N  N  17  
5YB  N20  C15   SING  N  N  18  
5YB  C15  C16   SING  N  N  19  
5YB  C15  C13   SING  N  N  20  
5YB  C13  O14   DOUB  N  N  21  
5YB  C13  N12   SING  N  N  22  
5YB  C16  C17   SING  N  N  23  
5YB  C17  O18   DOUB  N  N  24  
5YB  C17  O19   SING  N  N  25  
5YB  N12  C08   SING  N  N  26  
5YB  C08  C07   SING  N  N  27  
5YB  C08  C09   SING  N  N  28  
5YB  C09  O10   DOUB  N  N  29  
5YB  C09  O11   SING  N  N  30  
5YB  C07  C04   SING  N  N  31  
5YB  C04  C05   DOUB  Y  N  32  
5YB  C04  C03   SING  Y  N  33  
5YB  C03  C02   DOUB  Y  N  34  
5YB  C05  C06   SING  Y  N  35  
5YB  C02  C01   SING  Y  N  36  
5YB  C06  C01   DOUB  Y  N  37  
5YB  C29  H291  SING  N  N  38  
5YB  C30  H301  SING  N  N  39  
5YB  C32  H321  SING  N  N  40  
5YB  C33  H331  SING  N  N  41  
5YB  N35  H351  SING  N  N  42  
5YB  N36  H362  SING  N  N  43  
5YB  N36  H361  SING  N  N  44  
5YB  N25  H251  SING  N  N  45  
5YB  C24  H241  SING  N  N  46  
5YB  C24  H242  SING  N  N  47  
5YB  C23  H232  SING  N  N  48  
5YB  C23  H231  SING  N  N  49  
5YB  N20  H201  SING  N  N  50  
5YB  C15  H151  SING  N  N  51  
5YB  C16  H161  SING  N  N  52  
5YB  C16  H162  SING  N  N  53  
5YB  O19  H2    SING  N  N  54  
5YB  N12  H121  SING  N  N  55  
5YB  C08  H081  SING  N  N  56  
5YB  O11  H3    SING  N  N  57  
5YB  C07  H071  SING  N  N  58  
5YB  C07  H072  SING  N  N  59  
5YB  C03  H031  SING  N  N  60  
5YB  C05  H051  SING  N  N  61  
5YB  C02  H021  SING  N  N  62  
5YB  C06  H061  SING  N  N  63  
5YB  C01  H011  SING  N  N  64  
#   #
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
5YB  SMILES            ACDLabs               12.01  "C(c1ccc(\C(=N)N)cc1)(=O)NCCC(=O)NC(CC(=O)O)C(=O)NC(Cc2ccccc2)C(=O)O"  
5YB  InChI             InChI                 1.03   "InChI=1S/C24H27N5O7/c25-21(26)15-6-8-16(9-7-15)22(33)27-11-10-19(30)28-17(13-20(31)32)23(34)29-18(24(35)36)12-14-4-2-1-3-5-14/h1-9,17-18H,10-13H2,(H3,25,26)(H,27,33)(H,28,30)(H,29,34)(H,31,32)(H,35,36)/t17-,18-/m0/s1"  
5YB  InChIKey          InChI                 1.03   XPXOBWWMCFKOKQ-ROUUACIJSA-N  
5YB  SMILES_CANONICAL  CACTVS                3.385  "NC(=N)c1ccc(cc1)C(=O)NCCC(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](Cc2ccccc2)C(O)=O"  
5YB  SMILES            CACTVS                3.385  "NC(=N)c1ccc(cc1)C(=O)NCCC(=O)N[CH](CC(O)=O)C(=O)N[CH](Cc2ccccc2)C(O)=O"  
5YB  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "[H]/N=C(/c1ccc(cc1)C(=O)NCCC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc2ccccc2)C(=O)O)\N"  
5YB  SMILES            "OpenEye OEToolkits"  1.7.6  "c1ccc(cc1)CC(C(=O)O)NC(=O)C(CC(=O)O)NC(=O)CCNC(=O)c2ccc(cc2)C(=N)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
5YB  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine"  
5YB  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "(3S)-3-[3-[(4-carbamimidoylphenyl)carbonylamino]propanoylamino]-4-oxidanylidene-4-[[(2S)-1-oxidanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]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
5YB  "Create component"          2016-01-05  RCSB  
5YB  "Modify subcomponent list"  2016-01-27  RCSB  
5YB  "Initial release"           2016-02-03  RCSB  
5YB  "Modify synonyms"           2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5YB
_pdbx_chem_comp_synonyms.name        Ro-435054
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
