data_GYD
# 
_chem_comp.id                                    GYD 
_chem_comp.name                                  "N~1~-{5-[(3-{[3-(D-arginylamino)propyl]amino}propyl)amino]pentyl}-N~2~-[(2,4-dihydroxyphenyl)acetyl]-D-aspartamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H52 N10 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-06-05 
_chem_comp.pdbx_modified_date                    2018-08-17 
_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                        636.787 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     GYD 
_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        6DM2 
_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 
GYD N   N1  N 0 1 N N N 162.605 163.117 108.963 -9.548  0.376  -0.474 N   GYD 1  
GYD CA  C1  C 0 1 N N R 162.024 161.992 108.258 -8.310  -0.102 0.146  CA  GYD 2  
GYD C   C2  C 0 1 N N N 161.639 162.387 106.834 -7.130  0.577  -0.501 C   GYD 3  
GYD O   O1  O 0 1 N N N 160.626 162.951 106.637 -7.306  1.382  -1.391 O   GYD 4  
GYD CB  C3  C 0 1 N N N 163.107 160.934 108.167 -8.329  0.222  1.641  CB  GYD 5  
GYD CG  C4  C 0 1 N N N 163.872 160.564 109.432 -8.517  1.705  1.831  CG  GYD 6  
GYD OD1 O2  O 0 1 N N N 164.796 161.230 109.757 -8.533  2.443  0.868  OD1 GYD 7  
GYD ND2 N2  N 0 1 N N N 163.451 159.438 110.246 -8.667  2.212  3.070  ND2 GYD 8  
GYD CAB C5  C 0 1 Y N N 162.093 163.216 114.911 -14.747 -1.773 0.753  CAB GYD 9  
GYD CAC C6  C 0 1 Y N N 161.841 163.346 113.561 -13.739 -0.845 0.537  CAC GYD 10 
GYD CAI C7  C 0 1 Y N N 162.299 161.965 115.449 -15.087 -2.668 -0.249 CAI GYD 11 
GYD CAJ C8  C 0 1 Y N N 161.814 162.236 112.727 -13.075 -0.815 -0.681 CAJ GYD 12 
GYD CAK C9  C 0 1 N N N 161.520 162.382 111.225 -11.975 0.189  -0.914 CAK GYD 13 
GYD CAL C10 C 0 1 N N N 162.397 163.333 110.388 -10.677 -0.354 -0.376 CAL GYD 14 
GYD CAQ C11 C 0 1 N N N 162.069 162.478 104.378 -4.732  0.951  -0.718 CAQ GYD 15 
GYD CAR C12 C 0 1 N N N 161.664 161.276 103.531 -3.438  0.452  -0.071 CAR GYD 16 
GYD CAS C13 C 0 1 N N N 161.015 161.696 102.210 -2.241  1.142  -0.727 CAS GYD 17 
GYD CAT C14 C 0 1 N N N 162.023 162.219 101.181 -0.947  0.642  -0.081 CAT GYD 18 
GYD CAU C15 C 0 1 N N N 161.405 162.501 99.804  0.250   1.332  -0.737 CAU GYD 19 
GYD CAW C16 C 0 1 N N N 161.902 161.607 97.644  2.666   1.495  -0.722 CAW GYD 20 
GYD CAX C17 C 0 1 N N N 161.889 162.471 96.387  3.938   0.971  -0.051 CAX GYD 21 
GYD CAY C18 C 0 1 N N N 161.870 161.625 95.120  5.160   1.640  -0.682 CAY GYD 22 
GYD CBA C19 C 0 1 N N N 162.635 161.747 92.900  7.578   1.760  -0.620 CBA GYD 23 
GYD CBB C20 C 0 1 N N N 161.831 161.848 91.610  8.826   1.212  0.075  CBB GYD 24 
GYD CBC C21 C 0 1 N N N 162.611 162.614 90.547  10.073  1.860  -0.531 CBC GYD 25 
GYD CBE C22 C 0 1 N N N 163.058 162.006 88.050  12.490  1.766  -0.237 CBE GYD 26 
GYD CBF C23 C 0 1 N N R 162.553 163.285 87.348  13.719  1.227  0.447  CBF GYD 27 
GYD CBG C24 C 0 1 N N N 162.347 162.931 85.873  14.067  -0.144 -0.135 CBG GYD 28 
GYD CBH C25 C 0 1 N N N 162.672 164.050 84.885  15.239  -0.746 0.644  CBH GYD 29 
GYD CBI C26 C 0 1 N N N 161.972 163.838 83.543  15.587  -2.117 0.062  CBI GYD 30 
GYD CBK C27 C 0 1 N N N 162.485 163.509 81.102  17.200  -3.931 0.462  CBK GYD 31 
GYD CBM C28 C 0 1 Y N N 162.261 160.846 114.636 -14.424 -2.631 -1.467 CBM GYD 32 
GYD CBN C29 C 0 1 Y N N 162.015 160.977 113.277 -13.416 -1.709 -1.678 CBN GYD 33 
GYD NAG N3  N 0 1 N N N 163.320 163.349 80.180  18.198  -4.444 1.125  NAG GYD 34 
GYD NAP N4  N 0 1 N N N 162.490 162.070 105.704 -5.879  0.291  -0.090 NAP GYD 35 
GYD NAV N5  N 0 1 N N N 162.414 162.385 98.759  1.492   0.853  -0.116 NAV GYD 36 
GYD NAZ N6  N 0 1 N N N 161.977 162.484 93.960  6.381   1.138  -0.038 NAZ GYD 37 
GYD NBD N7  N 0 1 N N N 163.069 161.733 89.488  11.268  1.336  0.134  NBD GYD 38 
GYD NBJ N8  N 0 1 N N N 162.936 163.650 82.474  16.709  -2.694 0.807  NBJ GYD 39 
GYD NBL N9  N 0 1 N N N 161.263 163.545 80.836  16.639  -4.627 -0.582 NBL GYD 40 
GYD NBP N10 N 0 1 N N N 161.278 163.792 87.829  14.842  2.150  0.234  NBP GYD 41 
GYD OAA O3  O 0 1 N N N 161.635 164.626 113.038 -13.403 0.035  1.517  OAA GYD 42 
GYD OAD O4  O 0 1 N N N 162.915 164.275 110.878 -10.647 -1.449 0.146  OAD GYD 43 
GYD OAF O5  O 0 1 N N N 163.494 161.144 87.363  12.599  2.588  -1.123 OAF GYD 44 
GYD OAH O6  O 0 1 N N N 162.549 161.846 116.818 -16.070 -3.583 -0.038 OAH GYD 45 
GYD H1  H1  H 0 1 N N N 163.168 163.767 108.453 -9.557  1.221  -0.951 H1  GYD 46 
GYD H2  H2  H 0 1 N N N 161.147 161.596 108.792 -8.228  -1.180 0.009  H2  GYD 47 
GYD H3  H3  H 0 1 N N N 162.632 160.015 107.795 -9.150  -0.312 2.118  H3  GYD 48 
GYD H4  H4  H 0 1 N N N 163.846 161.288 107.433 -7.385  -0.085 2.091  H4  GYD 49 
GYD H5  H5  H 0 1 N N N 163.942 159.219 111.089 -8.655  1.622  3.840  H5  GYD 50 
GYD H6  H6  H 0 1 N N N 162.670 158.881 109.964 -8.788  3.167  3.193  H6  GYD 51 
GYD H7  H7  H 0 1 N N N 162.129 164.091 115.543 -15.262 -1.800 1.702  H7  GYD 52 
GYD H8  H8  H 0 1 N N N 160.482 162.732 111.131 -11.875 0.376  -1.983 H8  GYD 53 
GYD H9  H9  H 0 1 N N N 161.611 161.381 110.779 -12.219 1.120  -0.403 H9  GYD 54 
GYD H10 H10 H 0 1 N N N 162.900 163.001 103.883 -4.814  2.030  -0.581 H10 GYD 55 
GYD H11 H11 H 0 1 N N N 161.210 163.159 104.468 -4.718  0.720  -1.783 H11 GYD 56 
GYD H12 H12 H 0 1 N N N 160.947 160.666 104.100 -3.452  0.683  0.994  H12 GYD 57 
GYD H13 H13 H 0 1 N N N 162.561 160.678 103.311 -3.357  -0.626 -0.208 H13 GYD 58 
GYD H14 H14 H 0 1 N N N 160.283 162.490 102.417 -2.227  0.911  -1.793 H14 GYD 59 
GYD H15 H15 H 0 1 N N N 160.499 160.824 101.782 -2.323  2.220  -0.590 H15 GYD 60 
GYD H16 H16 H 0 1 N N N 162.817 161.467 101.059 -0.961  0.873  0.985  H16 GYD 61 
GYD H17 H17 H 0 1 N N N 162.459 163.153 101.565 -0.865  -0.436 -0.218 H17 GYD 62 
GYD H18 H18 H 0 1 N N N 160.990 163.520 99.795  0.264   1.101  -1.802 H18 GYD 63 
GYD H19 H19 H 0 1 N N N 160.601 161.776 99.613  0.169   2.411  -0.600 H19 GYD 64 
GYD H20 H20 H 0 1 N N N 160.879 161.272 97.870  2.601   2.574  -0.585 H20 GYD 65 
GYD H21 H21 H 0 1 N N N 162.547 160.731 97.481  2.697   1.265  -1.787 H21 GYD 66 
GYD H22 H22 H 0 1 N N N 162.789 163.103 96.380  3.907   1.201  1.014  H22 GYD 67 
GYD H23 H23 H 0 1 N N N 160.993 163.109 96.403  4.003   -0.108 -0.188 H23 GYD 68 
GYD H24 H24 H 0 1 N N N 160.927 161.060 95.071  5.190   1.410  -1.747 H24 GYD 69 
GYD H25 H25 H 0 1 N N N 162.717 160.924 95.135  5.095   2.720  -0.545 H25 GYD 70 
GYD H26 H26 H 0 1 N N N 162.722 160.690 93.192  7.529   2.840  -0.483 H26 GYD 71 
GYD H27 H27 H 0 1 N N N 163.639 162.165 92.736  7.625   1.530  -1.685 H27 GYD 72 
GYD H28 H28 H 0 1 N N N 160.886 162.374 91.814  8.779   1.441  1.140  H28 GYD 73 
GYD H29 H29 H 0 1 N N N 161.615 160.835 91.239  8.874   0.132  -0.062 H29 GYD 74 
GYD H30 H30 H 0 1 N N N 163.483 163.091 91.018  10.120  1.631  -1.596 H30 GYD 75 
GYD H31 H31 H 0 1 N N N 161.960 163.387 90.113  10.024  2.940  -0.394 H31 GYD 76 
GYD H32 H32 H 0 1 N N N 163.325 164.064 87.427  13.527  1.130  1.516  H32 GYD 77 
GYD H33 H33 H 0 1 N N N 161.293 162.650 85.734  13.202  -0.802 -0.056 H33 GYD 78 
GYD H34 H34 H 0 1 N N N 162.990 162.070 85.636  14.346  -0.034 -1.183 H34 GYD 79 
GYD H35 H35 H 0 1 N N N 163.759 164.076 84.720  16.104  -0.088 0.565  H35 GYD 80 
GYD H36 H36 H 0 1 N N N 162.343 165.009 85.311  14.960  -0.856 1.692  H36 GYD 81 
GYD H37 H37 H 0 1 N N N 161.353 164.719 83.318  14.722  -2.776 0.140  H37 GYD 82 
GYD H38 H38 H 0 1 N N N 161.331 162.947 83.609  15.865  -2.007 -0.987 H38 GYD 83 
GYD H39 H39 H 0 1 N N N 162.424 159.867 115.061 -14.689 -3.329 -2.247 H39 GYD 84 
GYD H40 H40 H 0 1 N N N 161.980 160.100 112.647 -12.897 -1.684 -2.625 H40 GYD 85 
GYD H41 H41 H 0 1 N N N 164.259 163.337 80.523  18.594  -3.953 1.862  H41 GYD 86 
GYD H42 H42 H 0 1 N N N 163.351 161.579 105.837 -5.738  -0.352 0.623  H42 GYD 87 
GYD H43 H43 H 0 1 N N N 163.224 161.932 99.132  1.560   -0.152 -0.173 H43 GYD 88 
GYD H45 H45 H 0 1 N N N 162.514 163.296 94.190  6.432   0.132  -0.095 H45 GYD 89 
GYD H47 H47 H 0 1 N N N 163.431 160.845 89.771  11.180  0.679  0.843  H47 GYD 90 
GYD H48 H48 H 0 1 N N N 163.913 163.618 82.684  17.105  -2.203 1.544  H48 GYD 91 
GYD H49 H49 H 0 1 N N N 160.595 163.671 81.570  15.896  -4.245 -1.076 H49 GYD 92 
GYD H50 H50 H 0 1 N N N 160.954 163.448 79.890  16.985  -5.499 -0.826 H50 GYD 93 
GYD H51 H51 H 0 1 N N N 161.360 164.039 88.795  15.040  2.256  -0.750 H51 GYD 94 
GYD H52 H52 H 0 1 N N N 161.019 164.600 87.299  14.664  3.044  0.665  H52 GYD 95 
GYD H54 H54 H 0 1 N N N 162.059 164.694 112.191 -12.711 -0.285 2.112  H54 GYD 96 
GYD H55 H55 H 0 1 N N N 162.539 162.707 117.218 -16.953 -3.275 -0.285 H55 GYD 97 
# 
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 
GYD NAG CBK DOUB N N 1  
GYD NBL CBK SING N N 2  
GYD CBK NBJ SING N N 3  
GYD NBJ CBI SING N N 4  
GYD CBI CBH SING N N 5  
GYD CBH CBG SING N N 6  
GYD CBG CBF SING N N 7  
GYD CBF NBP SING N N 8  
GYD CBF CBE SING N N 9  
GYD OAF CBE DOUB N N 10 
GYD CBE NBD SING N N 11 
GYD NBD CBC SING N N 12 
GYD CBC CBB SING N N 13 
GYD CBB CBA SING N N 14 
GYD CBA NAZ SING N N 15 
GYD NAZ CAY SING N N 16 
GYD CAY CAX SING N N 17 
GYD CAX CAW SING N N 18 
GYD CAW NAV SING N N 19 
GYD NAV CAU SING N N 20 
GYD CAU CAT SING N N 21 
GYD CAT CAS SING N N 22 
GYD CAS CAR SING N N 23 
GYD CAR CAQ SING N N 24 
GYD CAQ NAP SING N N 25 
GYD NAP C   SING N N 26 
GYD O   C   DOUB N N 27 
GYD C   CA  SING N N 28 
GYD CB  CA  SING N N 29 
GYD CB  CG  SING N N 30 
GYD CA  N   SING N N 31 
GYD N   CAL SING N N 32 
GYD CG  OD1 DOUB N N 33 
GYD CG  ND2 SING N N 34 
GYD CAL OAD DOUB N N 35 
GYD CAL CAK SING N N 36 
GYD CAK CAJ SING N N 37 
GYD CAJ CBN DOUB Y N 38 
GYD CAJ CAC SING Y N 39 
GYD OAA CAC SING N N 40 
GYD CBN CBM SING Y N 41 
GYD CAC CAB DOUB Y N 42 
GYD CBM CAI DOUB Y N 43 
GYD CAB CAI SING Y N 44 
GYD CAI OAH SING N N 45 
GYD N   H1  SING N N 46 
GYD CA  H2  SING N N 47 
GYD CB  H3  SING N N 48 
GYD CB  H4  SING N N 49 
GYD ND2 H5  SING N N 50 
GYD ND2 H6  SING N N 51 
GYD CAB H7  SING N N 52 
GYD CAK H8  SING N N 53 
GYD CAK H9  SING N N 54 
GYD CAQ H10 SING N N 55 
GYD CAQ H11 SING N N 56 
GYD CAR H12 SING N N 57 
GYD CAR H13 SING N N 58 
GYD CAS H14 SING N N 59 
GYD CAS H15 SING N N 60 
GYD CAT H16 SING N N 61 
GYD CAT H17 SING N N 62 
GYD CAU H18 SING N N 63 
GYD CAU H19 SING N N 64 
GYD CAW H20 SING N N 65 
GYD CAW H21 SING N N 66 
GYD CAX H22 SING N N 67 
GYD CAX H23 SING N N 68 
GYD CAY H24 SING N N 69 
GYD CAY H25 SING N N 70 
GYD CBA H26 SING N N 71 
GYD CBA H27 SING N N 72 
GYD CBB H28 SING N N 73 
GYD CBB H29 SING N N 74 
GYD CBC H30 SING N N 75 
GYD CBC H31 SING N N 76 
GYD CBF H32 SING N N 77 
GYD CBG H33 SING N N 78 
GYD CBG H34 SING N N 79 
GYD CBH H35 SING N N 80 
GYD CBH H36 SING N N 81 
GYD CBI H37 SING N N 82 
GYD CBI H38 SING N N 83 
GYD CBM H39 SING N N 84 
GYD CBN H40 SING N N 85 
GYD NAG H41 SING N N 86 
GYD NAP H42 SING N N 87 
GYD NAV H43 SING N N 88 
GYD NAZ H45 SING N N 89 
GYD NBD H47 SING N N 90 
GYD NBJ H48 SING N N 91 
GYD NBL H49 SING N N 92 
GYD NBL H50 SING N N 93 
GYD NBP H51 SING N N 94 
GYD NBP H52 SING N N 95 
GYD OAA H54 SING N N 96 
GYD OAH H55 SING N N 97 
# 
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 
GYD SMILES           ACDLabs              12.01 "N(C(Cc1c(cc(O)cc1)O)=O)C(C(=O)NCCCCCNCCCNCCCNC(C(N)CCCN\C(=N)N)=O)CC(=O)N" 
GYD InChI            InChI                1.03  
;InChI=1S/C29H52N10O6/c30-22(7-4-15-38-29(32)33)27(44)36-16-6-13-35-12-5-11-34-10-2-1-3-14-37-28(45)23(19-25(31)42)39-26(43)17-20-8-9-21(40)18-24(20)41/h8-9,18,22-23,34-35,40-41H,1-7,10-17,19,30H2,(H2,31,42)(H,36,44)(H,37,45)(H,39,43)(H4,32,33,38)/t22-,23-/m1/s1
;
GYD InChIKey         InChI                1.03  FTNICLJXPYLDAH-DHIUTWEWSA-N 
GYD SMILES_CANONICAL CACTVS               3.385 "N[C@H](CCCNC(N)=N)C(=O)NCCCNCCCNCCCCCNC(=O)[C@@H](CC(N)=O)NC(=O)Cc1ccc(O)cc1O" 
GYD SMILES           CACTVS               3.385 "N[CH](CCCNC(N)=N)C(=O)NCCCNCCCNCCCCCNC(=O)[CH](CC(N)=O)NC(=O)Cc1ccc(O)cc1O" 
GYD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C(\N)/NCCC[C@H](C(=O)NCCCNCCCNCCCCCNC(=O)[C@@H](CC(=O)N)NC(=O)Cc1ccc(cc1O)O)N" 
GYD SMILES           "OpenEye OEToolkits" 2.0.6 "c1cc(c(cc1O)O)CC(=O)NC(CC(=O)N)C(=O)NCCCCCNCCCNCCCNC(=O)C(CCCNC(=N)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 
GYD "SYSTEMATIC NAME" ACDLabs              12.01 "N~1~-{5-[(3-{[3-(D-arginylamino)propyl]amino}propyl)amino]pentyl}-N~2~-[(2,4-dihydroxyphenyl)acetyl]-D-aspartamide"                                                   
GYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-~{N}-[5-[3-[3-[[(2~{R})-2-azanyl-5-carbamimidamido-pentanoyl]amino]propylamino]propylamino]pentyl]-2-[2-[2,4-bis(oxidanyl)phenyl]ethanoylamino]butanediamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
GYD "Create component" 2018-06-05 RCSB 
GYD "Initial release"  2018-08-22 RCSB 
# 
