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 #