data_VL5 # _chem_comp.id VL5 _chem_comp.name "(2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H34 N8 O10 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "AIC499 (bound)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-27 _chem_comp.pdbx_modified_date 2021-07-30 _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 670.715 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VL5 _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 7ONK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 VL5 C10 C1 C 0 1 Y N N -3.588 -16.865 -1.747 -5.873 -0.285 0.573 C10 VL5 1 VL5 C11 C2 C 0 1 Y N N -2.631 -16.946 -2.754 -5.011 -0.462 1.656 C11 VL5 2 VL5 C12 C3 C 0 1 Y N N -2.986 -16.742 -4.079 -3.861 0.291 1.749 C12 VL5 3 VL5 C13 C4 C 0 1 Y N N -4.311 -16.471 -4.397 -3.559 1.226 0.767 C13 VL5 4 VL5 C14 C5 C 0 1 Y N N -5.270 -16.390 -3.395 -4.416 1.405 -0.313 C14 VL5 5 VL5 C15 C6 C 0 1 Y N N -4.912 -16.589 -2.069 -5.564 0.651 -0.415 C15 VL5 6 VL5 C17 C7 C 0 1 N N N -3.721 -16.534 -6.740 -2.178 2.910 -0.183 C17 VL5 7 VL5 C18 C8 C 0 1 N N S -4.340 -16.107 -8.062 -0.865 3.645 0.095 C18 VL5 8 VL5 C19 C9 C 0 1 N N N -3.306 -16.196 -9.139 -0.919 4.269 1.466 C19 VL5 9 VL5 C2 C10 C 0 1 N N N -0.072 -15.834 -0.937 -10.298 -1.049 0.105 C2 VL5 10 VL5 C24 C11 C 0 1 N N N -7.156 -17.373 -9.680 2.538 2.576 -0.365 C24 VL5 11 VL5 C25 C12 C 0 1 Y N N -8.035 -17.019 -10.826 3.817 3.176 -0.804 C25 VL5 12 VL5 C27 C13 C 0 1 Y N N -8.657 -15.784 -12.598 5.977 3.083 -1.393 C27 VL5 13 VL5 C3 C14 C 0 1 N N R -1.086 -15.928 0.207 -9.182 -1.716 -0.702 C3 VL5 14 VL5 C30 C15 C 0 1 Y N N -9.206 -17.724 -11.158 3.958 4.498 -1.020 C30 VL5 15 VL5 C31 C16 C 0 1 N N N -7.450 -18.493 -8.786 2.475 1.136 -0.022 C31 VL5 16 VL5 C34 C17 C 0 1 N N S -8.921 -19.318 -7.031 3.556 -0.996 0.449 C34 VL5 17 VL5 C35 C18 C 0 1 N N N -8.222 -19.653 -5.697 4.726 -1.767 -0.167 C35 VL5 18 VL5 C36 C19 C 0 1 N N N -7.134 -18.625 -5.401 4.624 -1.713 -1.692 C36 VL5 19 VL5 C37 C20 C 0 1 N N N -7.631 -21.055 -5.823 6.045 -1.134 0.279 C37 VL5 20 VL5 C39 C21 C 0 1 N N N -10.355 -18.944 -6.815 3.656 -1.049 1.952 C39 VL5 21 VL5 C4 C22 C 0 1 N N N -1.948 -14.666 0.268 -9.608 -1.812 -2.170 C4 VL5 22 VL5 C5 C23 C 0 1 N N N -1.073 -13.421 0.305 -10.920 -2.598 -2.262 C5 VL5 23 VL5 C6 C24 C 0 1 N N N -0.134 -13.417 -0.896 -11.985 -1.905 -1.409 C6 VL5 24 VL5 C8 C25 C 0 1 N N N -3.204 -17.079 -0.310 -7.108 -1.092 0.470 C8 VL5 25 VL5 N1 N1 N 0 1 N N N 0.735 -14.604 -0.852 -11.530 -1.838 -0.014 N1 VL5 26 VL5 N23 N2 N 0 1 N N N -6.144 -16.669 -9.404 1.468 3.314 -0.280 N23 VL5 27 VL5 N26 N3 N 0 1 Y N N -7.747 -15.940 -11.630 4.915 2.447 -1.010 N26 VL5 28 VL5 N28 N4 N 0 1 N N N -8.575 -14.722 -13.570 7.205 2.501 -1.658 N28 VL5 29 VL5 N33 N5 N 0 1 N N N -8.305 -18.252 -7.800 3.603 0.399 0.006 N33 VL5 30 VL5 N38 N6 N 0 1 N N N -9.133 -19.732 -4.521 4.679 -3.166 0.278 N38 VL5 31 VL5 N7 N7 N 0 1 N N N -1.915 -17.121 0.053 -7.959 -0.917 -0.600 N7 VL5 32 VL5 N9 N8 N 0 1 N N N -4.118 -17.221 0.553 -7.392 -1.970 1.391 N9 VL5 33 VL5 O16 O1 O 0 1 N N N -4.664 -16.273 -5.703 -2.426 1.967 0.862 O16 VL5 34 VL5 O20 O2 O 0 1 N N N -2.524 -15.237 -9.290 -1.801 5.247 1.724 O20 VL5 35 VL5 O21 O3 O 0 1 N N N -3.269 -17.227 -9.839 -0.168 3.888 2.333 O21 VL5 36 VL5 O22 O4 O 0 1 N N N -5.419 -16.972 -8.411 0.222 2.720 0.035 O22 VL5 37 VL5 O32 O5 O 0 1 N N N -6.899 -19.580 -8.928 1.405 0.619 0.234 O32 VL5 38 VL5 O40 O6 O 0 1 N N N -10.739 -17.784 -6.952 3.756 -0.027 2.587 O40 VL5 39 VL5 O41 O7 O 0 1 N N N -9.660 -18.539 -4.140 5.784 -3.935 -0.293 O41 VL5 40 VL5 O43 O8 O 0 1 N N N -10.575 -18.946 -1.886 4.698 -6.102 -0.654 O43 VL5 41 VL5 O44 O9 O 0 1 N N N -10.124 -16.662 -2.628 7.029 -5.936 -0.347 O44 VL5 42 VL5 O45 O10 O 0 1 N N N -8.305 -18.094 -2.145 5.412 -5.431 1.491 O45 VL5 43 VL5 S29 S1 S 0 1 Y N N -9.916 -16.954 -12.550 5.617 4.802 -1.526 S29 VL5 44 VL5 S42 S2 S 0 1 N N N -9.681 -18.061 -2.674 5.801 -5.399 0.124 S42 VL5 45 VL5 H1 H1 H 0 1 N N N -1.605 -17.169 -2.502 -5.245 -1.188 2.421 H1 VL5 46 VL5 H2 H2 H 0 1 N N N -2.239 -16.793 -4.857 -3.193 0.155 2.587 H2 VL5 47 VL5 H3 H3 H 0 1 N N N -6.297 -16.172 -3.649 -4.178 2.132 -1.075 H3 VL5 48 VL5 H4 H4 H 0 1 N N N -5.659 -16.530 -1.291 -6.229 0.790 -1.254 H4 VL5 49 VL5 H5 H5 H 0 1 N N N -3.486 -17.608 -6.768 -2.995 3.630 -0.225 H5 VL5 50 VL5 H6 H6 H 0 1 N N N -2.799 -15.962 -6.558 -2.105 2.386 -1.136 H6 VL5 51 VL5 H7 H7 H 0 1 N N N -4.692 -15.068 -7.977 -0.720 4.425 -0.653 H7 VL5 52 VL5 H8 H8 H 0 1 N N N -0.614 -15.839 -1.894 -10.003 -0.991 1.153 H8 VL5 53 VL5 H9 H9 H 0 1 N N N 0.599 -16.704 -0.891 -10.472 -0.043 -0.279 H9 VL5 54 VL5 H10 H10 H 0 1 N N N -0.526 -16.003 1.151 -8.998 -2.716 -0.311 H10 VL5 55 VL5 H11 H11 H 0 1 N N N -9.596 -18.589 -10.642 3.185 5.244 -0.902 H11 VL5 56 VL5 H12 H12 H 0 1 N N N -8.905 -20.233 -7.641 2.616 -1.447 0.132 H12 VL5 57 VL5 H13 H13 H 0 1 N N N -6.643 -18.874 -4.449 4.659 -0.675 -2.023 H13 VL5 58 VL5 H14 H14 H 0 1 N N N -6.390 -18.636 -6.211 5.457 -2.262 -2.132 H14 VL5 59 VL5 H15 H15 H 0 1 N N N -7.585 -17.624 -5.330 3.684 -2.164 -2.010 H15 VL5 60 VL5 H16 H16 H 0 1 N N N -7.124 -21.325 -4.885 6.117 -1.173 1.366 H16 VL5 61 VL5 H17 H17 H 0 1 N N N -8.437 -21.776 -6.025 6.878 -1.683 -0.160 H17 VL5 62 VL5 H18 H18 H 0 1 N N N -6.906 -21.074 -6.650 6.080 -0.096 -0.051 H18 VL5 63 VL5 H19 H19 H 0 1 N Y N -11.065 -19.708 -6.534 3.638 -2.002 2.461 H19 VL5 64 VL5 H20 H20 H 0 1 N N N -2.595 -14.627 -0.621 -9.755 -0.811 -2.573 H20 VL5 65 VL5 H21 H21 H 0 1 N N N -2.571 -14.697 1.174 -8.835 -2.326 -2.741 H21 VL5 66 VL5 H22 H22 H 0 1 N N N -0.481 -13.418 1.232 -11.250 -2.634 -3.300 H22 VL5 67 VL5 H23 H23 H 0 1 N N N -1.710 -12.525 0.274 -10.762 -3.613 -1.895 H23 VL5 68 VL5 H24 H24 H 0 1 N N N 0.486 -12.509 -0.872 -12.151 -0.896 -1.786 H24 VL5 69 VL5 H25 H25 H 0 1 N N N -0.726 -13.432 -1.823 -12.915 -2.470 -1.461 H25 VL5 70 VL5 H26 H26 H 0 1 N N N 1.248 -14.605 0.006 -11.406 -2.763 0.370 H26 VL5 71 VL5 H27 H27 H 0 1 N N N -9.354 -14.780 -14.194 7.952 3.052 -1.942 H27 VL5 72 VL5 H28 H28 H 0 1 N N N -8.589 -13.839 -13.101 7.319 1.543 -1.560 H28 VL5 73 VL5 H29 H29 H 0 1 N N N -8.533 -17.304 -7.579 4.446 0.793 -0.267 H29 VL5 74 VL5 H30 H30 H 0 1 N N N -9.887 -20.348 -4.750 4.679 -3.226 1.285 H30 VL5 75 VL5 H31 H31 H 0 1 N N N -1.500 -18.014 0.227 -7.747 -0.264 -1.286 H31 VL5 76 VL5 H32 H32 H 0 1 N N N -3.748 -17.358 1.472 -8.203 -2.499 1.323 H32 VL5 77 VL5 H33 H33 H 0 1 N N N -1.924 -15.426 -10.002 -1.798 5.616 2.618 H33 VL5 78 VL5 H34 H34 H 0 1 N N N -10.078 -19.361 -1.191 4.621 -7.047 -0.461 H34 VL5 79 # # 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 VL5 N28 C27 SING N N 1 VL5 C27 S29 SING Y N 2 VL5 C27 N26 DOUB Y N 3 VL5 S29 C30 SING Y N 4 VL5 N26 C25 SING Y N 5 VL5 C30 C25 DOUB Y N 6 VL5 C25 C24 SING N N 7 VL5 O21 C19 DOUB N N 8 VL5 C24 N23 DOUB N Z 9 VL5 C24 C31 SING N N 10 VL5 N23 O22 SING N N 11 VL5 O20 C19 SING N N 12 VL5 C19 C18 SING N N 13 VL5 O32 C31 DOUB N N 14 VL5 C31 N33 SING N N 15 VL5 O22 C18 SING N N 16 VL5 C18 C17 SING N N 17 VL5 N33 C34 SING N N 18 VL5 C34 C39 SING N N 19 VL5 C34 C35 SING N N 20 VL5 O40 C39 DOUB N N 21 VL5 C17 O16 SING N N 22 VL5 C37 C35 SING N N 23 VL5 O16 C13 SING N N 24 VL5 C35 C36 SING N N 25 VL5 C35 N38 SING N N 26 VL5 N38 O41 SING N N 27 VL5 C13 C12 DOUB Y N 28 VL5 C13 C14 SING Y N 29 VL5 O41 S42 SING N N 30 VL5 C12 C11 SING Y N 31 VL5 C14 C15 DOUB Y N 32 VL5 C11 C10 DOUB Y N 33 VL5 S42 O44 DOUB N N 34 VL5 S42 O45 DOUB N N 35 VL5 S42 O43 SING N N 36 VL5 C15 C10 SING Y N 37 VL5 C10 C8 SING N N 38 VL5 C2 N1 SING N N 39 VL5 C2 C3 SING N N 40 VL5 C6 N1 SING N N 41 VL5 C6 C5 SING N N 42 VL5 C8 N7 SING N N 43 VL5 C8 N9 DOUB N N 44 VL5 N7 C3 SING N N 45 VL5 C3 C4 SING N N 46 VL5 C4 C5 SING N N 47 VL5 C11 H1 SING N N 48 VL5 C12 H2 SING N N 49 VL5 C14 H3 SING N N 50 VL5 C15 H4 SING N N 51 VL5 C17 H5 SING N N 52 VL5 C17 H6 SING N N 53 VL5 C18 H7 SING N N 54 VL5 C2 H8 SING N N 55 VL5 C2 H9 SING N N 56 VL5 C3 H10 SING N N 57 VL5 C30 H11 SING N N 58 VL5 C34 H12 SING N N 59 VL5 C36 H13 SING N N 60 VL5 C36 H14 SING N N 61 VL5 C36 H15 SING N N 62 VL5 C37 H16 SING N N 63 VL5 C37 H17 SING N N 64 VL5 C37 H18 SING N N 65 VL5 C39 H19 SING N N 66 VL5 C4 H20 SING N N 67 VL5 C4 H21 SING N N 68 VL5 C5 H22 SING N N 69 VL5 C5 H23 SING N N 70 VL5 C6 H24 SING N N 71 VL5 C6 H25 SING N N 72 VL5 N1 H26 SING N N 73 VL5 N28 H27 SING N N 74 VL5 N28 H28 SING N N 75 VL5 N33 H29 SING N N 76 VL5 N38 H30 SING N N 77 VL5 N7 H31 SING N N 78 VL5 N9 H32 SING N N 79 VL5 O20 H33 SING N N 80 VL5 O43 H34 SING N N 81 # # 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 VL5 InChI InChI 1.03 "InChI=1S/C25H34N8O10S2/c1-25(2,33-43-45(38,39)40)19(11-34)31-22(35)20(17-13-44-24(27)30-17)32-42-18(23(36)37)12-41-16-7-5-14(6-8-16)21(26)29-15-4-3-9-28-10-15/h5-8,11,13,15,18-19,28,33H,3-4,9-10,12H2,1-2H3,(H2,26,29)(H2,27,30)(H,31,35)(H,36,37)(H,38,39,40)/b32-20-/t15-,18+,19-/m1/s1" VL5 InChIKey InChI 1.03 NFNVPYWCKFTXAX-OOLKDPNPSA-N VL5 SMILES_CANONICAL CACTVS 3.385 "CC(C)(NO[S](O)(=O)=O)[C@H](NC(=O)C(=N\O[C@@H](COc1ccc(cc1)C(=N)N[C@@H]2CCCNC2)C(O)=O)/c3csc(N)n3)C=O" VL5 SMILES CACTVS 3.385 "CC(C)(NO[S](O)(=O)=O)[CH](NC(=O)C(=NO[CH](COc1ccc(cc1)C(=N)N[CH]2CCCNC2)C(O)=O)c3csc(N)n3)C=O" VL5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/c1ccc(cc1)OC[C@@H](C(=O)O)O/N=C(/c2csc(n2)N)\C(=O)N[C@H](C=O)C(C)(C)NOS(=O)(=O)O)\N[C@@H]3CCCNC3" VL5 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C(C=O)NC(=O)C(=NOC(COc1ccc(cc1)C(=N)NC2CCCNC2)C(=O)O)c3csc(n3)N)NOS(=O)(=O)O" # _pdbx_chem_comp_identifier.comp_id VL5 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{S})-2-[(~{Z})-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2~{S})-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[~{N}-[(3~{R})-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VL5 _pdbx_chem_comp_synonyms.name "AIC499 (bound)" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VL5 "Create component" 2021-05-27 PDBE VL5 "Initial release" 2021-08-04 RCSB ##