data_VS3 # _chem_comp.id VS3 _chem_comp.name "3-[N-[BENZYLOXYCARBONYL]-PHENYLALANINYL-AMINO]-5-PHENYL-PENTANE-1-SULFONIC ACID 4-NITRO-PHENYL ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C34 H35 N3 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-06-09 _chem_comp.pdbx_modified_date 2024-09-27 _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 645.722 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VS3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1F2B _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 VS3 C1 C1 C 0 1 Y N N N N N 1.221 -13.016 1.201 7.240 -1.233 1.405 C1 VS3 1 VS3 C2 C2 C 0 1 Y N N N N N 1.038 -12.349 -0.022 7.420 -2.513 1.894 C2 VS3 2 VS3 C3 C3 C 0 1 Y N N N N N -0.260 -12.036 -0.468 8.215 -2.723 3.006 C3 VS3 3 VS3 C4 C4 C 0 1 Y N N N N N -1.371 -12.392 0.315 8.830 -1.653 3.628 C4 VS3 4 VS3 C5 C5 C 0 1 Y N N N N N -1.190 -13.047 1.543 8.650 -0.373 3.138 C5 VS3 5 VS3 C6 C6 C 0 1 Y N N N N N 0.108 -13.358 1.988 7.859 -0.163 2.024 C6 VS3 6 VS3 C7 C7 C 0 1 N N N N N N 2.603 -13.268 1.705 6.373 -1.005 0.194 C7 VS3 7 VS3 O1 O1 O 0 1 N N N N N N 3.057 -12.107 2.406 5.003 -0.775 0.615 O1 VS3 8 VS3 C8 C8 C 0 1 N N N N N N 4.108 -12.158 3.231 4.045 -0.546 -0.304 C8 VS3 9 VS3 O2 O2 O 0 1 N N N N N N 4.704 -13.207 3.526 4.328 -0.532 -1.485 O2 VS3 10 VS3 N1 N1 N 0 1 N N N N N N 4.357 -10.898 3.714 2.773 -0.333 0.087 N1 VS3 11 VS3 C9 C9 C 0 1 N N S N N N 5.400 -10.598 4.706 1.732 -0.084 -0.912 C9 VS3 12 VS3 C10 C10 C 0 1 N N N N N N 5.702 -9.080 4.803 1.194 -1.419 -1.431 C10 VS3 13 VS3 C11 C11 C 0 1 Y N N N N N 6.036 -8.465 3.465 2.287 -2.149 -2.168 C11 VS3 14 VS3 C12 C12 C 0 1 Y N N N N N 5.334 -7.315 3.087 3.121 -3.015 -1.486 C12 VS3 15 VS3 C13 C13 C 0 1 Y N N N N N 5.573 -6.733 1.838 4.124 -3.684 -2.162 C13 VS3 16 VS3 C14 C14 C 0 1 Y N N N N N 6.519 -7.295 0.965 4.292 -3.488 -3.520 C14 VS3 17 VS3 C15 C15 C 0 1 Y N N N N N 7.228 -8.436 1.344 3.457 -2.623 -4.202 C15 VS3 18 VS3 C16 C16 C 0 1 Y N N N N N 6.989 -9.020 2.593 2.452 -1.957 -3.527 C16 VS3 19 VS3 C17 C17 C 0 1 N N N N N N 4.940 -11.061 6.028 0.609 0.699 -0.283 C17 VS3 20 VS3 O3 O3 O 0 1 N N N N N N 3.755 -11.039 6.389 0.672 1.018 0.886 O3 VS3 21 VS3 N2 N2 N 0 1 N N N N N N 5.935 -11.427 6.853 -0.466 1.046 -1.018 N2 VS3 22 VS3 C18 C18 C 0 1 N N S N N N 5.549 -11.754 8.218 -1.558 1.807 -0.406 C18 VS3 23 VS3 C19 C19 C 0 1 N N N N N N 5.700 -13.320 8.449 -1.227 3.300 -0.455 C19 VS3 24 VS3 C20 C20 C 0 1 N N N N N N 4.653 -14.164 7.734 -0.001 3.580 0.417 C20 VS3 25 VS3 C21 C21 C 0 1 Y N N N N N 5.009 -15.609 7.903 0.325 5.050 0.370 C21 VS3 26 VS3 C22 C22 C 0 1 Y N N N N N 4.459 -16.430 8.903 -0.239 5.913 1.291 C22 VS3 27 VS3 C23 C23 C 0 1 Y N N N N N 4.860 -17.777 9.023 0.060 7.262 1.248 C23 VS3 28 VS3 C24 C24 C 0 1 Y N N N N N 5.815 -18.295 8.132 0.922 7.748 0.283 C24 VS3 29 VS3 C25 C25 C 0 1 Y N N N N N 6.364 -17.477 7.124 1.486 6.885 -0.638 C25 VS3 30 VS3 C26 C26 C 0 1 Y N N N N N 5.963 -16.137 7.016 1.191 5.536 -0.592 C26 VS3 31 VS3 C28 C28 C 0 1 N N N N N N 7.101 -11.718 9.897 -3.252 0.077 -1.023 C28 VS3 32 VS3 S1 S1 S 0 1 N N N N N N 8.120 -11.797 11.150 -4.790 -0.231 -1.935 S1 VS3 33 VS3 O4 O4 O 0 1 N N N N N N 8.146 -13.247 11.390 -5.903 0.391 -1.309 O4 VS3 34 VS3 O5 O5 O 0 1 N N N N N N 7.561 -10.980 12.217 -4.585 -0.176 -3.340 O5 VS3 35 VS3 O29 O29 O 0 1 N N N N N N 9.520 -11.275 10.775 -5.047 -1.711 -1.689 O29 VS3 36 VS3 C30 C30 C 0 1 Y N N N N N 10.704 -11.956 10.994 -5.500 -1.824 -0.413 C30 VS3 37 VS3 C31 C31 C 0 1 Y N N N N N 11.498 -11.691 9.871 -6.860 -1.750 -0.149 C31 VS3 38 VS3 C32 C32 C 0 1 Y N N N N N 12.533 -12.535 9.551 -7.318 -1.865 1.149 C32 VS3 39 VS3 C33 C33 C 0 1 Y N N N N N 12.792 -13.646 10.376 -6.422 -2.055 2.185 C33 VS3 40 VS3 N3 N3 N 1 1 N N N N N N 13.968 -14.457 10.047 -6.915 -2.178 3.575 N3 VS3 41 VS3 O8 O8 O 0 1 N N N N N N 14.279 -15.411 10.793 -6.127 -2.350 4.488 O8 VS3 42 VS3 O9 O9 O -1 1 N N N N N N 14.746 -14.167 8.974 -8.109 -2.113 3.806 O9 VS3 43 VS3 C34 C34 C 0 1 Y N N N N N 12.019 -13.912 11.568 -5.065 -2.123 1.925 C34 VS3 44 VS3 C35 C35 C 0 1 Y N N N N N 10.970 -13.047 11.877 -4.603 -2.014 0.628 C35 VS3 45 VS3 C27 C27 C 0 1 N N N N N N 6.369 -10.895 9.180 -2.855 1.547 -1.175 C27 VS3 46 VS3 H21 1H2 H 0 1 N N N N N N 1.913 -12.071 -0.632 6.939 -3.350 1.409 H21 VS3 47 VS3 H31 1H3 H 0 1 N N N N N N -0.406 -11.513 -1.428 8.355 -3.723 3.389 H31 VS3 48 VS3 H41 1H4 H 0 1 N N N N N N -2.389 -12.156 -0.035 9.450 -1.816 4.496 H41 VS3 49 VS3 H51 1H5 H 0 1 N N N N N N -2.065 -13.316 2.156 9.130 0.464 3.624 H51 VS3 50 VS3 H61 1H6 H 0 1 N N N N N N 0.253 -13.870 2.954 7.719 0.837 1.641 H61 VS3 51 VS3 H71 1H7 H 0 1 N N N N N N 2.668 -14.192 2.325 6.413 -1.882 -0.452 H71 VS3 52 VS3 H72 2H7 H 0 1 N N N N N N 3.302 -13.576 0.893 6.736 -0.134 -0.353 H72 VS3 53 VS3 HN11 1HN1 H 0 0 N N N N N N 3.755 -10.170 3.328 2.548 -0.345 1.031 HN11 VS3 54 VS3 H91 1H9 H 0 1 N N N N N N 6.332 -11.117 4.384 2.152 0.485 -1.741 H91 VS3 55 VS3 H101 1H10 H 0 0 N N N N N N 4.862 -8.535 5.294 0.854 -2.025 -0.592 H101 VS3 56 VS3 H102 2H10 H 0 0 N N N N N N 6.507 -8.879 5.547 0.359 -1.236 -2.108 H102 VS3 57 VS3 H121 1H12 H 0 0 N N N N N N 4.593 -6.868 3.772 2.990 -3.168 -0.425 H121 VS3 58 VS3 H131 1H13 H 0 0 N N N N N N 5.014 -5.829 1.541 4.777 -4.360 -1.629 H131 VS3 59 VS3 H141 1H14 H 0 0 N N N N N N 6.705 -6.838 -0.021 5.076 -4.010 -4.048 H141 VS3 60 VS3 H151 1H15 H 0 0 N N N N N N 7.973 -8.874 0.659 3.589 -2.470 -5.263 H151 VS3 61 VS3 H161 1H16 H 0 0 N N N N N N 7.553 -9.919 2.890 1.799 -1.281 -4.060 H161 VS3 62 VS3 HN21 1HN2 H 0 0 N N N N N N 6.884 -11.453 6.481 -0.517 0.790 -1.953 HN21 VS3 63 VS3 H181 1H18 H 0 0 N N N N N N 4.477 -11.517 8.412 -1.682 1.496 0.631 H181 VS3 64 VS3 H191 1H19 H 0 0 N N N N N N 6.726 -13.656 8.172 -1.016 3.593 -1.483 H191 VS3 65 VS3 H192 2H19 H 0 0 N N N N N N 5.709 -13.553 9.539 -2.076 3.873 -0.081 H192 VS3 66 VS3 H201 1H20 H 0 0 N N N N N N 3.615 -13.936 8.073 -0.212 3.287 1.445 H201 VS3 67 VS3 H202 2H20 H 0 0 N N N N N N 4.530 -13.876 6.663 0.848 3.007 0.043 H202 VS3 68 VS3 H221 1H22 H 0 0 N N N N N N 3.708 -16.015 9.597 -0.913 5.533 2.045 H221 VS3 69 VS3 H231 1H23 H 0 0 N N N N N N 4.429 -18.421 9.808 -0.381 7.936 1.967 H231 VS3 70 VS3 H241 1H24 H 0 0 N N N N N N 6.134 -19.346 8.224 1.155 8.802 0.249 H241 VS3 71 VS3 H251 1H25 H 0 0 N N N N N N 7.107 -17.885 6.419 2.160 7.265 -1.392 H251 VS3 72 VS3 H261 1H26 H 0 0 N N N N N N 6.399 -15.496 6.231 1.632 4.862 -1.311 H261 VS3 73 VS3 H281 1H28 H 0 0 N N N N N N 7.713 -12.200 9.099 -3.403 -0.151 0.032 H281 VS3 74 VS3 H282 2H28 H 0 0 N N N N N N 6.332 -12.464 10.206 -2.460 -0.556 -1.422 H282 VS3 75 VS3 H311 1H31 H 0 0 N N N N N N 11.306 -10.811 9.233 -7.560 -1.603 -0.958 H311 VS3 76 VS3 H321 1H32 H 0 0 N N N N N N 13.140 -12.325 8.654 -8.376 -1.808 1.355 H321 VS3 77 VS3 H341 1H34 H 0 0 N N N N N N 12.227 -14.765 12.234 -4.367 -2.271 2.736 H341 VS3 78 VS3 H351 1H35 H 0 0 N N N N N N 10.371 -13.219 12.787 -3.544 -2.072 0.425 H351 VS3 79 VS3 H271 1H27 H 0 0 N N N N N N 6.969 -10.109 8.664 -2.704 1.775 -2.230 H271 VS3 80 VS3 H272 2H27 H 0 0 N N N N N N 5.743 -10.210 9.799 -3.647 2.181 -0.777 H272 VS3 81 # 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 VS3 C1 C2 DOUB Y N 1 VS3 C1 C6 SING Y N 2 VS3 C1 C7 SING N N 3 VS3 C2 C3 SING Y N 4 VS3 C2 H21 SING N N 5 VS3 C3 C4 DOUB Y N 6 VS3 C3 H31 SING N N 7 VS3 C4 C5 SING Y N 8 VS3 C4 H41 SING N N 9 VS3 C5 C6 DOUB Y N 10 VS3 C5 H51 SING N N 11 VS3 C6 H61 SING N N 12 VS3 C7 O1 SING N N 13 VS3 C7 H71 SING N N 14 VS3 C7 H72 SING N N 15 VS3 O1 C8 SING N N 16 VS3 C8 O2 DOUB N N 17 VS3 C8 N1 SING N N 18 VS3 N1 C9 SING N N 19 VS3 N1 HN11 SING N N 20 VS3 C9 C10 SING N N 21 VS3 C9 C17 SING N N 22 VS3 C9 H91 SING N N 23 VS3 C10 C11 SING N N 24 VS3 C10 H101 SING N N 25 VS3 C10 H102 SING N N 26 VS3 C11 C12 DOUB Y N 27 VS3 C11 C16 SING Y N 28 VS3 C12 C13 SING Y N 29 VS3 C12 H121 SING N N 30 VS3 C13 C14 DOUB Y N 31 VS3 C13 H131 SING N N 32 VS3 C14 C15 SING Y N 33 VS3 C14 H141 SING N N 34 VS3 C15 C16 DOUB Y N 35 VS3 C15 H151 SING N N 36 VS3 C16 H161 SING N N 37 VS3 C17 O3 DOUB N N 38 VS3 C17 N2 SING N N 39 VS3 N2 C18 SING N N 40 VS3 N2 HN21 SING N N 41 VS3 C18 C19 SING N N 42 VS3 C18 C27 SING N N 43 VS3 C18 H181 SING N N 44 VS3 C19 C20 SING N N 45 VS3 C19 H191 SING N N 46 VS3 C19 H192 SING N N 47 VS3 C20 C21 SING N N 48 VS3 C20 H201 SING N N 49 VS3 C20 H202 SING N N 50 VS3 C21 C22 DOUB Y N 51 VS3 C21 C26 SING Y N 52 VS3 C22 C23 SING Y N 53 VS3 C22 H221 SING N N 54 VS3 C23 C24 DOUB Y N 55 VS3 C23 H231 SING N N 56 VS3 C24 C25 SING Y N 57 VS3 C24 H241 SING N N 58 VS3 C25 C26 DOUB Y N 59 VS3 C25 H251 SING N N 60 VS3 C26 H261 SING N N 61 VS3 C28 S1 SING N N 62 VS3 C28 C27 SING N N 63 VS3 C28 H281 SING N N 64 VS3 C28 H282 SING N N 65 VS3 S1 O4 DOUB N N 66 VS3 S1 O5 DOUB N N 67 VS3 S1 O29 SING N N 68 VS3 O29 C30 SING N N 69 VS3 C30 C31 DOUB Y N 70 VS3 C30 C35 SING Y N 71 VS3 C31 C32 SING Y N 72 VS3 C31 H311 SING N N 73 VS3 C32 C33 DOUB Y N 74 VS3 C32 H321 SING N N 75 VS3 C33 N3 SING N N 76 VS3 C33 C34 SING Y N 77 VS3 N3 O8 DOUB N N 78 VS3 N3 O9 SING N N 79 VS3 C34 C35 DOUB Y N 80 VS3 C34 H341 SING N N 81 VS3 C35 H351 SING N N 82 VS3 C27 H271 SING N N 83 VS3 C27 H272 SING N N 84 # 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 VS3 SMILES ACDLabs 10.04 "O=S(=O)(Oc1ccc(cc1)[N+]([O-])=O)CCC(NC(=O)C(NC(=O)OCc2ccccc2)Cc3ccccc3)CCc4ccccc4" VS3 SMILES_CANONICAL CACTVS 3.341 "[O-][N+](=O)c1ccc(O[S](=O)(=O)CC[C@H](CCc2ccccc2)NC(=O)[C@H](Cc3ccccc3)NC(=O)OCc4ccccc4)cc1" VS3 SMILES CACTVS 3.341 "[O-][N+](=O)c1ccc(O[S](=O)(=O)CC[CH](CCc2ccccc2)NC(=O)[CH](Cc3ccccc3)NC(=O)OCc4ccccc4)cc1" VS3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CC[C@@H](CCS(=O)(=O)Oc2ccc(cc2)[N+](=O)[O-])NC(=O)[C@H](Cc3ccccc3)NC(=O)OCc4ccccc4" VS3 SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CCC(CCS(=O)(=O)Oc2ccc(cc2)[N+](=O)[O-])NC(=O)C(Cc3ccccc3)NC(=O)OCc4ccccc4" VS3 InChI InChI 1.03 "InChI=1S/C34H35N3O8S/c38-33(32(24-27-12-6-2-7-13-27)36-34(39)44-25-28-14-8-3-9-15-28)35-29(17-16-26-10-4-1-5-11-26)22-23-46(42,43)45-31-20-18-30(19-21-31)37(40)41/h1-15,18-21,29,32H,16-17,22-25H2,(H,35,38)(H,36,39)/t29-,32-/m0/s1" VS3 InChIKey InChI 1.03 WABCRPSWXFHXDH-NYDCQLBNSA-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 VS3 "SYSTEMATIC NAME" ACDLabs 10.04 "4-nitrophenyl (3S)-3-({N-[(benzyloxy)carbonyl]-L-phenylalanyl}amino)-5-phenylpentane-1-sulfonate" VS3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(4-nitrophenyl) (3S)-5-phenyl-3-[[(2S)-3-phenyl-2-phenylmethoxycarbonylamino-propanoyl]amino]pentane-1-sulfonate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VS3 "Create component" 2000-06-09 RCSB VS3 "Modify descriptor" 2011-06-04 RCSB VS3 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id VS3 _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C27 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #