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 ? ##