data_YBH
# 
_chem_comp.id                                    YBH 
_chem_comp.name                                  "4-OXO-3-{6-[4-(QUINOXALIN-2-YLOXY)-BENZOYLAMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-BUTYRIC ACID" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H28 N4 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-01-09 
_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                        560.621 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YBH 
_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        1RWX 
_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 
YBH O39  O39  O 0 1 N N N N N N 33.145 58.113 3.491  -8.178 -0.696 1.984  O39  YBH 1  
YBH C31  C31  C 0 1 N N N N N N 33.388 58.862 4.426  -8.557 0.446  2.090  C31  YBH 2  
YBH C17  C17  C 0 1 N N S N N N 33.271 60.358 4.245  -8.009 1.510  1.174  C17  YBH 3  
YBH C12  C12  C 0 1 N N N N N N 34.437 60.853 3.389  -9.154 2.134  0.374  C12  YBH 4  
YBH C6   C6   C 0 1 N N N N N N 34.024 61.994 2.484  -8.625 3.279  -0.450 C6   YBH 5  
YBH O38  O38  O 0 1 N N N N N N 32.810 62.251 2.324  -7.452 3.567  -0.403 O38  YBH 6  
YBH O36  O36  O 0 1 N N N N N N 34.929 62.643 1.918  -9.457 3.980  -1.237 O36  YBH 7  
YBH N4   N4   N 0 1 N N N N N N 33.222 61.076 5.512  -7.040 0.910  0.253  N4   YBH 8  
YBH C18  C18  C 0 1 N N N N N N 32.078 61.378 6.136  -5.756 0.756  0.632  C18  YBH 9  
YBH O35  O35  O 0 1 N N N N N N 30.986 60.980 5.758  -5.402 1.115  1.736  O35  YBH 10 
YBH C8   C8   C 0 1 N N R N N N 32.190 62.249 7.362  -4.759 0.139  -0.315 C8   YBH 11 
YBH C28  C28  C 0 1 Y N N N N N 31.932 61.469 8.626  -5.203 -1.256 -0.671 C28  YBH 12 
YBH S41  S41  S 0 1 Y N N N N N 33.176 60.857 9.623  -5.475 -2.658 0.400  S41  YBH 13 
YBH C9   C9   C 0 1 Y N N N N N 30.661 61.173 9.130  -5.505 -1.771 -1.888 C9   YBH 14 
YBH C15  C15  C 0 1 Y N N N N N 30.784 60.585 10.419 -5.890 -3.096 -1.979 C15  YBH 15 
YBH C7   C7   C 0 1 Y N N N N N 32.055 60.384 10.799 -5.965 -3.837 -0.847 C7   YBH 16 
YBH C11  C11  C 0 1 N N N N N N 31.239 63.446 7.267  -3.386 0.082  0.356  C11  YBH 17 
YBH C25  C25  C 0 1 N N N N N N 31.628 64.561 8.235  -2.349 -0.429 -0.646 C25  YBH 18 
YBH C13  C13  C 0 1 N N N N N N 30.516 65.596 8.378  -0.975 -0.486 0.025  C13  YBH 19 
YBH C14  C14  C 0 1 N N N N N N 30.615 66.331 9.711  0.061  -0.997 -0.978 C14  YBH 20 
YBH N3   N3   N 0 1 N N N N N N 31.467 67.505 9.637  1.377  -1.052 -0.335 N3   YBH 21 
YBH C33  C33  C 0 1 N N N N N N 31.945 68.123 10.721 2.450  -1.475 -1.032 C33  YBH 22 
YBH O37  O37  O 0 1 N N N N N N 31.370 68.073 11.799 2.327  -1.810 -2.194 O37  YBH 23 
YBH C16  C16  C 0 1 Y N N N N N 33.223 68.910 10.614 3.775  -1.530 -0.385 C16  YBH 24 
YBH C20  C20  C 0 1 Y N N N N N 33.507 69.912 11.546 4.889  -1.968 -1.106 C20  YBH 25 
YBH C21  C21  C 0 1 Y N N N N N 34.689 70.646 11.452 6.124  -2.018 -0.498 C21  YBH 26 
YBH C22  C22  C 0 1 Y N N N N N 35.598 70.378 10.427 6.263  -1.634 0.831  C22  YBH 27 
YBH C23  C23  C 0 1 Y N N N N N 35.311 69.384 9.489  5.157  -1.198 1.551  C23  YBH 28 
YBH C24  C24  C 0 1 Y N N N N N 34.130 68.648 9.585  3.920  -1.139 0.949  C24  YBH 29 
YBH O34  O34  O 0 1 N N N N N N 36.754 71.115 10.338 7.482  -1.685 1.426  O34  YBH 30 
YBH C26  C26  C 0 1 Y N N N N N 38.016 70.622 10.575 8.161  -0.582 1.023  C26  YBH 31 
YBH C27  C27  C 0 1 Y N N N N N 39.017 71.506 10.976 9.500  -0.410 1.409  C27  YBH 32 
YBH N1   N1   N 0 1 Y N N N N N 40.259 71.056 11.211 10.173 0.650  1.029  N1   YBH 33 
YBH N2   N2   N 0 1 Y N N N N N 38.309 69.320 10.417 7.560  0.315  0.268  N2   YBH 34 
YBH C30  C30  C 0 1 Y N N N N N 39.555 68.871 10.641 8.230  1.405  -0.125 C30  YBH 35 
YBH C29  C29  C 0 1 Y N N N N N 40.549 69.757 11.050 9.582  1.577  0.266  C29  YBH 36 
YBH C10  C10  C 0 1 Y N N N N N 41.847 69.299 11.280 10.280 2.721  -0.156 C10  YBH 37 
YBH C32  C32  C 0 1 Y N N N N N 42.147 67.948 11.105 9.653  3.647  -0.932 C32  YBH 38 
YBH C19  C19  C 0 1 Y N N N N N 41.151 67.062 10.697 8.324  3.479  -1.316 C19  YBH 39 
YBH C5   C5   C 0 1 Y N N N N N 39.854 67.522 10.466 7.616  2.383  -0.926 C5   YBH 40 
YBH H31  H31  H 0 1 N N N N N N 33.674 58.269 5.311  -9.289 0.705  2.841  H31  YBH 41 
YBH H17  H17  H 0 1 N N N N N N 32.304 60.566 3.730  -7.517 2.281  1.767  H17  YBH 42 
YBH H121 1H12 H 0 0 N N N N N N 34.897 60.020 2.808  -9.918 2.502  1.059  H121 YBH 43 
YBH H122 2H12 H 0 0 N N N N N N 35.314 61.131 4.019  -9.589 1.382  -0.285 H122 YBH 44 
YBH H36  H36  H 0 1 N N N N N N 34.670 63.359 1.350  -9.117 4.715  -1.766 H36  YBH 45 
YBH HN4  HN4  H 0 1 N N N N N N 34.058 61.394 6.003  -7.323 0.623  -0.629 HN4  YBH 46 
YBH H8   H8   H 0 1 N N N N N N 33.238 62.628 7.406  -4.696 0.743  -1.220 H8   YBH 47 
YBH H9   H9   H 0 1 N N N N N N 29.716 61.371 8.598  -5.437 -1.158 -2.775 H9   YBH 48 
YBH H15  H15  H 0 1 N N N N N N 29.948 60.303 11.081 -6.132 -3.532 -2.937 H15  YBH 49 
YBH H7   H7   H 0 1 N N N N N N 32.152 59.947 11.807 -6.248 -4.873 -0.730 H7   YBH 50 
YBH H111 1H11 H 0 0 N N N N N N 30.179 63.134 7.414  -3.104 1.079  0.694  H111 YBH 51 
YBH H112 2H11 H 0 0 N N N N N N 31.167 63.825 6.221  -3.427 -0.593 1.211  H112 YBH 52 
YBH H251 1H25 H 0 0 N N N N N N 32.592 65.038 7.941  -2.630 -1.426 -0.984 H251 YBH 53 
YBH H252 2H25 H 0 0 N N N N N N 31.933 64.151 9.226  -2.308 0.246  -1.502 H252 YBH 54 
YBH H131 1H13 H 0 0 N N N N N N 29.509 65.138 8.236  -0.694 0.511  0.362  H131 YBH 55 
YBH H132 2H13 H 0 0 N N N N N N 30.504 66.306 7.518  -1.017 -1.161 0.880  H132 YBH 56 
YBH H141 1H14 H 0 0 N N N N N N 30.948 65.644 10.524 -0.220 -1.994 -1.316 H141 YBH 57 
YBH H142 2H14 H 0 0 N N N N N N 29.604 66.593 10.101 0.103  -0.322 -1.833 H142 YBH 58 
YBH HN3  HN3  H 0 1 N N N N N N 31.752 67.929 8.754  1.475  -0.784 0.592  HN3  YBH 59 
YBH H20  H20  H 0 1 N N N N N N 32.794 70.125 12.360 4.782  -2.267 -2.138 H20  YBH 60 
YBH H21  H21  H 0 1 N N N N N N 34.905 71.438 12.188 6.986  -2.357 -1.054 H21  YBH 61 
YBH H23  H23  H 0 1 N N N N N N 36.020 69.179 8.669  5.269  -0.900 2.583  H23  YBH 62 
YBH H24  H24  H 0 1 N N N N N N 33.913 67.858 8.846  3.062  -0.800 1.509  H24  YBH 63 
YBH H27  H27  H 0 1 N N N N N N 38.822 72.583 11.110 9.979  -1.156 2.025  H27  YBH 64 
YBH H10  H10  H 0 1 N N N N N N 42.634 70.003 11.599 11.310 2.865  0.135  H10  YBH 65 
YBH H32  H32  H 0 1 N N N N N N 43.171 67.581 11.289 10.193 4.525  -1.254 H32  YBH 66 
YBH H19  H19  H 0 1 N N N N N N 41.390 65.994 10.557 7.849  4.228  -1.931 H19  YBH 67 
YBH H5   H5   H 0 1 N N N N N N 39.066 66.820 10.145 6.587  2.266  -1.231 H5   YBH 68 
# 
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 
YBH O39 C31  DOUB N N 1  
YBH C31 C17  SING N N 2  
YBH C31 H31  SING N N 3  
YBH C17 C12  SING N N 4  
YBH C17 N4   SING N N 5  
YBH C17 H17  SING N N 6  
YBH C12 C6   SING N N 7  
YBH C12 H121 SING N N 8  
YBH C12 H122 SING N N 9  
YBH C6  O38  DOUB N N 10 
YBH C6  O36  SING N N 11 
YBH O36 H36  SING N N 12 
YBH N4  C18  SING N N 13 
YBH N4  HN4  SING N N 14 
YBH C18 O35  DOUB N N 15 
YBH C18 C8   SING N N 16 
YBH C8  C28  SING N N 17 
YBH C8  C11  SING N N 18 
YBH C8  H8   SING N N 19 
YBH C28 S41  SING Y N 20 
YBH C28 C9   DOUB Y N 21 
YBH S41 C7   SING Y N 22 
YBH C9  C15  SING Y N 23 
YBH C9  H9   SING N N 24 
YBH C15 C7   DOUB Y N 25 
YBH C15 H15  SING N N 26 
YBH C7  H7   SING N N 27 
YBH C11 C25  SING N N 28 
YBH C11 H111 SING N N 29 
YBH C11 H112 SING N N 30 
YBH C25 C13  SING N N 31 
YBH C25 H251 SING N N 32 
YBH C25 H252 SING N N 33 
YBH C13 C14  SING N N 34 
YBH C13 H131 SING N N 35 
YBH C13 H132 SING N N 36 
YBH C14 N3   SING N N 37 
YBH C14 H141 SING N N 38 
YBH C14 H142 SING N N 39 
YBH N3  C33  SING N N 40 
YBH N3  HN3  SING N N 41 
YBH C33 O37  DOUB N N 42 
YBH C33 C16  SING N N 43 
YBH C16 C20  DOUB Y N 44 
YBH C16 C24  SING Y N 45 
YBH C20 C21  SING Y N 46 
YBH C20 H20  SING N N 47 
YBH C21 C22  DOUB Y N 48 
YBH C21 H21  SING N N 49 
YBH C22 C23  SING Y N 50 
YBH C22 O34  SING N N 51 
YBH C23 C24  DOUB Y N 52 
YBH C23 H23  SING N N 53 
YBH C24 H24  SING N N 54 
YBH O34 C26  SING N N 55 
YBH C26 C27  DOUB Y N 56 
YBH C26 N2   SING Y N 57 
YBH C27 N1   SING Y N 58 
YBH C27 H27  SING N N 59 
YBH N1  C29  DOUB Y N 60 
YBH N2  C30  DOUB Y N 61 
YBH C30 C29  SING Y N 62 
YBH C30 C5   SING Y N 63 
YBH C29 C10  SING Y N 64 
YBH C10 C32  DOUB Y N 65 
YBH C10 H10  SING N N 66 
YBH C32 C19  SING Y N 67 
YBH C32 H32  SING N N 68 
YBH C19 C5   DOUB Y N 69 
YBH C19 H19  SING N N 70 
YBH C5  H5   SING N N 71 
# 
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 
YBH SMILES           ACDLabs              10.04 "O=C(O)CC(C=O)NC(=O)C(c1sccc1)CCCCNC(=O)c4ccc(Oc2nc3c(nc2)cccc3)cc4"                                                                                                                                                                    
YBH SMILES_CANONICAL CACTVS               3.341 "OC(=O)C[C@H](NC(=O)[C@@H](CCCCNC(=O)c1ccc(Oc2cnc3ccccc3n2)cc1)c4sccc4)C=O"                                                                                                                                                             
YBH SMILES           CACTVS               3.341 "OC(=O)C[CH](NC(=O)[CH](CCCCNC(=O)c1ccc(Oc2cnc3ccccc3n2)cc1)c4sccc4)C=O"                                                                                                                                                                
YBH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)ncc(n2)Oc3ccc(cc3)C(=O)NCCCC[C@@H](c4cccs4)C(=O)N[C@@H](CC(=O)O)C=O"                                                                                                                                                        
YBH SMILES           "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)ncc(n2)Oc3ccc(cc3)C(=O)NCCCCC(c4cccs4)C(=O)NC(CC(=O)O)C=O"                                                                                                                                                                  
YBH InChI            InChI                1.03  "InChI=1S/C29H28N4O6S/c34-18-20(16-27(35)36)32-29(38)22(25-9-5-15-40-25)6-3-4-14-30-28(37)19-10-12-21(13-11-19)39-26-17-31-23-7-1-2-8-24(23)33-26/h1-2,5,7-13,15,17-18,20,22H,3-4,6,14,16H2,(H,30,37)(H,32,38)(H,35,36)/t20-,22-/m0/s1" 
YBH InChIKey         InChI                1.03  DJLHSAXTGGXZPX-UNMCSNQZSA-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 
YBH "SYSTEMATIC NAME" ACDLabs              10.04 "(3S)-4-oxo-3-{[(2R)-6-({[4-(quinoxalin-2-yloxy)phenyl]carbonyl}amino)-2-thiophen-2-ylhexanoyl]amino}butanoic acid" 
YBH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(3S)-4-oxo-3-[[(2R)-6-[(4-quinoxalin-2-yloxyphenyl)carbonylamino]-2-thiophen-2-yl-hexanoyl]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 
YBH "Create component"  2004-01-09 RCSB 
YBH "Modify descriptor" 2011-06-04 RCSB 
YBH "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YBH 
_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               C31 
_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      ? 
# 
