data_DN1
# 
_chem_comp.id                                    DN1 
_chem_comp.name                                  
;3-({(2S)-2-[({(1R)-1-[({(1R)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARB
ONYL]-2,3-DIHYDRO-1H-INDOL-2-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H31 F2 N3 O7 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "PEPTIDOMIMETIC INHIBITOR" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-07-14 
_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                        567.602 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DN1 
_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        1W3C 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
DN1 N1   N1   N 0 1 N N N N N N 65.013 25.387 3.574  0.226  0.471  3.284  N1   DN1 1  
DN1 C2   C2   C 0 1 N N S N N N 65.928 24.187 3.760  0.331  -0.964 3.014  C2   DN1 2  
DN1 C1   C1   C 0 1 N N N N N N 66.050 23.414 2.401  0.941  -1.198 1.656  C1   DN1 3  
DN1 O2   O2   O 0 1 N N N N N N 65.271 22.486 2.085  1.662  -2.156 1.471  O2   DN1 4  
DN1 N3   N3   N 0 1 N N N N N N 67.070 23.739 1.562  0.686  -0.342 0.646  N3   DN1 5  
DN1 C4   C4   C 0 1 N N R N N N 67.781 22.723 0.825  1.390  -0.485 -0.630 C4   DN1 6  
DN1 C5   C5   C 0 1 N N N N N N 68.609 23.266 -0.326 2.777  0.149  -0.523 C5   DN1 7  
DN1 C6   C6   C 0 1 N N N N N N 66.884 24.958 -1.052 4.898  0.628  -1.753 C6   DN1 8  
DN1 C7   C7   C 0 1 N N N N N N 69.291 25.435 -1.476 3.793  -1.600 -1.989 C7   DN1 9  
DN1 C8   C8   C 0 1 N N N N N N 68.305 24.776 -0.524 3.553  -0.098 -1.818 C8   DN1 10 
DN1 C9   C9   C 0 1 N N N N N N 67.489 21.266 0.916  0.604  0.203  -1.716 C9   DN1 11 
DN1 O10  O10  O 0 1 N N N N N N 67.870 20.482 1.809  -0.323 0.927  -1.426 O10  DN1 12 
DN1 N11  N11  N 0 1 N N N N N N 66.640 20.669 -0.038 0.934  0.014  -3.009 N11  DN1 13 
DN1 C12  C12  C 0 1 N N R N N N 66.341 19.223 0.235  0.093  0.576  -4.069 C12  DN1 14 
DN1 C13  C13  C 0 1 N N N N N N 66.635 18.881 1.690  -0.981 -0.439 -4.460 C13  DN1 15 
DN1 C14  C14  C 0 1 N N N N N N 65.552 18.751 2.698  -1.846 -0.762 -3.240 C14  DN1 16 
DN1 F15  F15  F 0 1 N N N N N N 64.411 19.089 2.426  -2.829 -1.691 -3.598 F15  DN1 17 
DN1 F16  F16  F 0 1 N N N N N N 65.812 19.398 3.720  -1.043 -1.299 -2.228 F16  DN1 18 
DN1 C17  C17  C 0 1 N N R N N N 67.141 18.300 -0.830 0.958  0.899  -5.289 C17  DN1 19 
DN1 C18  C18  C 0 1 N N N N N N 67.666 16.999 -0.072 0.093  1.478  -6.379 C18  DN1 20 
DN1 O19  O19  O 0 1 N N N N N N 68.127 17.057 1.108  -0.595 2.609  -6.161 O19  DN1 21 
DN1 O20  O20  O 0 1 N N N N N N 67.548 15.894 -0.675 0.018  0.923  -7.450 O20  DN1 22 
DN1 O21  O21  O 0 1 N N N N N N 68.312 19.004 -1.294 1.582  -0.296 -5.760 O21  DN1 23 
DN1 C22  C22  C 0 1 N N N N N N 65.223 23.290 4.840  -1.046 -1.625 3.096  C22  DN1 24 
DN1 C23  C23  C 0 1 N N N N N N 67.273 24.729 4.349  1.253  -1.515 4.114  C23  DN1 25 
DN1 C24  C24  C 0 1 Y N N N N N 65.760 26.496 4.011  0.980  0.804  4.410  C24  DN1 26 
DN1 C25  C25  C 0 1 Y N N N N N 67.030 26.199 4.469  1.610  -0.306 4.950  C25  DN1 27 
DN1 C26  C26  C 0 1 Y N N N N N 65.279 27.789 4.018  1.162  2.048  5.017  C26  DN1 28 
DN1 C27  C27  C 0 1 Y N N N N N 67.878 27.196 4.935  2.405  -0.183 6.073  C27  DN1 29 
DN1 C28  C28  C 0 1 Y N N N N N 67.408 28.515 4.942  2.580  1.051  6.669  C28  DN1 30 
DN1 C29  C29  C 0 1 Y N N N N N 66.111 28.818 4.484  1.957  2.165  6.138  C29  DN1 31 
DN1 C30  C30  C 0 1 Y N N N N N 66.270 22.486 5.612  -1.943 -1.048 2.031  C30  DN1 32 
DN1 C31  C31  C 0 1 Y N N N N N 67.214 21.581 5.011  -2.017 -1.604 0.779  C31  DN1 33 
DN1 C32  C32  C 0 1 Y N N N N N 68.301 21.310 5.818  -2.842 -1.047 -0.146 C32  DN1 34 
DN1 S33  S33  S 0 1 Y N N N N N 68.203 22.158 7.300  -3.551 0.285  0.706  S33  DN1 35 
DN1 C34  C34  C 0 1 Y N N N N N 66.735 22.876 6.861  -2.735 0.063  2.276  C34  DN1 36 
DN1 C35  C35  C 0 1 N N N N N N 66.014 23.924 7.617  -2.862 0.854  3.502  C35  DN1 37 
DN1 O36  O36  O 0 1 N N N N N N 66.506 24.130 8.761  -2.220 0.551  4.490  O36  DN1 38 
DN1 O37  O37  O 0 1 N N N N N N 65.025 24.446 7.020  -3.691 1.918  3.536  O37  DN1 39 
DN1 H1   H1   H 0 1 N N N N N N 64.060 25.388 3.210  -0.291 1.099  2.756  H1   DN1 40 
DN1 H3   H3   H 0 1 N N N N N N 67.337 24.717 1.452  0.037  0.368  0.765  H3   DN1 41 
DN1 H4   H4   H 0 1 N N N N N N 68.638 22.684 1.537  1.492  -1.543 -0.872 H4   DN1 42 
DN1 H5C1 1H5C H 0 0 N N N N N N 68.459 22.681 -1.263 3.316  -0.294 0.314  H5C1 DN1 43 
DN1 H5C2 2H5C H 0 0 N N N N N N 69.698 23.072 -0.188 2.674  1.222  -0.361 H5C2 DN1 44 
DN1 H6C1 1H6C H 0 0 N N N N N N 66.666 26.042 -1.194 5.451  0.451  -2.676 H6C1 DN1 45 
DN1 H6C2 2H6C H 0 0 N N N N N N 66.129 24.462 -0.399 4.727  1.698  -1.631 H6C2 DN1 46 
DN1 H6C3 3H6C H 0 0 N N N N N N 66.706 24.370 -1.983 5.474  0.253  -0.907 H6C3 DN1 47 
DN1 H7C1 1H7C H 0 0 N N N N N N 69.073 26.519 -1.618 4.411  -1.965 -1.168 H7C1 DN1 48 
DN1 H7C2 2H7C H 0 0 N N N N N N 69.331 24.899 -2.453 2.837  -2.123 -1.984 H7C2 DN1 49 
DN1 H7C3 3H7C H 0 0 N N N N N N 70.343 25.274 -1.144 4.302  -1.781 -2.935 H7C3 DN1 50 
DN1 H8   H8   H 0 1 N N N N N N 68.380 25.283 0.466  2.978  0.276  -2.664 H8   DN1 51 
DN1 H11  H11  H 0 1 N N N N N N 66.263 21.173 -0.840 1.728  -0.493 -3.238 H11  DN1 52 
DN1 H12  H12  H 0 1 N N N N N N 65.250 19.066 0.065  -0.383 1.489  -3.709 H12  DN1 53 
DN1 H13  H13  H 0 1 N N N N N N 67.370 19.626 2.074  -1.607 -0.021 -5.249 H13  DN1 54 
DN1 H13D H13D H 0 0 N N N N N N 67.230 17.938 1.705  -0.505 -1.351 -4.820 H13D DN1 55 
DN1 H14  H14  H 0 1 N N N N N N 65.511 17.677 2.995  -2.322 0.149  -2.881 H14  DN1 56 
DN1 H17  H17  H 0 1 N N N N N N 66.482 18.021 -1.685 1.723  1.623  -5.010 H17  DN1 57 
DN1 H19  H19  H 0 1 N N N N N N 68.439 16.281 1.559  -1.150 2.980  -6.860 H19  DN1 58 
DN1 H21  H21  H 0 1 N N N N N N 68.781 18.463 -1.918 0.871  -0.908 -5.996 H21  DN1 59 
DN1 H221 1H22 H 0 0 N N N N N N 64.438 22.636 4.393  -0.944 -2.699 2.943  H221 DN1 60 
DN1 H222 2H22 H 0 0 N N N N N N 64.570 23.887 5.518  -1.480 -1.437 4.078  H222 DN1 61 
DN1 H231 1H23 H 0 0 N N N N N N 68.179 24.456 3.760  0.725  -2.253 4.719  H231 DN1 62 
DN1 H232 2H23 H 0 0 N N N N N N 67.597 24.235 5.294  2.150  -1.952 3.676  H232 DN1 63 
DN1 H26  H26  H 0 1 N N N N N N 64.258 28.010 3.663  0.678  2.922  4.608  H26  DN1 64 
DN1 H27  H27  H 0 1 N N N N N N 68.894 26.955 5.290  2.891  -1.055 6.487  H27  DN1 65 
DN1 H28  H28  H 0 1 N N N N N N 68.060 29.325 5.310  3.202  1.145  7.547  H28  DN1 66 
DN1 H29  H29  H 0 1 N N N N N N 65.751 29.861 4.492  2.093  3.131  6.602  H29  DN1 67 
DN1 H31  H31  H 0 1 N N N N N N 67.082 21.147 4.006  -1.427 -2.474 0.532  H31  DN1 68 
DN1 H32  H32  H 0 1 N N N N N N 69.127 20.633 5.542  -3.014 -1.359 -1.165 H32  DN1 69 
DN1 H37  H37  H 0 1 N N N N N N 64.562 25.118 7.505  -3.775 2.440  4.345  H37  DN1 70 
# 
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 
DN1 N1  C2   SING N N 1  
DN1 N1  C24  SING N N 2  
DN1 N1  H1   SING N N 3  
DN1 C2  C1   SING N N 4  
DN1 C2  C22  SING N N 5  
DN1 C2  C23  SING N N 6  
DN1 C1  O2   DOUB N N 7  
DN1 C1  N3   SING N N 8  
DN1 N3  C4   SING N N 9  
DN1 N3  H3   SING N N 10 
DN1 C4  C5   SING N N 11 
DN1 C4  C9   SING N N 12 
DN1 C4  H4   SING N N 13 
DN1 C5  C8   SING N N 14 
DN1 C5  H5C1 SING N N 15 
DN1 C5  H5C2 SING N N 16 
DN1 C6  C8   SING N N 17 
DN1 C6  H6C1 SING N N 18 
DN1 C6  H6C2 SING N N 19 
DN1 C6  H6C3 SING N N 20 
DN1 C7  C8   SING N N 21 
DN1 C7  H7C1 SING N N 22 
DN1 C7  H7C2 SING N N 23 
DN1 C7  H7C3 SING N N 24 
DN1 C8  H8   SING N N 25 
DN1 C9  O10  DOUB N N 26 
DN1 C9  N11  SING N N 27 
DN1 N11 C12  SING N N 28 
DN1 N11 H11  SING N N 29 
DN1 C12 C13  SING N N 30 
DN1 C12 C17  SING N N 31 
DN1 C12 H12  SING N N 32 
DN1 C13 C14  SING N N 33 
DN1 C13 H13  SING N N 34 
DN1 C13 H13D SING N N 35 
DN1 C14 F15  SING N N 36 
DN1 C14 F16  SING N N 37 
DN1 C14 H14  SING N N 38 
DN1 C17 C18  SING N N 39 
DN1 C17 O21  SING N N 40 
DN1 C17 H17  SING N N 41 
DN1 C18 O19  SING N N 42 
DN1 C18 O20  DOUB N N 43 
DN1 O19 H19  SING N N 44 
DN1 O21 H21  SING N N 45 
DN1 C22 C30  SING N N 46 
DN1 C22 H221 SING N N 47 
DN1 C22 H222 SING N N 48 
DN1 C23 C25  SING N N 49 
DN1 C23 H231 SING N N 50 
DN1 C23 H232 SING N N 51 
DN1 C24 C25  DOUB Y N 52 
DN1 C24 C26  SING Y N 53 
DN1 C25 C27  SING Y N 54 
DN1 C26 C29  DOUB Y N 55 
DN1 C26 H26  SING N N 56 
DN1 C27 C28  DOUB Y N 57 
DN1 C27 H27  SING N N 58 
DN1 C28 C29  SING Y N 59 
DN1 C28 H28  SING N N 60 
DN1 C29 H29  SING N N 61 
DN1 C30 C31  SING Y N 62 
DN1 C30 C34  DOUB Y N 63 
DN1 C31 C32  DOUB Y N 64 
DN1 C31 H31  SING N N 65 
DN1 C32 S33  SING Y N 66 
DN1 C32 H32  SING N N 67 
DN1 S33 C34  SING Y N 68 
DN1 C34 C35  SING N N 69 
DN1 C35 O36  DOUB N N 70 
DN1 C35 O37  SING N N 71 
DN1 O37 H37  SING N N 72 
# 
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 
DN1 SMILES           ACDLabs              10.04 "O=C(O)C(O)C(NC(=O)C(NC(=O)C2(Nc1ccccc1C2)Cc3c(scc3)C(=O)O)CC(C)C)CC(F)F"                                                                                                                                                                    
DN1 SMILES_CANONICAL CACTVS               3.341 "CC(C)C[C@@H](NC(=O)[C@]1(Cc2ccccc2N1)Cc3ccsc3C(O)=O)C(=O)N[C@H](CC(F)F)[C@@H](O)C(O)=O"                                                                                                                                                     
DN1 SMILES           CACTVS               3.341 "CC(C)C[CH](NC(=O)[C]1(Cc2ccccc2N1)Cc3ccsc3C(O)=O)C(=O)N[CH](CC(F)F)[CH](O)C(O)=O"                                                                                                                                                           
DN1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)CC(C(=O)N[C@H](CC(F)F)[C@H](C(=O)O)O)NC(=O)[C@]1(Cc2ccccc2N1)Cc3ccsc3C(=O)O"                                                                                                                                                           
DN1 SMILES           "OpenEye OEToolkits" 1.5.0 "CC(C)CC(C(=O)NC(CC(F)F)C(C(=O)O)O)NC(=O)C1(Cc2ccccc2N1)Cc3ccsc3C(=O)O"                                                                                                                                                                      
DN1 InChI            InChI                1.03  "InChI=1S/C26H31F2N3O7S/c1-13(2)9-18(22(33)29-17(10-19(27)28)20(32)23(34)35)30-25(38)26(11-14-5-3-4-6-16(14)31-26)12-15-7-8-39-21(15)24(36)37/h3-8,13,17-20,31-32H,9-12H2,1-2H3,(H,29,33)(H,30,38)(H,34,35)(H,36,37)/t17-,18-,20-,26+/m1/s1" 
DN1 InChIKey         InChI                1.03  BEFPIHVRQQQFFB-DUFVWYDBSA-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 
DN1 "SYSTEMATIC NAME" ACDLabs              10.04 "3-{[N-({(2S)-2-[(2-carboxythiophen-3-yl)methyl]-2,3-dihydro-1H-indol-2-yl}carbonyl)-D-leucyl]amino}-3,4,5-trideoxy-5,5-difluoro-D-erythro-pentonic acid"                     
DN1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-[[(2S)-2-[[1-[[(2R,3R)-5,5-difluoro-1,2-dihydroxy-1-oxo-pentan-3-yl]amino]-4-methyl-1-oxo-pentan-2-yl]carbamoyl]-1,3-dihydroindol-2-yl]methyl]thiophene-2-carboxylic 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 
DN1 "Create component"  2004-07-14 EBI  
DN1 "Modify descriptor" 2011-06-04 RCSB 
DN1 "Modify synonyms"   2020-06-05 PDBE 
DN1 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      DN1 
_pdbx_chem_comp_synonyms.name         "PEPTIDOMIMETIC INHIBITOR" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            DN1 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_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               C17 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
