data_DN2
# 
_chem_comp.id                                    DN2 
_chem_comp.name                                  "3-({(2S)-2-[({(1S)-1-[({(1S)-1-[(R)-CARBOXY(HYDROXY)METHYL]-3,3-DIFLUOROPROPYL}AMINO)CARBONYL]-3-METHYLBUTYL}AMINO)CARBONYL]-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                     DN2 
_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 
DN2 N1   N1   N 0 1 N N N N N N 23.451 29.490 -3.548 -0.621 0.100  -2.715 N1   DN2 1  
DN2 C2   C2   C 0 1 N N S N N N 22.731 28.141 -3.638 0.164  -1.132 -2.619 C2   DN2 2  
DN2 C1   C1   C 0 1 N N N N N N 22.836 27.409 -2.250 0.210  -1.613 -1.192 C1   DN2 3  
DN2 O2   O2   O 0 1 N N N N N N 23.849 26.691 -2.081 0.127  -2.798 -0.948 O2   DN2 4  
DN2 N3   N3   N 0 1 N N N N N N 21.891 27.571 -1.270 0.344  -0.726 -0.186 N3   DN2 5  
DN2 C4   C4   C 0 1 N N S N N N 21.777 26.599 -0.170 0.261  -1.178 1.204  C4   DN2 6  
DN2 C5   C5   C 0 1 N N N N N N 20.540 26.876 0.710  1.666  -1.487 1.725  C5   DN2 7  
DN2 C6   C6   C 0 1 N N N N N N 19.050 28.708 1.753  3.713  -2.866 1.339  C6   DN2 8  
DN2 C7   C7   C 0 1 N N N N N N 21.599 28.756 1.972  1.460  -3.946 1.334  C7   DN2 9  
DN2 C8   C8   C 0 1 N N N N N N 20.397 28.355 1.121  2.241  -2.683 0.964  C8   DN2 10 
DN2 C9   C9   C 0 1 N N N N N N 21.674 25.174 -0.773 -0.360 -0.096 2.048  C9   DN2 11 
DN2 O10  O10  O 0 1 N N N N N N 21.032 24.974 -1.814 -0.701 0.950  1.537  O10  DN2 12 
DN2 N11  N11  N 0 1 N N N N N N 22.691 24.339 -0.303 -0.539 -0.290 3.369  N11  DN2 13 
DN2 C12  C12  C 0 1 N N S N N N 22.653 22.892 -0.482 -1.144 0.762  4.189  C12  DN2 14 
DN2 C13  C13  C 0 1 N N N N N N 23.843 22.194 -1.158 -2.662 0.577  4.217  C13  DN2 15 
DN2 C14  C14  C 0 1 N N N N N N 24.381 22.882 -2.398 -3.213 0.661  2.792  C14  DN2 16 
DN2 F15  F15  F 0 1 N N N N N N 23.524 22.801 -3.276 -4.601 0.492  2.818  F15  DN2 17 
DN2 F16  F16  F 0 1 N N N N N N 24.462 24.083 -2.169 -2.905 1.912  2.246  F16  DN2 18 
DN2 C17  C17  C 0 1 N N R N N N 22.105 22.080 0.824  -0.593 0.678  5.614  C17  DN2 19 
DN2 C18  C18  C 0 1 N N N N N N 21.715 20.677 0.112  0.901  0.860  5.587  C18  DN2 20 
DN2 O19  O19  O 0 1 N N N N N N 20.751 20.742 -0.706 1.431  1.994  5.101  O19  DN2 21 
DN2 O20  O20  O 0 1 N N N N N N 22.444 19.716 0.444  1.624  -0.014 6.002  O20  DN2 22 
DN2 O21  O21  O 0 1 N N N N N N 20.794 22.640 1.142  -0.908 -0.599 6.172  O21  DN2 23 
DN2 C22  C22  C 0 1 N N N N N N 23.601 27.388 -4.707 1.581  -0.904 -3.148 C22  DN2 24 
DN2 C23  C23  C 0 1 N N N N N N 21.318 28.420 -4.225 -0.576 -2.151 -3.502 C23  DN2 25 
DN2 C24  C24  C 0 1 Y N N N N N 22.544 30.430 -4.059 -1.722 -0.096 -3.549 C24  DN2 26 
DN2 C25  C25  C 0 1 Y N N N N N 21.335 29.893 -4.470 -1.763 -1.389 -4.046 C25  DN2 27 
DN2 C26  C26  C 0 1 Y N N N N N 22.803 31.782 -4.182 -2.726 0.803  -3.917 C26  DN2 28 
DN2 C27  C27  C 0 1 Y N N N N N 20.334 30.688 -5.016 -2.781 -1.782 -4.894 C27  DN2 29 
DN2 C28  C28  C 0 1 Y N N N N N 20.569 32.055 -5.132 -3.770 -0.886 -5.254 C28  DN2 30 
DN2 C29  C29  C 0 1 Y N N N N N 21.803 32.595 -4.718 -3.739 0.406  -4.763 C29  DN2 31 
DN2 C30  C30  C 0 1 Y N N N N N 22.953 26.231 -5.473 2.219  0.236  -2.398 C30  DN2 32 
DN2 C31  C31  C 0 1 Y N N N N N 22.109 25.252 -4.836 2.985  0.019  -1.280 C31  DN2 33 
DN2 C32  C32  C 0 1 Y N N N N N 21.093 24.785 -5.638 3.539  1.081  -0.638 C32  DN2 34 
DN2 S33  S33  S 0 1 Y N N N N N 21.124 25.529 -7.174 3.007  2.435  -1.582 S33  DN2 35 
DN2 C34  C34  C 0 1 Y N N N N N 22.478 26.455 -6.770 2.064  1.551  -2.811 C34  DN2 36 
DN2 C35  C35  C 0 1 N N N N N N 22.969 27.628 -7.528 1.314  2.077  -3.954 C35  DN2 37 
DN2 O36  O36  O 0 1 N N N N N N 23.970 28.199 -6.981 1.279  3.405  -4.183 O36  DN2 38 
DN2 O37  O37  O 0 1 N N N N N N 22.389 27.954 -8.594 0.724  1.315  -4.696 O37  DN2 39 
DN2 H1   H1   H 0 1 N N N N N N 24.390 29.667 -3.192 -0.406 0.932  -2.264 H1   DN2 40 
DN2 H3   H3   H 0 1 N N N N N N 21.261 28.372 -1.303 0.496  0.210  -0.383 H3   DN2 41 
DN2 H4   H4   H 0 1 N N N N N N 22.693 26.659 0.463  -0.351 -2.078 1.258  H4   DN2 42 
DN2 H5C1 1H5C H 0 0 N N N N N N 20.538 26.215 1.608  1.616  -1.722 2.788  H5C1 DN2 43 
DN2 H5C2 2H5C H 0 0 N N N N N N 19.611 26.513 0.211  2.308  -0.618 1.576  H5C2 DN2 44 
DN2 H6C1 1H6C H 0 0 N N N N N N 18.947 29.778 2.050  4.123  -3.718 0.797  H6C1 DN2 45 
DN2 H6C2 2H6C H 0 0 N N N N N N 18.842 28.041 2.622  4.270  -1.966 1.076  H6C2 DN2 46 
DN2 H6C3 3H6C H 0 0 N N N N N N 18.214 28.409 1.078  3.796  -3.043 2.412  H6C3 DN2 47 
DN2 H7C1 1H7C H 0 0 N N N N N N 21.496 29.826 2.269  1.569  -4.141 2.401  H7C1 DN2 48 
DN2 H7C2 2H7C H 0 0 N N N N N N 22.568 28.550 1.460  0.406  -3.803 1.096  H7C2 DN2 49 
DN2 H7C3 3H7C H 0 0 N N N N N N 21.740 28.084 2.850  1.849  -4.792 0.768  H7C3 DN2 50 
DN2 H8   H8   H 0 1 N N N N N N 20.467 28.950 0.180  2.159  -2.505 -0.107 H8   DN2 51 
DN2 H11  H11  H 0 1 N N N N N N 23.486 24.755 0.181  -0.267 -1.126 3.778  H11  DN2 52 
DN2 H12  H12  H 0 1 N N N N N N 21.831 22.755 -1.223 -0.904 1.737  3.764  H12  DN2 53 
DN2 H131 1H13 H 0 0 N N N N N N 23.583 21.135 -1.390 -2.902 -0.397 4.642  H131 DN2 54 
DN2 H132 2H13 H 0 0 N N N N N N 24.664 22.038 -0.420 -3.112 1.360  4.827  H132 DN2 55 
DN2 H14  H14  H 0 1 N N N N N N 25.356 22.452 -2.725 -2.762 -0.121 2.182  H14  DN2 56 
DN2 H17  H17  H 0 1 N N N N N N 22.817 22.005 1.679  -1.044 1.461  6.224  H17  DN2 57 
DN2 H19  H19  H 0 1 N N N N N N 20.522 19.919 -1.123 2.390  2.111  5.083  H19  DN2 58 
DN2 H21  H21  H 0 1 N N N N N N 20.475 22.167 1.902  -0.492 -1.262 5.604  H21  DN2 59 
DN2 H221 1H22 H 0 0 N N N N N N 24.541 27.028 -4.226 2.172  -1.809 -3.005 H221 DN2 60 
DN2 H222 2H22 H 0 0 N N N N N N 24.006 28.128 -5.436 1.538  -0.662 -4.210 H222 DN2 61 
DN2 H231 1H23 H 0 0 N N N N N N 20.473 28.065 -3.589 0.065  -2.487 -4.316 H231 DN2 62 
DN2 H232 2H23 H 0 0 N N N N N N 21.056 27.804 -5.117 -0.910 -2.999 -2.904 H232 DN2 63 
DN2 H26  H26  H 0 1 N N N N N N 23.771 32.206 -3.866 -2.708 1.814  -3.537 H26  DN2 64 
DN2 H27  H27  H 0 1 N N N N N N 19.379 30.247 -5.348 -2.804 -2.792 -5.277 H27  DN2 65 
DN2 H28  H28  H 0 1 N N N N N N 19.790 32.715 -5.548 -4.565 -1.194 -5.916 H28  DN2 66 
DN2 H29  H29  H 0 1 N N N N N N 21.982 33.679 -4.819 -4.511 1.107  -5.043 H29  DN2 67 
DN2 H31  H31  H 0 1 N N N N N N 22.263 24.908 -3.799 3.144  -0.984 -0.914 H31  DN2 68 
DN2 H32  H32  H 0 1 N N N N N N 20.354 24.027 -5.328 4.160  1.082  0.244  H32  DN2 69 
DN2 H36  H36  H 0 1 N N N N N N 24.285 28.951 -7.467 0.784  3.753  -4.937 H36  DN2 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 
DN2 N1  C2   SING N N 1  
DN2 N1  C24  SING N N 2  
DN2 N1  H1   SING N N 3  
DN2 C2  C1   SING N N 4  
DN2 C2  C22  SING N N 5  
DN2 C2  C23  SING N N 6  
DN2 C1  O2   DOUB N N 7  
DN2 C1  N3   SING N N 8  
DN2 N3  C4   SING N N 9  
DN2 N3  H3   SING N N 10 
DN2 C4  C5   SING N N 11 
DN2 C4  C9   SING N N 12 
DN2 C4  H4   SING N N 13 
DN2 C5  C8   SING N N 14 
DN2 C5  H5C1 SING N N 15 
DN2 C5  H5C2 SING N N 16 
DN2 C6  C8   SING N N 17 
DN2 C6  H6C1 SING N N 18 
DN2 C6  H6C2 SING N N 19 
DN2 C6  H6C3 SING N N 20 
DN2 C7  C8   SING N N 21 
DN2 C7  H7C1 SING N N 22 
DN2 C7  H7C2 SING N N 23 
DN2 C7  H7C3 SING N N 24 
DN2 C8  H8   SING N N 25 
DN2 C9  O10  DOUB N N 26 
DN2 C9  N11  SING N N 27 
DN2 N11 C12  SING N N 28 
DN2 N11 H11  SING N N 29 
DN2 C12 C13  SING N N 30 
DN2 C12 C17  SING N N 31 
DN2 C12 H12  SING N N 32 
DN2 C13 C14  SING N N 33 
DN2 C13 H131 SING N N 34 
DN2 C13 H132 SING N N 35 
DN2 C14 F15  SING N N 36 
DN2 C14 F16  SING N N 37 
DN2 C14 H14  SING N N 38 
DN2 C17 C18  SING N N 39 
DN2 C17 O21  SING N N 40 
DN2 C17 H17  SING N N 41 
DN2 C18 O19  SING N N 42 
DN2 C18 O20  DOUB N N 43 
DN2 O19 H19  SING N N 44 
DN2 O21 H21  SING N N 45 
DN2 C22 C30  SING N N 46 
DN2 C22 H221 SING N N 47 
DN2 C22 H222 SING N N 48 
DN2 C23 C25  SING N N 49 
DN2 C23 H231 SING N N 50 
DN2 C23 H232 SING N N 51 
DN2 C24 C25  DOUB Y N 52 
DN2 C24 C26  SING Y N 53 
DN2 C25 C27  SING Y N 54 
DN2 C26 C29  DOUB Y N 55 
DN2 C26 H26  SING N N 56 
DN2 C27 C28  DOUB Y N 57 
DN2 C27 H27  SING N N 58 
DN2 C28 C29  SING Y N 59 
DN2 C28 H28  SING N N 60 
DN2 C29 H29  SING N N 61 
DN2 C30 C31  SING Y N 62 
DN2 C30 C34  DOUB Y N 63 
DN2 C31 C32  DOUB Y N 64 
DN2 C31 H31  SING N N 65 
DN2 C32 S33  SING Y N 66 
DN2 C32 H32  SING N N 67 
DN2 S33 C34  SING Y N 68 
DN2 C34 C35  SING N N 69 
DN2 C35 O36  SING N N 70 
DN2 C35 O37  DOUB N N 71 
DN2 O36 H36  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 
DN2 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"                                                                                                                                                                    
DN2 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"                                                                                                                                                     
DN2 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"                                                                                                                                                           
DN2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)C[C@@H](C(=O)N[C@@H](CC(F)F)[C@H](C(=O)O)O)NC(=O)[C@]1(Cc2ccccc2N1)Cc3ccsc3C(=O)O"                                                                                                                                                     
DN2 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"                                                                                                                                                                      
DN2 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-/m0/s1" 
DN2 InChIKey         InChI                1.03  BEFPIHVRQQQFFB-QUPVEMFASA-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 
DN2 "SYSTEMATIC NAME" ACDLabs              10.04 "3-{[N-({(2S)-2-[(2-carboxythiophen-3-yl)methyl]-2,3-dihydro-1H-indol-2-yl}carbonyl)-L-leucyl]amino}-3,4,5-trideoxy-5,5-difluoro-L-threo-pentonic acid"                            
DN2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-[[(2S)-2-[[(2S)-1-[[(2R,3S)-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 
DN2 "Create component"  2004-07-14 EBI  
DN2 "Modify descriptor" 2011-06-04 RCSB 
DN2 "Modify synonyms"   2021-03-01 PDBE 
DN2 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      DN2 
_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                            DN2 
_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      ? 
# 
