data_V2M
# 
_chem_comp.id                                    V2M 
_chem_comp.name                                  "N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H34 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-06-19 
_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                        474.550 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V2M 
_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        6XHL 
_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 
V2M C1  C1  C 0 1 N N N N N N 23.489 58.040 29.143 8.561  1.833  0.237  C1  V2M 1  
V2M O2  O1  O 0 1 N N N N N N 23.844 56.700 29.515 7.167  1.617  0.005  O2  V2M 2  
V2M C3  C2  C 0 1 Y N N N N N 24.719 56.529 30.554 6.650  0.431  0.415  C3  V2M 3  
V2M C4  C3  C 0 1 Y N N N N N 25.256 57.549 31.331 7.458  -0.503 1.031  C4  V2M 4  
V2M C5  C4  C 0 1 Y N N N N N 26.090 57.253 32.406 6.935  -1.717 1.452  C5  V2M 5  
V2M C6  C5  C 0 1 Y N N N N N 26.504 55.948 32.647 5.602  -2.012 1.263  C6  V2M 6  
V2M C7  C6  C 0 1 Y N N N N N 26.003 54.935 31.837 4.765  -1.089 0.644  C7  V2M 7  
V2M N8  N1  N 0 1 Y N N N N N 26.239 53.575 31.876 3.427  -1.101 0.325  N8  V2M 8  
V2M C9  C7  C 0 1 Y N N N N N 25.493 52.969 30.883 3.106  0.095  -0.292 C9  V2M 9  
V2M C10 C8  C 0 1 Y N N N N N 24.808 53.930 30.174 4.222  0.868  -0.370 C10 V2M 10 
V2M C11 C9  C 0 1 Y N N N N N 25.103 55.199 30.789 5.287  0.148  0.219  C11 V2M 11 
V2M C12 C10 C 0 1 N N N N N N 25.599 51.508 30.693 1.774  0.469  -0.785 C12 V2M 12 
V2M O13 O2  O 0 1 N N N N N N 26.340 50.828 31.407 1.603  1.551  -1.315 O13 V2M 13 
V2M N14 N2  N 0 1 N N N N N N 24.918 51.001 29.664 0.741  -0.386 -0.650 N14 V2M 14 
V2M C15 C11 C 0 1 N N S N N N 25.002 49.589 29.327 -0.609 0.029  -1.041 C15 V2M 15 
V2M C17 C12 C 0 1 N N N N N N 23.948 49.200 28.287 -0.832 -0.290 -2.520 C17 V2M 16 
V2M C18 C13 C 0 1 N N N N N N 22.511 49.354 28.761 -2.187 0.267  -2.963 C18 V2M 17 
V2M C19 C14 C 0 1 N N N N N N 22.125 48.240 29.744 -2.150 1.796  -2.917 C19 V2M 18 
V2M C20 C15 C 0 1 N N N N N N 21.561 49.394 27.564 -2.485 -0.193 -4.392 C20 V2M 19 
V2M C21 C16 C 0 1 N N N N N N 26.403 49.232 28.833 -1.623 -0.713 -0.208 C21 V2M 20 
V2M O22 O3  O 0 1 N N N N N N 27.000 49.963 28.038 -1.303 -1.727 0.376  O22 V2M 21 
V2M N23 N3  N 0 1 N N N N N N 26.913 48.088 29.308 -2.885 -0.250 -0.113 N23 V2M 22 
V2M C24 C17 C 0 1 N N S N N N 28.133 47.495 28.774 -3.847 -0.921 0.766  C24 V2M 23 
V2M C26 C18 C 0 1 N N N N N N 29.159 47.267 29.884 -4.932 0.072  1.186  C26 V2M 24 
V2M C27 C19 C 0 1 N N S N N N 29.743 48.581 30.425 -4.308 1.179  2.038  C27 V2M 25 
V2M C29 C20 C 0 1 N N N N N N 30.559 49.360 29.433 -5.391 2.181  2.502  C29 V2M 26 
V2M C30 C21 C 0 1 N N N N N N 31.660 49.729 30.225 -5.308 3.264  1.404  C30 V2M 27 
V2M N31 N4  N 0 1 N N N N N N 31.771 49.167 31.437 -3.944 3.179  0.872  N31 V2M 28 
V2M C32 C22 C 0 1 N N N N N N 30.667 48.392 31.611 -3.360 2.016  1.208  C32 V2M 29 
V2M O33 O4  O 0 1 N N N N N N 30.366 47.722 32.597 -2.237 1.686  0.892  O33 V2M 30 
V2M C34 C23 C 0 1 N N S N N N 27.813 46.248 27.948 -4.489 -2.092 0.019  C34 V2M 31 
V2M O35 O5  O 0 1 N N N N N N 29.015 45.602 27.530 -5.427 -2.746 0.877  O35 V2M 32 
V2M C36 C24 C 0 1 N N N N N N 27.032 46.627 26.691 -3.403 -3.086 -0.401 C36 V2M 33 
V2M O37 O6  O 0 1 N N N N N N 26.642 45.505 25.913 -2.652 -3.484 0.748  O37 V2M 34 
V2M H1  H1  H 0 1 N N N N N N 22.784 58.012 28.299 8.763  1.779  1.307  H1  V2M 35 
V2M H2  H2  H 0 1 N N N N N N 23.017 58.545 29.999 9.138  1.067  -0.280 H2  V2M 36 
V2M H3  H3  H 0 1 N N N N N N 24.394 58.590 28.846 8.844  2.816  -0.137 H3  V2M 37 
V2M H4  H4  H 0 1 N N N N N N 25.025 58.578 31.099 8.505  -0.288 1.187  H4  V2M 38 
V2M H5  H5  H 0 1 N N N N N N 26.419 58.047 33.060 7.578  -2.439 1.932  H5  V2M 39 
V2M H6  H6  H 0 1 N N N N N N 27.198 55.726 33.444 5.207  -2.961 1.595  H6  V2M 40 
V2M H7  H7  H 0 1 N N N N N N 26.848 53.107 32.516 2.810  -1.828 0.503  H7  V2M 41 
V2M H8  H8  H 0 1 N N N N N N 24.170 53.764 29.318 4.285  1.851  -0.812 H8  V2M 42 
V2M H9  H9  H 0 1 N N N N N N 24.339 51.603 29.114 0.891  -1.276 -0.295 H9  V2M 43 
V2M H10 H10 H 0 1 N N N N N N 24.808 48.999 30.235 -0.721 1.101  -0.879 H10 V2M 44 
V2M H11 H11 H 0 1 N N N N N N 24.109 48.147 28.012 -0.041 0.166  -3.114 H11 V2M 45 
V2M H12 H12 H 0 1 N N N N N N 24.088 49.836 27.401 -0.819 -1.370 -2.666 H12 V2M 46 
V2M H13 H13 H 0 1 N N N N N N 22.429 50.314 29.291 -2.966 -0.098 -2.294 H13 V2M 47 
V2M H14 H14 H 0 1 N N N N N N 22.827 48.239 30.591 -3.136 2.191  -3.160 H14 V2M 48 
V2M H15 H15 H 0 1 N N N N N N 21.104 48.415 30.114 -1.864 2.122  -1.916 H15 V2M 49 
V2M H16 H16 H 0 1 N N N N N N 22.168 47.268 29.231 -1.422 2.164  -3.640 H16 V2M 50 
V2M H17 H17 H 0 1 N N N N N N 20.526 49.506 27.920 -2.512 -1.282 -4.425 H17 V2M 51 
V2M H18 H18 H 0 1 N N N N N N 21.820 50.246 26.919 -3.450 0.204  -4.707 H18 V2M 52 
V2M H19 H19 H 0 1 N N N N N N 21.653 48.459 26.992 -1.706 0.172  -5.061 H19 V2M 53 
V2M H20 H20 H 0 1 N N N N N N 26.439 47.624 30.056 -3.157 0.526  -0.626 H20 V2M 54 
V2M H21 H21 H 0 1 N N N N N N 28.577 48.225 28.081 -3.332 -1.293 1.651  H21 V2M 55 
V2M H22 H22 H 0 1 N N N N N N 28.670 46.731 30.711 -5.387 0.511  0.298  H22 V2M 56 
V2M H23 H23 H 0 1 N N N N N N 29.980 46.654 29.485 -5.695 -0.447 1.766  H23 V2M 57 
V2M H24 H24 H 0 1 N N N N N N 28.902 49.213 30.748 -3.788 0.752  2.896  H24 V2M 58 
V2M H25 H25 H 0 1 N N N N N N 30.013 50.241 29.064 -6.375 1.712  2.515  H25 V2M 59 
V2M H26 H26 H 0 1 N N N N N N 30.865 48.735 28.581 -5.146 2.596  3.479  H26 V2M 60 
V2M H27 H27 H 0 1 N N N N N N 32.570 49.476 29.661 -6.034 3.060  0.617  H27 V2M 61 
V2M H28 H28 H 0 1 N N N N N N 31.610 50.818 30.371 -5.485 4.251  1.834  H28 V2M 62 
V2M H29 H29 H 0 1 N N N N N N 32.520 49.293 32.087 -3.517 3.873  0.345  H29 V2M 63 
V2M H30 H30 H 0 1 N Y N N N N 27.202 45.564 28.556 -5.003 -1.721 -0.866 H30 V2M 64 
V2M H31 H31 H 0 1 N N N N N N 29.523 45.354 28.293 -6.144 -2.175 1.182  H31 V2M 65 
V2M H32 H32 H 0 1 N N N N N N 27.664 47.279 26.071 -3.868 -3.962 -0.853 H32 V2M 66 
V2M H33 H33 H 0 1 N N N N N N 26.127 47.174 26.994 -2.738 -2.613 -1.124 H33 V2M 67 
V2M H34 H34 H 0 1 N N N N N N 26.162 45.801 25.148 -1.945 -4.115 0.555  H34 V2M 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 
V2M O37 C36 SING N N 1  
V2M C36 C34 SING N N 2  
V2M O35 C34 SING N N 3  
V2M C20 C18 SING N N 4  
V2M C34 C24 SING N N 5  
V2M O22 C21 DOUB N N 6  
V2M C17 C18 SING N N 7  
V2M C17 C15 SING N N 8  
V2M C18 C19 SING N N 9  
V2M C24 N23 SING N N 10 
V2M C24 C26 SING N N 11 
V2M C21 N23 SING N N 12 
V2M C21 C15 SING N N 13 
V2M C1  O2  SING N N 14 
V2M C15 N14 SING N N 15 
V2M C29 C30 SING N N 16 
V2M C29 C27 SING N N 17 
V2M O2  C3  SING N N 18 
V2M N14 C12 SING N N 19 
V2M C26 C27 SING N N 20 
V2M C10 C11 SING Y N 21 
V2M C10 C9  DOUB Y N 22 
V2M C30 N31 SING N N 23 
V2M C27 C32 SING N N 24 
V2M C3  C11 DOUB Y N 25 
V2M C3  C4  SING Y N 26 
V2M C12 C9  SING N N 27 
V2M C12 O13 DOUB N N 28 
V2M C11 C7  SING Y N 29 
V2M C9  N8  SING Y N 30 
V2M C4  C5  DOUB Y N 31 
V2M N31 C32 SING N N 32 
V2M C32 O33 DOUB N N 33 
V2M C7  N8  SING Y N 34 
V2M C7  C6  DOUB Y N 35 
V2M C5  C6  SING Y N 36 
V2M C1  H1  SING N N 37 
V2M C1  H2  SING N N 38 
V2M C1  H3  SING N N 39 
V2M C4  H4  SING N N 40 
V2M C5  H5  SING N N 41 
V2M C6  H6  SING N N 42 
V2M N8  H7  SING N N 43 
V2M C10 H8  SING N N 44 
V2M N14 H9  SING N N 45 
V2M C15 H10 SING N N 46 
V2M C17 H11 SING N N 47 
V2M C17 H12 SING N N 48 
V2M C18 H13 SING N N 49 
V2M C19 H14 SING N N 50 
V2M C19 H15 SING N N 51 
V2M C19 H16 SING N N 52 
V2M C20 H17 SING N N 53 
V2M C20 H18 SING N N 54 
V2M C20 H19 SING N N 55 
V2M N23 H20 SING N N 56 
V2M C24 H21 SING N N 57 
V2M C26 H22 SING N N 58 
V2M C26 H23 SING N N 59 
V2M C27 H24 SING N N 60 
V2M C29 H25 SING N N 61 
V2M C29 H26 SING N N 62 
V2M C30 H27 SING N N 63 
V2M C30 H28 SING N N 64 
V2M N31 H29 SING N N 65 
V2M C34 H30 SING N N 66 
V2M O35 H31 SING N N 67 
V2M C36 H32 SING N N 68 
V2M C36 H33 SING N N 69 
V2M O37 H34 SING N N 70 
# 
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 
V2M SMILES           ACDLabs              12.01 "COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C(O)CO"                                                                                                                                                                   
V2M InChI            InChI                1.06  "InChI=1S/C24H34N4O6/c1-13(2)9-18(23(32)27-17(20(30)12-29)10-14-7-8-25-22(14)31)28-24(33)19-11-15-16(26-19)5-4-6-21(15)34-3/h4-6,11,13-14,17-18,20,26,29-30H,7-10,12H2,1-3H3,(H,25,31)(H,27,32)(H,28,33)/t14-,17-,18-,20+/m0/s1" 
V2M InChIKey         InChI                1.06  FDQSUXUTXIGUIA-PRIDNEQBSA-N                                                                                                                                                                                                      
V2M SMILES_CANONICAL CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)CO"                                                                                                                                                
V2M SMILES           CACTVS               3.385 "COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)CO"                                                                                                                                                       
V2M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](CO)O)NC(=O)c2cc3c([nH]2)cccc3OC"                                                                                                                                               
V2M SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(CO)O)NC(=O)c2cc3c([nH]2)cccc3OC"                                                                                                                                                                   
# 
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 
V2M "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide"                                            
V2M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(2~{S})-1-[[(2~{S},3~{S})-3,4-bis(oxidanyl)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1~{H}-indole-2-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V2M "Create component"   2020-06-19 RCSB 
V2M "Initial release"    2020-07-08 RCSB 
V2M "Other modification" 2022-07-26 RCSB 
V2M "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      V2M 
_pdbx_chem_comp_synonyms.name         "N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            V2M 
_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               C34 
_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      ? 
# 
