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 ? #