data_VR4 # _chem_comp.id VR4 _chem_comp.name "N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H38 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms " GC376 alpha-ketoamide analog (bound form)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-09-09 _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 538.635 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VR4 _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 7K0H _chem_comp.pdbx_subcomponent_list "P6S LEU UZ4 ABN" _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 VR4 C33 C23 C 0 1 N N N N N N 20.216 23.445 -3.567 -6.098 0.298 -0.632 C21 P6S 1 VR4 C34 C24 C 0 1 Y N N N N N 20.472 24.917 -3.316 -7.137 0.236 0.458 C22 P6S 2 VR4 C36 C26 C 0 1 Y N N N N N 21.660 26.671 -2.096 -8.603 1.346 1.991 C24 P6S 3 VR4 C38 C28 C 0 1 Y N N N N N 20.030 27.259 -3.738 -8.534 -1.046 1.920 C26 P6S 4 VR4 C02 C1 C 0 1 N N N N N N 20.450 21.403 -2.364 -3.726 0.378 -0.881 C19 P6S 5 VR4 C35 C25 C 0 1 Y N N N N N 21.415 25.312 -2.346 -7.650 1.403 0.991 C23 P6S 6 VR4 C37 C27 C 0 1 Y N N N N N 20.961 27.647 -2.796 -9.043 0.121 2.458 C25 P6S 7 VR4 C39 C29 C 0 1 Y N N N N N 19.788 25.913 -3.990 -7.581 -0.989 0.920 C27 P6S 8 VR4 O32 O6 O 0 1 N N N N N N 20.669 22.752 -2.435 -4.774 0.322 -0.038 O20 P6S 9 VR4 O01 O1 O 0 1 N N N N N N 19.719 20.813 -3.132 -3.913 0.406 -2.082 O28 P6S 10 VR4 N03 N1 N 0 1 N N N N N N 21.107 20.845 -1.335 -2.470 0.403 -0.395 N LEU 11 VR4 C04 C2 C 0 1 N N S N N N 21.159 19.423 -1.160 -1.328 0.353 -1.311 CA LEU 12 VR4 C05 C3 C 0 1 N N N N N N 19.809 18.983 -0.599 -0.157 -0.296 -0.620 C LEU 13 VR4 O27 O5 O 0 1 N N N N N N 19.262 19.643 0.292 -0.172 -0.449 0.583 O LEU 14 VR4 C28 C19 C 0 1 N N N N N N 22.250 19.014 -0.186 -0.948 1.774 -1.732 CB LEU 15 VR4 C29 C20 C 0 1 N N N N N N 23.620 19.161 -0.736 0.153 1.715 -2.792 CG LEU 16 VR4 C30 C21 C 0 1 N N N N N N 24.648 19.070 0.408 -0.407 1.102 -4.076 CD1 LEU 17 VR4 C31 C22 C 0 1 N N N N N N 23.890 18.072 -1.718 0.659 3.130 -3.081 CD2 LEU 18 VR4 N06 N2 N 0 1 N N N N N N 19.205 17.823 -1.048 0.907 -0.706 -1.338 N19 UZ4 19 VR4 C07 C4 C 0 1 N N S N N N 18.059 17.268 -0.476 1.999 -1.431 -0.683 C20 UZ4 20 VR4 C08 C5 C 0 1 N N N N N N 16.957 17.006 -1.538 1.693 -2.930 -0.691 C21 UZ4 21 VR4 C09 C6 C 0 1 N N S N N N 16.361 18.306 -2.045 2.762 -3.673 0.113 C22 UZ4 22 VR4 C13 C9 C 0 1 N N N N N N 15.553 19.131 -0.992 2.568 -5.202 -0.012 C23 UZ4 23 VR4 C12 C8 C 0 1 N N N N N N 14.300 19.656 -1.715 2.954 -5.685 1.404 C24 UZ4 24 VR4 N11 N3 N 0 1 N N N N N N 14.208 18.812 -2.900 2.706 -4.542 2.289 N25 UZ4 25 VR4 C10 C7 C 0 1 N N N N N N 15.336 18.043 -3.112 2.599 -3.398 1.592 C26 UZ4 26 VR4 O14 O2 O 0 1 N N N N N N 15.447 17.270 -4.073 2.401 -2.304 2.077 O27 UZ4 27 VR4 C15 C10 C 0 1 N N R N N N 18.512 15.951 0.332 3.306 -1.173 -1.434 C28 UZ4 28 VR4 O26 O4 O 0 1 N N N N N N 19.733 16.261 1.018 3.178 -1.625 -2.783 O29 UZ4 29 VR4 C16 C11 C 0 1 N N N N N N 17.532 15.479 1.383 3.607 0.304 -1.425 C31 UZ4 30 VR4 O25 O3 O 0 1 N N N N N N 16.408 15.091 1.078 3.613 0.928 -2.466 O32 UZ4 31 VR4 N17 N4 N 0 1 N N N N N N 17.938 15.540 2.727 3.871 0.931 -0.262 N ABN 32 VR4 C18 C12 C 0 1 N N N N N N 17.094 15.137 3.860 4.163 2.367 -0.254 C ABN 33 VR4 C19 C13 C 0 1 Y N N N N N 16.364 16.298 4.467 4.420 2.819 1.161 C1 ABN 34 VR4 C20 C14 C 0 1 Y N N N N N 15.543 16.184 5.594 5.703 2.789 1.673 C2 ABN 35 VR4 C21 C15 C 0 1 Y N N N N N 14.860 17.303 6.103 5.939 3.204 2.971 C3 ABN 36 VR4 C22 C16 C 0 1 Y N N N N N 14.991 18.558 5.502 4.891 3.648 3.756 C4 ABN 37 VR4 C23 C17 C 0 1 Y N N N N N 15.791 18.680 4.380 3.608 3.678 3.243 C5 ABN 38 VR4 C24 C18 C 0 1 Y N N N N N 16.471 17.555 3.883 3.373 3.269 1.944 C6 ABN 39 VR4 H27 H27 H 0 1 N N N N N N 19.140 23.268 -3.713 -6.192 -0.578 -1.274 H7 P6S 40 VR4 H28 H28 H 0 1 N N N N N N 20.767 23.112 -4.459 -6.247 1.201 -1.225 H8 P6S 41 VR4 H30 H30 H 0 1 N N N N N N 22.394 26.959 -1.358 -9.004 2.258 2.408 H9 P6S 42 VR4 H32 H32 H 0 1 N N N N N N 19.482 28.011 -4.287 -8.877 -2.003 2.285 H10 P6S 43 VR4 H29 H29 H 0 1 N N N N N N 21.955 24.561 -1.789 -7.307 2.360 0.627 H20 P6S 44 VR4 H31 H31 H 0 1 N N N N N N 21.144 28.694 -2.606 -9.783 0.076 3.242 H21 P6S 45 VR4 H33 H33 H 0 1 N N N N N N 19.049 25.639 -4.729 -7.183 -1.901 0.501 H22 P6S 46 VR4 H34 H34 H 0 1 N N N N N N 21.571 21.435 -0.675 -2.321 0.455 0.562 H LEU 47 VR4 H1 H1 H 0 1 N N N N N N 21.329 18.923 -2.125 -1.596 -0.228 -2.194 HA LEU 48 VR4 H18 H18 H 0 1 N N N N N N 22.167 19.642 0.714 -1.823 2.277 -2.144 HB2 LEU 49 VR4 H19 H19 H 0 1 N N N N N N 22.096 17.960 0.087 -0.588 2.326 -0.863 HB3 LEU 50 VR4 H20 H20 H 0 1 N N N N N N 23.720 20.139 -1.230 0.977 1.103 -2.426 HG LEU 51 VR4 H21 H21 H 0 1 N N N N N N 24.457 19.870 1.138 0.395 0.989 -4.806 HD11 LEU 52 VR4 H22 H22 H 0 1 N N N N N N 24.559 18.092 0.904 -0.837 0.125 -3.855 HD12 LEU 53 VR4 H23 H23 H 0 1 N N N N N N 25.663 19.182 -0.001 -1.180 1.754 -4.484 HD13 LEU 54 VR4 H24 H24 H 0 1 N N N N N N 24.907 18.186 -2.122 1.058 3.568 -2.166 HD21 LEU 55 VR4 H25 H25 H 0 1 N N N N N N 23.802 17.097 -1.217 1.443 3.089 -3.836 HD22 LEU 56 VR4 H26 H26 H 0 1 N N N N N N 23.160 18.130 -2.539 -0.165 3.743 -3.447 HD23 LEU 57 VR4 H35 H35 H 0 1 N N N N N N 19.614 17.353 -1.830 0.950 -0.522 -2.290 H2 UZ4 58 VR4 H2 H2 H 0 1 N N N N N N 17.643 17.968 0.264 2.097 -1.086 0.347 H4 UZ4 59 VR4 H3 H3 H 0 1 N N N N N N 16.160 16.399 -1.085 0.715 -3.104 -0.243 H5 UZ4 60 VR4 H4 H4 H 0 1 N N N N N N 17.398 16.459 -2.385 1.692 -3.295 -1.718 H6 UZ4 61 VR4 H5 H5 H 0 1 N N N N N N 17.162 18.940 -2.452 3.758 -3.387 -0.223 H7 UZ4 62 VR4 H8 H8 H 0 1 N N N N N N 15.263 18.489 -0.147 1.529 -5.446 -0.237 H8 UZ4 63 VR4 H9 H9 H 0 1 N N N N N N 16.158 19.972 -0.622 3.237 -5.620 -0.764 H9 UZ4 64 VR4 H6 H6 H 0 1 N N N N N N 14.422 20.713 -1.994 2.333 -6.531 1.697 H10 UZ4 65 VR4 H7 H7 H 0 1 N N N N N N 13.406 19.544 -1.083 4.008 -5.964 1.432 H11 UZ4 66 VR4 H36 H36 H 0 1 N N N N N N 13.408 18.792 -3.500 2.628 -4.603 3.254 H12 UZ4 67 VR4 H10 H10 H 0 1 N N N N N N 18.678 15.144 -0.397 4.118 -1.712 -0.946 H13 UZ4 68 VR4 H38 H38 H 0 1 N N N N N N 20.025 15.500 1.505 2.472 -1.187 -3.279 H14 UZ4 69 VR4 H37 H37 H 0 1 N N N N N N 18.858 15.879 2.924 3.866 0.432 0.570 HN2 ABN 70 VR4 H11 H11 H 0 1 N N N N N N 16.357 14.401 3.508 5.046 2.561 -0.863 H1 ABN 71 VR4 H12 H12 H 0 1 N N N N N N 17.731 14.678 4.630 3.313 2.913 -0.661 H2A ABN 72 VR4 H13 H13 H 0 1 N N N N N N 15.432 15.225 6.079 6.522 2.442 1.060 H2 ABN 73 VR4 H14 H14 H 0 1 N N N N N N 14.226 17.191 6.970 6.942 3.181 3.372 H3 ABN 74 VR4 H15 H15 H 0 1 N N N N N N 14.477 19.417 5.906 5.075 3.972 4.769 H4 ABN 75 VR4 H16 H16 H 0 1 N N N N N N 15.893 19.636 3.888 2.789 4.025 3.856 H5 ABN 76 VR4 H17 H17 H 0 1 N N N N N N 17.101 17.672 3.014 2.371 3.292 1.543 H6 ABN 77 # 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 VR4 O14 C10 DOUB N N 1 VR4 C39 C38 DOUB Y N 2 VR4 C39 C34 SING Y N 3 VR4 C38 C37 SING Y N 4 VR4 C33 C34 SING N N 5 VR4 C33 O32 SING N N 6 VR4 C34 C35 DOUB Y N 7 VR4 O01 C02 DOUB N N 8 VR4 C10 N11 SING N N 9 VR4 C10 C09 SING N N 10 VR4 N11 C12 SING N N 11 VR4 C37 C36 DOUB Y N 12 VR4 O32 C02 SING N N 13 VR4 C02 N03 SING N N 14 VR4 C35 C36 SING Y N 15 VR4 C09 C08 SING N N 16 VR4 C09 C13 SING N N 17 VR4 C31 C29 SING N N 18 VR4 C12 C13 SING N N 19 VR4 C08 C07 SING N N 20 VR4 N03 C04 SING N N 21 VR4 C04 C05 SING N N 22 VR4 C04 C28 SING N N 23 VR4 N06 C05 SING N N 24 VR4 N06 C07 SING N N 25 VR4 C29 C28 SING N N 26 VR4 C29 C30 SING N N 27 VR4 C05 O27 DOUB N N 28 VR4 C07 C15 SING N N 29 VR4 C15 O26 SING N N 30 VR4 C15 C16 SING N N 31 VR4 O25 C16 DOUB N N 32 VR4 C16 N17 SING N N 33 VR4 N17 C18 SING N N 34 VR4 C18 C19 SING N N 35 VR4 C24 C23 DOUB Y N 36 VR4 C24 C19 SING Y N 37 VR4 C23 C22 SING Y N 38 VR4 C19 C20 DOUB Y N 39 VR4 C22 C21 DOUB Y N 40 VR4 C20 C21 SING Y N 41 VR4 C04 H1 SING N N 42 VR4 C07 H2 SING N N 43 VR4 C08 H3 SING N N 44 VR4 C08 H4 SING N N 45 VR4 C09 H5 SING N N 46 VR4 C12 H6 SING N N 47 VR4 C12 H7 SING N N 48 VR4 C13 H8 SING N N 49 VR4 C13 H9 SING N N 50 VR4 C15 H10 SING N N 51 VR4 C18 H11 SING N N 52 VR4 C18 H12 SING N N 53 VR4 C20 H13 SING N N 54 VR4 C21 H14 SING N N 55 VR4 C22 H15 SING N N 56 VR4 C23 H16 SING N N 57 VR4 C24 H17 SING N N 58 VR4 C28 H18 SING N N 59 VR4 C28 H19 SING N N 60 VR4 C29 H20 SING N N 61 VR4 C30 H21 SING N N 62 VR4 C30 H22 SING N N 63 VR4 C30 H23 SING N N 64 VR4 C31 H24 SING N N 65 VR4 C31 H25 SING N N 66 VR4 C31 H26 SING N N 67 VR4 C33 H27 SING N N 68 VR4 C33 H28 SING N N 69 VR4 C35 H29 SING N N 70 VR4 C36 H30 SING N N 71 VR4 C37 H31 SING N N 72 VR4 C38 H32 SING N N 73 VR4 C39 H33 SING N N 74 VR4 N03 H34 SING N N 75 VR4 N06 H35 SING N N 76 VR4 N11 H36 SING N N 77 VR4 N17 H37 SING N N 78 VR4 O26 H38 SING N N 79 # 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 VR4 SMILES ACDLabs 12.01 "C(c1ccccc1)OC(NC(C(=O)NC(C(O)C(NCc2ccccc2)=O)CC3CCNC3=O)CC(C)C)=O" VR4 InChI InChI 1.03 "InChI=1S/C29H38N4O6/c1-19(2)15-24(33-29(38)39-18-21-11-7-4-8-12-21)27(36)32-23(16-22-13-14-30-26(22)35)25(34)28(37)31-17-20-9-5-3-6-10-20/h3-12,19,22-25,34H,13-18H2,1-2H3,(H,30,35)(H,31,37)(H,32,36)(H,33,38)/t22-,23-,24-,25+/m0/s1" VR4 InChIKey InChI 1.03 MPMTWRHFCLPCDF-OJJQZRKESA-N VR4 SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)C(=O)NCc3ccccc3" VR4 SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)C(=O)NCc3ccccc3" VR4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3" VR4 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3" # 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 VR4 "SYSTEMATIC NAME" ACDLabs 12.01 "N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide" VR4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]pentan-2-yl]carbamate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VR4 _pdbx_chem_comp_synonyms.name "GC376 alpha-ketoamide analog (bound form)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VR4 "Create component" 2020-09-09 RCSB VR4 "Initial release" 2021-01-13 RCSB VR4 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id VR4 _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 C15 _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 ? #