data_VPP # _chem_comp.id VPP _chem_comp.name "(2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H29 N5 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(5S)-Penicilloic Acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-07-18 _chem_comp.pdbx_modified_date 2021-03-01 _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 535.570 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VPP _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 4KQQ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 VPP S S S 0 1 N N N -7.297 5.636 24.052 5.074 -1.254 -1.498 S VPP 1 VPP O01 O01 O 0 1 N N N -4.489 3.620 23.416 3.610 -3.061 -0.054 O01 VPP 2 VPP O02 O02 O 0 1 N N N -7.923 4.789 19.678 5.859 -0.292 2.462 O02 VPP 3 VPP O03 O03 O 0 1 N N N -9.791 5.857 19.940 7.563 0.984 1.866 O03 VPP 4 VPP O06 O06 O 0 1 N N N -2.419 6.896 24.607 -0.227 -1.382 -0.930 O06 VPP 5 VPP O04 O04 O 0 1 N N N 0.406 9.686 21.863 -3.199 0.867 1.774 O04 VPP 6 VPP O05 O05 O 0 1 N N N 1.159 7.674 25.271 -5.538 1.016 2.012 O05 VPP 7 VPP O O O 0 1 N N N 3.523 7.861 26.511 -8.013 0.145 1.235 O VPP 8 VPP N02 N02 N 0 1 N N N -6.622 6.193 21.630 4.280 0.265 0.427 N02 VPP 9 VPP N03 N03 N 0 1 N N N -3.836 6.931 22.727 1.395 -0.116 -0.100 N03 VPP 10 VPP N04 N04 N 0 1 N N N -0.517 8.377 23.515 -2.294 -0.036 -0.042 N04 VPP 11 VPP N01 N01 N 0 1 N N N 1.883 9.026 23.533 -4.589 -0.147 0.371 N01 VPP 12 VPP N N N 0 1 N N N 4.534 8.640 24.581 -7.081 -1.376 -0.096 N VPP 13 VPP C17 C17 C 0 1 N N S -6.144 6.442 22.964 3.713 -0.181 -0.876 C17 VPP 14 VPP C19 C19 C 0 1 N N N -8.641 5.531 22.910 6.420 -0.233 -0.776 C19 VPP 15 VPP C18 C18 C 0 1 N N S -8.107 6.176 21.632 5.698 0.611 0.291 C18 VPP 16 VPP C20 C20 C 0 1 N N R -4.737 5.959 23.240 2.427 -0.984 -0.673 C20 VPP 17 VPP C01 C01 C 0 1 N N N -4.441 4.616 22.650 2.695 -2.132 0.266 C01 VPP 18 VPP C02 C02 C 0 1 N N N -9.023 4.110 22.708 7.486 -1.123 -0.134 C02 VPP 19 VPP C03 C03 C 0 1 N N N -9.833 6.352 23.454 7.045 0.668 -1.844 C03 VPP 20 VPP C04 C04 C 0 1 N N N -8.627 5.578 20.351 6.379 0.401 1.619 C04 VPP 21 VPP C21 C21 C 0 1 N N N -2.688 7.344 23.502 0.092 -0.404 -0.288 C21 VPP 22 VPP CA CA C 0 1 N N R -1.821 8.396 22.893 -0.970 0.489 0.301 CA VPP 23 VPP C05 C05 C 0 1 Y N N -2.536 9.714 23.002 -0.821 1.881 -0.256 C05 VPP 24 VPP C06 C06 C 0 1 N N N 0.582 9.070 22.901 -3.355 0.251 0.739 C06 VPP 25 VPP C07 C07 C 0 1 Y N N -3.150 10.247 21.841 -1.321 2.181 -1.510 C07 VPP 26 VPP C08 C08 C 0 1 Y N N -2.604 10.402 24.221 -0.190 2.860 0.488 C08 VPP 27 VPP C09 C09 C 0 1 N N N 3.006 9.764 22.902 -4.761 -0.994 -0.810 C09 VPP 28 VPP C10 C10 C 0 1 N N N 4.387 9.073 23.175 -5.860 -2.026 -0.573 C10 VPP 29 VPP C11 C11 C 0 1 N N N 2.085 8.288 24.746 -5.661 0.232 1.095 C11 VPP 30 VPP C12 C12 C 0 1 Y N N -3.838 11.474 21.921 -1.184 3.458 -2.021 C12 VPP 31 VPP C13 C13 C 0 1 Y N N -3.282 11.636 24.285 -0.054 4.137 -0.023 C13 VPP 32 VPP C14 C14 C 0 1 N N N 3.400 8.248 25.354 -7.006 -0.329 0.752 C14 VPP 33 VPP C15 C15 C 0 1 N N N 5.887 8.606 25.151 -8.388 -1.857 -0.549 C15 VPP 34 VPP C16 C16 C 0 1 Y N N -3.903 12.172 23.135 -0.549 4.435 -1.278 C16 VPP 35 VPP C C C 0 1 N N N 6.560 7.327 24.709 -8.787 -1.120 -1.829 C VPP 36 VPP O07 O07 O 0 1 N N N -4.133 4.472 21.419 2.086 -2.217 1.306 O07 VPP 37 VPP H1 H1 H 0 1 N N N -4.271 2.834 22.929 3.747 -3.779 0.579 H1 VPP 38 VPP H2 H2 H 0 1 N N N -9.961 5.392 19.129 7.961 0.820 2.732 H2 VPP 39 VPP H3 H3 H 0 1 N N N -6.279 5.309 21.312 4.146 -0.437 1.139 H3 VPP 40 VPP H5 H5 H 0 1 N N N -3.997 7.331 21.825 1.649 0.666 0.414 H5 VPP 41 VPP H6 H6 H 0 1 N N N -0.379 7.882 24.373 -2.408 -0.589 -0.830 H6 VPP 42 VPP H7 H7 H 0 1 N N N -6.207 7.516 23.194 3.545 0.665 -1.542 H7 VPP 43 VPP H8 H8 H 0 1 N N N -8.440 7.224 21.649 5.779 1.664 0.021 H8 VPP 44 VPP H9 H9 H 0 1 N N N -4.610 5.890 24.330 2.085 -1.371 -1.632 H9 VPP 45 VPP H10 H10 H 0 1 N N N -9.400 3.693 23.654 8.241 -0.499 0.343 H10 VPP 46 VPP H11 H11 H 0 1 N N N -9.809 4.047 21.941 7.020 -1.766 0.614 H11 VPP 47 VPP H12 H12 H 0 1 N N N -8.143 3.537 22.379 7.955 -1.740 -0.901 H12 VPP 48 VPP H13 H13 H 0 1 N N N -10.213 5.883 24.374 6.276 1.311 -2.272 H13 VPP 49 VPP H14 H14 H 0 1 N N N -9.501 7.377 23.676 7.822 1.282 -1.390 H14 VPP 50 VPP H15 H15 H 0 1 N N N -10.633 6.380 22.700 7.481 0.051 -2.629 H15 VPP 51 VPP H16 H16 H 0 1 N N N -1.704 8.163 21.824 -0.860 0.517 1.385 H16 VPP 52 VPP H17 H17 H 0 1 N N N -3.091 9.717 20.902 -1.817 1.417 -2.090 H17 VPP 53 VPP H18 H18 H 0 1 N N N -2.140 9.990 25.105 0.196 2.627 1.470 H18 VPP 54 VPP H19 H19 H 0 1 N N N 3.033 10.786 23.309 -5.031 -0.371 -1.663 H19 VPP 55 VPP H20 H20 H 0 1 N N N 2.838 9.806 21.816 -3.824 -1.508 -1.023 H20 VPP 56 VPP H21 H21 H 0 1 N N N 4.476 8.191 22.523 -5.522 -2.747 0.171 H21 VPP 57 VPP H22 H22 H 0 1 N N N 5.191 9.786 22.939 -6.071 -2.547 -1.507 H22 VPP 58 VPP H23 H23 H 0 1 N N N -4.318 11.879 21.042 -1.574 3.692 -3.001 H23 VPP 59 VPP H24 H24 H 0 1 N N N -3.327 12.175 25.220 0.439 4.902 0.559 H24 VPP 60 VPP H25 H25 H 0 1 N N N 6.463 9.472 24.792 -8.333 -2.927 -0.748 H25 VPP 61 VPP H26 H26 H 0 1 N N N 5.828 8.634 26.249 -9.133 -1.669 0.225 H26 VPP 62 VPP H27 H27 H 0 1 N N N -4.426 13.115 23.191 -0.442 5.433 -1.678 H27 VPP 63 VPP H28 H28 H 0 1 N N N 7.577 7.284 25.127 -9.760 -1.477 -2.166 H28 VPP 64 VPP H29 H29 H 0 1 N N N 5.979 6.464 25.067 -8.842 -0.049 -1.630 H29 VPP 65 VPP H30 H30 H 0 1 N N N 6.614 7.302 23.611 -8.043 -1.307 -2.603 H30 VPP 66 # # 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 VPP O02 C04 DOUB N N 1 VPP O03 C04 SING N N 2 VPP C04 C18 SING N N 3 VPP O07 C01 DOUB N N 4 VPP N02 C18 SING N N 5 VPP N02 C17 SING N N 6 VPP C18 C19 SING N N 7 VPP C07 C12 DOUB Y N 8 VPP C07 C05 SING Y N 9 VPP O04 C06 DOUB N N 10 VPP C12 C16 SING Y N 11 VPP C01 C20 SING N N 12 VPP C01 O01 SING N N 13 VPP C02 C19 SING N N 14 VPP N03 C20 SING N N 15 VPP N03 C21 SING N N 16 VPP CA C05 SING N N 17 VPP CA C21 SING N N 18 VPP CA N04 SING N N 19 VPP C06 N04 SING N N 20 VPP C06 N01 SING N N 21 VPP C09 C10 SING N N 22 VPP C09 N01 SING N N 23 VPP C19 C03 SING N N 24 VPP C19 S SING N N 25 VPP C17 C20 SING N N 26 VPP C17 S SING N N 27 VPP C05 C08 DOUB Y N 28 VPP C16 C13 DOUB Y N 29 VPP C10 N SING N N 30 VPP C21 O06 DOUB N N 31 VPP N01 C11 SING N N 32 VPP C08 C13 SING Y N 33 VPP N C15 SING N N 34 VPP N C14 SING N N 35 VPP C C15 SING N N 36 VPP C11 O05 DOUB N N 37 VPP C11 C14 SING N N 38 VPP C14 O DOUB N N 39 VPP O01 H1 SING N N 40 VPP O03 H2 SING N N 41 VPP N02 H3 SING N N 42 VPP N03 H5 SING N N 43 VPP N04 H6 SING N N 44 VPP C17 H7 SING N N 45 VPP C18 H8 SING N N 46 VPP C20 H9 SING N N 47 VPP C02 H10 SING N N 48 VPP C02 H11 SING N N 49 VPP C02 H12 SING N N 50 VPP C03 H13 SING N N 51 VPP C03 H14 SING N N 52 VPP C03 H15 SING N N 53 VPP CA H16 SING N N 54 VPP C07 H17 SING N N 55 VPP C08 H18 SING N N 56 VPP C09 H19 SING N N 57 VPP C09 H20 SING N N 58 VPP C10 H21 SING N N 59 VPP C10 H22 SING N N 60 VPP C12 H23 SING N N 61 VPP C13 H24 SING N N 62 VPP C15 H25 SING N N 63 VPP C15 H26 SING N N 64 VPP C16 H27 SING N N 65 VPP C H28 SING N N 66 VPP C H29 SING N N 67 VPP C H30 SING N N 68 # # 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 VPP SMILES ACDLabs 12.01 "O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3" VPP InChI InChI 1.03 "InChI=1S/C23H29N5O8S/c1-4-27-10-11-28(19(31)18(27)30)22(36)25-13(12-8-6-5-7-9-12)16(29)24-14(20(32)33)17-26-15(21(34)35)23(2,3)37-17/h5-9,13-15,17,26H,4,10-11H2,1-3H3,(H,24,29)(H,25,36)(H,32,33)(H,34,35)/t13-,14+,15+,17+/m1/s1" VPP InChIKey InChI 1.03 OKSUEATVFIVTFV-AESZEHBQSA-N VPP SMILES_CANONICAL CACTVS 3.385 "CCN1CCN(C(=O)N[C@@H](C(=O)N[C@@H]([C@H]2N[C@@H](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O" VPP SMILES CACTVS 3.385 "CCN1CCN(C(=O)N[CH](C(=O)N[CH]([CH]2N[CH](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O" VPP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@@H]([C@H]3N[C@H](C(S3)(C)C)C(=O)O)C(=O)O" VPP SMILES "OpenEye OEToolkits" 1.7.6 "CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C3NC(C(S3)(C)C)C(=O)O)C(=O)O" # # 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 VPP "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" VPP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S,4S)-2-[(1R)-1-[[(2R)-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-phenyl-ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-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 VPP "Create component" 2013-07-18 RCSB VPP "Initial release" 2013-11-06 RCSB VPP "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VPP _pdbx_chem_comp_synonyms.name "(5S)-Penicilloic Acid" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##