data_YPP # _chem_comp.id YPP _chem_comp.name "Hydrolyzed piperacillin" _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 "(2R,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.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-01-06 _chem_comp.pdbx_modified_date 2021-03-13 _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 YPP _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 3Q07 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 YPP C C C 0 1 N N N -4.368 -16.170 14.501 -2.279 -2.675 -1.156 C YPP 1 YPP N N N 0 1 N N N -6.191 -16.473 12.856 -1.395 -0.479 -0.623 N YPP 2 YPP O O O 0 1 N N N -3.855 -16.443 15.610 -1.859 -2.531 -2.280 O YPP 3 YPP CA CA C 0 1 N N R -5.582 -17.008 14.085 -2.381 -1.490 -0.231 CA YPP 4 YPP CB CB C 0 1 N N R -5.188 -18.481 13.944 -3.786 -0.892 -0.321 CB YPP 5 YPP NAE NAE N 0 1 N N N -4.220 -18.686 12.798 -3.952 0.238 0.636 NAE YPP 6 YPP CAG CAG C 0 1 N N S -4.931 -19.303 11.612 -5.371 0.503 0.893 CAG YPP 7 YPP CAH CAH C 0 1 N N N -6.002 -20.286 12.069 -6.240 -0.767 0.822 CAH YPP 8 YPP SAI SAI S 0 1 N N N -6.606 -19.534 13.557 -5.051 -2.071 0.310 SAI YPP 9 YPP CAJ CAJ C 0 1 N N N -3.913 -20.021 10.729 -5.872 1.493 -0.127 CAJ YPP 10 YPP OAK OAK O 0 1 N N N -2.739 -20.068 11.148 -5.255 1.671 -1.151 OAK YPP 11 YPP OAL OAL O 0 1 N N N -4.334 -20.512 9.659 -7.005 2.177 0.102 OAL YPP 12 YPP CAM CAM C 0 1 N N N -7.113 -20.412 11.027 -6.836 -1.089 2.193 CAM YPP 13 YPP CAN CAN C 0 1 N N N -5.382 -21.653 12.374 -7.345 -0.606 -0.224 CAN YPP 14 YPP CAP CAP C 0 1 N N N -7.516 -16.317 12.753 -0.129 -0.562 -0.168 CAP YPP 15 YPP OAQ OAQ O 0 1 N N N -8.310 -16.599 13.648 0.194 -1.473 0.565 OAQ YPP 16 YPP CAR CAR C 0 1 N N R -8.008 -15.705 11.441 0.886 0.477 -0.570 CAR YPP 17 YPP CAS CAS C 0 1 Y N N -8.039 -16.748 10.313 0.422 1.836 -0.112 CAS YPP 18 YPP CAT CAT C 0 1 Y N N -7.097 -16.690 9.291 -0.183 2.698 -1.007 CAT YPP 19 YPP CAU CAU C 0 1 Y N N -7.131 -17.619 8.257 -0.608 3.944 -0.586 CAU YPP 20 YPP CAV CAV C 0 1 Y N N -8.113 -18.603 8.237 -0.429 4.328 0.730 CAV YPP 21 YPP CAW CAW C 0 1 Y N N -9.067 -18.653 9.249 0.175 3.465 1.625 CAW YPP 22 YPP CAX CAX C 0 1 Y N N -9.031 -17.723 10.285 0.597 2.217 1.206 CAX YPP 23 YPP NAY NAY N 0 1 N N N -9.359 -15.137 11.622 2.176 0.166 0.051 NAY YPP 24 YPP CAZ CAZ C 0 1 N N N -9.839 -14.242 10.768 3.319 0.604 -0.514 CAZ YPP 25 YPP OBA OBA O 0 1 N N N -9.186 -13.843 9.804 3.276 1.330 -1.487 OBA YPP 26 YPP NBB NBB N 0 1 N N N -11.068 -13.737 10.929 4.509 0.236 0.001 NBB YPP 27 YPP CBC CBC C 0 1 N N N -11.463 -12.577 10.090 4.559 -0.548 1.235 CBC YPP 28 YPP CBD CBD C 0 1 N N N -12.409 -11.669 10.866 5.684 -1.577 1.170 CBD YPP 29 YPP NBE NBE N 0 1 N N N -13.525 -12.475 11.400 6.944 -0.937 0.793 NBE YPP 30 YPP CBF CBF C 0 1 N N N -13.263 -13.715 11.981 6.953 0.061 -0.114 CBF YPP 31 YPP OBG OBG O 0 1 N N N -14.146 -14.289 12.622 8.002 0.522 -0.511 OBG YPP 32 YPP CBH CBH C 0 1 N N N -12.006 -14.302 11.831 5.649 0.586 -0.626 CBH YPP 33 YPP OBI OBI O 0 1 N N N -11.730 -15.316 12.471 5.620 1.322 -1.591 OBI YPP 34 YPP CBJ CBJ C 0 1 N N N -14.912 -11.968 11.331 8.200 -1.380 1.403 CBJ YPP 35 YPP CBK CBK C 0 1 N N N -15.191 -11.012 12.493 8.811 -2.499 0.556 CBK YPP 36 YPP OXT OXT O 0 1 N N N -3.985 -15.281 13.706 -2.661 -3.891 -0.733 OXT YPP 37 YPP HN HN H 0 1 N N N -5.605 -16.222 12.086 -1.653 0.249 -1.209 HN YPP 38 YPP HA HA H 0 1 N N N -6.347 -16.946 14.873 -2.187 -1.810 0.792 HA YPP 39 YPP HB HB H 0 1 N N N -4.744 -18.750 14.914 -4.014 -0.580 -1.341 HB YPP 40 YPP HNAE HNAE H 0 0 N N N -3.838 -17.802 12.529 -3.456 0.058 1.496 HNAE YPP 41 YPP HAG HAG H 0 1 N N N -5.422 -18.502 11.040 -5.472 0.943 1.885 HAG YPP 42 YPP HAM HAM H 0 1 N N N -7.870 -21.126 11.382 -7.455 -0.256 2.525 HAM YPP 43 YPP HAMA HAMA H 0 0 N N N -7.581 -19.429 10.870 -7.446 -1.990 2.122 HAMA YPP 44 YPP HAMB HAMB H 0 0 N N N -6.687 -20.771 10.079 -6.031 -1.252 2.910 HAMB YPP 45 YPP HAN HAN H 0 1 N N N -6.169 -22.348 12.702 -6.897 -0.429 -1.202 HAN YPP 46 YPP HANA HANA H 0 0 N N N -4.899 -22.047 11.467 -7.948 -1.513 -0.258 HANA YPP 47 YPP HANB HANB H 0 0 N N N -4.632 -21.546 13.172 -7.978 0.240 0.044 HANB YPP 48 YPP HAR HAR H 0 1 N N N -7.304 -14.908 11.158 0.995 0.477 -1.655 HAR YPP 49 YPP HAT HAT H 0 1 N N N -6.338 -15.922 9.301 -0.323 2.398 -2.035 HAT YPP 50 YPP HAU HAU H 0 1 N N N -6.394 -17.576 7.469 -1.080 4.618 -1.286 HAU YPP 51 YPP HAV HAV H 0 1 N N N -8.135 -19.328 7.437 -0.760 5.302 1.058 HAV YPP 52 YPP HAW HAW H 0 1 N N N -9.835 -19.412 9.231 0.316 3.765 2.653 HAW YPP 53 YPP HAX HAX H 0 1 N N N -9.774 -17.759 11.068 1.065 1.542 1.906 HAX YPP 54 YPP HNAY HNAY H 0 0 N N N -9.919 -15.430 12.397 2.207 -0.355 0.868 HNAY YPP 55 YPP HBC HBC H 0 1 N N N -10.564 -12.009 9.809 4.731 0.121 2.079 HBC YPP 56 YPP HBCA HBCA H 0 0 N N N -11.970 -12.940 9.184 3.608 -1.063 1.373 HBCA YPP 57 YPP HBD HBD H 0 1 N N N -11.866 -11.195 11.697 5.798 -2.047 2.147 HBD YPP 58 YPP HBDA HBDA H 0 0 N N N -12.804 -10.890 10.197 5.432 -2.339 0.432 HBDA YPP 59 YPP HBJ HBJ H 0 1 N N N -15.053 -11.432 10.381 8.896 -0.543 1.453 HBJ YPP 60 YPP HBJA HBJA H 0 0 N N N -15.609 -12.817 11.387 8.005 -1.751 2.409 HBJA YPP 61 YPP HBK HBK H 0 1 N N N -16.226 -10.645 12.426 9.006 -2.128 -0.450 HBK YPP 62 YPP HBKA HBKA H 0 0 N N N -15.051 -11.543 13.446 9.745 -2.829 1.010 HBKA YPP 63 YPP HBKB HBKB H 0 0 N N N -14.496 -10.161 12.442 8.116 -3.337 0.506 HBKB YPP 64 YPP HAL HAL H 0 1 N N N -3.617 -20.935 9.201 -7.287 2.800 -0.581 HAL YPP 65 YPP HXT HXT H 0 1 N N N -3.232 -14.832 14.072 -2.582 -4.620 -1.364 HXT YPP 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 YPP C O DOUB N N 1 YPP C CA SING N N 2 YPP C OXT SING N N 3 YPP N CA SING N N 4 YPP N CAP SING N N 5 YPP CA CB SING N N 6 YPP CB NAE SING N N 7 YPP CB SAI SING N N 8 YPP NAE CAG SING N N 9 YPP CAG CAH SING N N 10 YPP CAG CAJ SING N N 11 YPP CAH SAI SING N N 12 YPP CAH CAM SING N N 13 YPP CAH CAN SING N N 14 YPP CAJ OAK DOUB N N 15 YPP CAJ OAL SING N N 16 YPP CAP OAQ DOUB N N 17 YPP CAP CAR SING N N 18 YPP CAR CAS SING N N 19 YPP CAR NAY SING N N 20 YPP CAS CAT DOUB Y N 21 YPP CAS CAX SING Y N 22 YPP CAT CAU SING Y N 23 YPP CAU CAV DOUB Y N 24 YPP CAV CAW SING Y N 25 YPP CAW CAX DOUB Y N 26 YPP NAY CAZ SING N N 27 YPP CAZ OBA DOUB N N 28 YPP CAZ NBB SING N N 29 YPP NBB CBC SING N N 30 YPP NBB CBH SING N N 31 YPP CBC CBD SING N N 32 YPP CBD NBE SING N N 33 YPP NBE CBF SING N N 34 YPP NBE CBJ SING N N 35 YPP CBF OBG DOUB N N 36 YPP CBF CBH SING N N 37 YPP CBH OBI DOUB N N 38 YPP CBJ CBK SING N N 39 YPP N HN SING N N 40 YPP CA HA SING N N 41 YPP CB HB SING N N 42 YPP NAE HNAE SING N N 43 YPP CAG HAG SING N N 44 YPP CAM HAM SING N N 45 YPP CAM HAMA SING N N 46 YPP CAM HAMB SING N N 47 YPP CAN HAN SING N N 48 YPP CAN HANA SING N N 49 YPP CAN HANB SING N N 50 YPP CAR HAR SING N N 51 YPP CAT HAT SING N N 52 YPP CAU HAU SING N N 53 YPP CAV HAV SING N N 54 YPP CAW HAW SING N N 55 YPP CAX HAX SING N N 56 YPP NAY HNAY SING N N 57 YPP CBC HBC SING N N 58 YPP CBC HBCA SING N N 59 YPP CBD HBD SING N N 60 YPP CBD HBDA SING N N 61 YPP CBJ HBJ SING N N 62 YPP CBJ HBJA SING N N 63 YPP CBK HBK SING N N 64 YPP CBK HBKA SING N N 65 YPP CBK HBKB SING N N 66 YPP OAL HAL SING N N 67 YPP OXT HXT 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 YPP 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" YPP SMILES_CANONICAL CACTVS 3.370 "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" YPP SMILES CACTVS 3.370 "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" YPP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "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" YPP SMILES "OpenEye OEToolkits" 1.7.0 "CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C3NC(C(S3)(C)C)C(=O)O)C(=O)O" YPP 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" YPP InChIKey InChI 1.03 OKSUEATVFIVTFV-WBTNSWJXSA-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 YPP "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,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" YPP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2R,4S)-2-[(1R)-1-[[(2R)-2-[(4-ethyl-2,3-dioxo-piperazin-1-yl)carbonylamino]-2-phenyl-ethanoyl]amino]-2-hydroxy-2-oxo-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 YPP "Create component" 2011-01-06 PDBJ YPP "Modify aromatic_flag" 2011-06-04 RCSB YPP "Modify descriptor" 2011-06-04 RCSB YPP "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YPP _pdbx_chem_comp_synonyms.name "(2R,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" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##