data_JPP
#
_chem_comp.id JPP
_chem_comp.name "Piperacillin (Open Form)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H29 N5 O7 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-07-18
_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 519.571
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JPP
_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 4KQO
_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
JPP S S S 0 1 N N N N N N -5.446 6.028 24.319 4.526 0.356 -1.337 S JPP 1
JPP O01 O01 O 0 1 N N N N N N -2.781 4.270 20.868 1.972 2.747 -1.436 O01 JPP 2
JPP O02 O02 O 0 1 N N N N N N -7.628 3.596 20.911 8.038 -0.391 1.664 O02 JPP 3
JPP O03 O03 O 0 1 N N N N N N -7.563 5.633 20.102 5.935 -0.611 2.305 O03 JPP 4
JPP O06 O06 O 0 1 N N N N N N -1.870 6.522 24.672 -0.106 1.523 0.851 O06 JPP 5
JPP O04 O04 O 0 1 N N N N N N 0.559 9.257 21.746 -3.157 -0.596 -1.871 O04 JPP 6
JPP O05 O05 O 0 1 N N N N N N 1.439 7.823 25.254 -5.496 -0.865 -1.953 O05 JPP 7
JPP O O O 0 1 N N N N N N 3.786 8.329 26.467 -7.945 -0.245 -0.902 O JPP 8
JPP N02 N02 N 0 1 N N N N N N -5.597 4.094 22.633 4.949 1.434 0.967 N02 JPP 9
JPP N03 N03 N 0 1 N N N N N N -2.775 5.980 22.653 1.511 0.463 -0.236 N03 JPP 10
JPP N04 N04 N 0 1 N N N N N N -0.234 8.254 23.624 -2.161 0.155 -0.034 N04 JPP 11
JPP N01 N01 N 0 1 N N N N N N 2.196 8.874 23.421 -4.484 0.166 -0.262 N01 JPP 12
JPP N N N 0 1 N N N N N N 4.770 8.696 24.436 -6.994 1.175 0.525 N JPP 13
JPP C17 C17 C 0 1 N N R N N N -4.669 4.557 23.665 3.877 0.588 0.371 C17 JPP 14
JPP C19 C19 C 0 1 N N N N N N -6.758 6.093 23.097 6.291 0.315 -0.829 C19 JPP 15
JPP C18 C18 C 0 1 N N S N N N -6.178 5.205 21.969 6.276 0.951 0.574 C18 JPP 16
JPP C20 C20 C 0 1 N N R N N N -3.248 4.693 23.150 2.536 1.325 0.356 C20 JPP 17
JPP C01 C01 C 0 1 N N N N N N -3.059 3.781 21.967 2.665 2.586 -0.460 C01 JPP 18
JPP C02 C02 C 0 1 N N N N N N -8.044 5.495 23.634 6.798 -1.127 -0.761 C02 JPP 19
JPP C03 C03 C 0 1 N N N N N N -6.993 7.533 22.629 7.147 1.141 -1.790 C03 JPP 20
JPP C04 C04 C 0 1 N N N N N N -7.171 4.783 20.952 6.737 -0.074 1.578 C04 JPP 21
JPP C21 C21 C 0 1 N N N N N N -2.074 6.856 23.518 0.213 0.645 0.078 C21 JPP 22
JPP CA CA C 0 1 N N R N N N -1.567 8.152 23.008 -0.842 -0.242 -0.531 CA JPP 23
JPP C05 C05 C 0 1 Y N N N N N -2.472 9.337 23.209 -0.573 -1.676 -0.151 C05 JPP 24
JPP C06 C06 C 0 1 N N N N N N 0.826 8.839 22.850 -3.263 -0.109 -0.762 C06 JPP 25
JPP C07 C07 C 0 1 Y N N N N N -3.672 9.443 22.337 -0.954 -2.144 1.093 C07 JPP 26
JPP C08 C08 C 0 1 Y N N N N N -2.236 10.316 24.150 0.049 -2.524 -1.048 C08 JPP 27
JPP C09 C09 C 0 1 N N N N N N 3.204 9.513 22.619 -4.608 0.863 1.018 C09 JPP 28
JPP C10 C10 C 0 1 N N N N N N 4.589 8.804 22.927 -5.777 1.844 0.984 C10 JPP 29
JPP C11 C11 C 0 1 N N N N N N 2.377 8.318 24.648 -5.588 -0.197 -0.945 C11 JPP 30
JPP C12 C12 C 0 1 Y N N N N N -4.545 10.502 22.465 -0.707 -3.459 1.442 C12 JPP 31
JPP C13 C13 C 0 1 Y N N N N N -3.185 11.476 24.288 0.296 -3.838 -0.699 C13 JPP 32
JPP C14 C14 C 0 1 N N N N N N 3.655 8.407 25.256 -6.930 0.235 -0.442 C14 JPP 33
JPP C15 C15 C 0 1 N N N N N N 6.123 8.843 24.928 -8.286 1.518 1.125 C15 JPP 34
JPP C16 C16 C 0 1 Y N N N N N -4.294 11.571 23.486 -0.080 -4.305 0.546 C16 JPP 35
JPP C C C 0 1 N N N N N N 6.863 7.579 24.680 -8.540 0.619 2.337 C JPP 36
JPP H1 H1 H 0 1 N N N N N N -8.244 3.518 20.192 8.286 -1.054 2.323 H1 JPP 37
JPP H2 H2 H 0 1 N N N N N N -6.319 3.548 23.058 4.861 1.474 1.971 H2 JPP 38
JPP H4 H4 H 0 1 N N N N N N -2.945 6.244 21.703 1.766 -0.240 -0.854 H4 JPP 39
JPP H5 H5 H 0 1 N N N N N N -0.071 7.926 24.554 -2.241 0.609 0.820 H5 JPP 40
JPP H6 H6 H 0 1 N N N N N N -4.667 3.834 24.494 3.793 -0.365 0.892 H6 JPP 41
JPP H7 H7 H 0 1 N N N N N N -5.388 5.781 21.465 6.973 1.789 0.587 H7 JPP 42
JPP H8 H8 H 0 1 N N N N N N -2.569 4.357 23.947 2.251 1.581 1.377 H8 JPP 43
JPP H9 H9 H 0 1 N N N N N N -3.165 2.712 22.078 3.377 3.345 -0.173 H9 JPP 44
JPP H10 H10 H 0 1 N N N N N N -8.442 6.137 24.433 6.726 -1.584 -1.747 H10 JPP 45
JPP H11 H11 H 0 1 N N N N N N -8.782 5.422 22.821 7.838 -1.131 -0.433 H11 JPP 46
JPP H12 H12 H 0 1 N N N N N N -7.841 4.492 24.037 6.192 -1.693 -0.053 H12 JPP 47
JPP H13 H13 H 0 1 N N N N N N -7.404 8.126 23.459 7.111 0.695 -2.784 H13 JPP 48
JPP H14 H14 H 0 1 N N N N N N -6.039 7.972 22.302 6.764 2.160 -1.834 H14 JPP 49
JPP H15 H15 H 0 1 N N N N N N -7.704 7.534 21.790 8.178 1.156 -1.436 H15 JPP 50
JPP H16 H16 H 0 1 N N N N N N -1.420 8.041 21.924 -0.817 -0.144 -1.616 H16 JPP 51
JPP H17 H17 H 0 1 N N N N N N -3.862 8.682 21.595 -1.443 -1.483 1.792 H17 JPP 52
JPP H18 H18 H 0 1 N N N N N N -1.368 10.251 24.790 0.343 -2.159 -2.021 H18 JPP 53
JPP H19 H19 H 0 1 N N N N N N 3.265 10.581 22.875 -4.774 0.134 1.811 H19 JPP 54
JPP H20 H20 H 0 1 N N N N N N 2.957 9.406 21.552 -3.686 1.409 1.221 H20 JPP 55
JPP H21 H21 H 0 1 N N N N N N 4.594 7.798 22.483 -5.539 2.663 0.305 H21 JPP 56
JPP H22 H22 H 0 1 N N N N N N 5.410 9.398 22.499 -5.941 2.243 1.985 H22 JPP 57
JPP H23 H23 H 0 1 N N N N N N -5.414 10.562 21.827 -1.004 -3.825 2.413 H23 JPP 58
JPP H24 H24 H 0 1 N N N N N N -2.991 12.241 25.025 0.782 -4.501 -1.400 H24 JPP 59
JPP H25 H25 H 0 1 N N N N N N 6.620 9.671 24.402 -8.273 2.561 1.442 H25 JPP 60
JPP H26 H26 H 0 1 N N N N N N 6.103 9.054 26.007 -9.078 1.371 0.391 H26 JPP 61
JPP H27 H27 H 0 1 N N N N N N -4.975 12.403 23.588 0.113 -5.332 0.819 H27 JPP 62
JPP H28 H28 H 0 1 N N N N N N 7.894 7.678 25.050 -8.552 -0.423 2.020 H28 JPP 63
JPP H29 H29 H 0 1 N N N N N N 6.363 6.752 25.206 -7.748 0.767 3.071 H29 JPP 64
JPP H30 H30 H 0 1 N N N N N N 6.880 7.370 23.600 -9.501 0.875 2.783 H30 JPP 65
#
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
JPP O03 C04 DOUB N N 1
JPP O01 C01 DOUB N N 2
JPP O02 C04 SING N N 3
JPP C04 C18 SING N N 4
JPP O04 C06 DOUB N N 5
JPP C01 C20 SING N N 6
JPP C18 N02 SING N N 7
JPP C18 C19 SING N N 8
JPP C07 C12 DOUB Y N 9
JPP C07 C05 SING Y N 10
JPP C12 C16 SING Y N 11
JPP C09 C10 SING N N 12
JPP C09 N01 SING N N 13
JPP C03 C19 SING N N 14
JPP N02 C17 SING N N 15
JPP N03 C20 SING N N 16
JPP N03 C21 SING N N 17
JPP C06 N01 SING N N 18
JPP C06 N04 SING N N 19
JPP C10 N SING N N 20
JPP CA C05 SING N N 21
JPP CA C21 SING N N 22
JPP CA N04 SING N N 23
JPP C19 C02 SING N N 24
JPP C19 S SING N N 25
JPP C20 C17 SING N N 26
JPP C05 C08 DOUB Y N 27
JPP N01 C11 SING N N 28
JPP C16 C13 DOUB Y N 29
JPP C21 O06 DOUB N N 30
JPP C17 S SING N N 31
JPP C08 C13 SING Y N 32
JPP N C15 SING N N 33
JPP N C14 SING N N 34
JPP C11 O05 DOUB N N 35
JPP C11 C14 SING N N 36
JPP C C15 SING N N 37
JPP C14 O DOUB N N 38
JPP O02 H1 SING N N 39
JPP N02 H2 SING N N 40
JPP N03 H4 SING N N 41
JPP N04 H5 SING N N 42
JPP C17 H6 SING N N 43
JPP C18 H7 SING N N 44
JPP C20 H8 SING N N 45
JPP C01 H9 SING N N 46
JPP C02 H10 SING N N 47
JPP C02 H11 SING N N 48
JPP C02 H12 SING N N 49
JPP C03 H13 SING N N 50
JPP C03 H14 SING N N 51
JPP C03 H15 SING N N 52
JPP CA H16 SING N N 53
JPP C07 H17 SING N N 54
JPP C08 H18 SING N N 55
JPP C09 H19 SING N N 56
JPP C09 H20 SING N N 57
JPP C10 H21 SING N N 58
JPP C10 H22 SING N N 59
JPP C12 H23 SING N N 60
JPP C13 H24 SING N N 61
JPP C15 H25 SING N N 62
JPP C15 H26 SING N N 63
JPP C16 H27 SING N N 64
JPP C H28 SING N N 65
JPP C H29 SING N N 66
JPP C H30 SING N N 67
#
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
JPP SMILES ACDLabs 12.01 "O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3"
JPP InChI InChI 1.03 "InChI=1S/C23H29N5O7S/c1-4-27-10-11-28(20(32)19(27)31)22(35)25-15(13-8-6-5-7-9-13)17(30)24-14(12-29)18-26-16(21(33)34)23(2,3)36-18/h5-9,12,14-16,18,26H,4,10-11H2,1-3H3,(H,24,30)(H,25,35)(H,33,34)/t14-,15-,16+,18-/m1/s1"
JPP InChIKey InChI 1.03 CJYMHKMECTVNSA-XLMAVXFVSA-N
JPP SMILES_CANONICAL CACTVS 3.385 "CCN1CCN(C(=O)N[C@@H](C(=O)N[C@H](C=O)[C@@H]2N[C@@H](C(O)=O)C(C)(C)S2)c3ccccc3)C(=O)C1=O"
JPP SMILES CACTVS 3.385 "CCN1CCN(C(=O)N[CH](C(=O)N[CH](C=O)[CH]2N[CH](C(O)=O)C(C)(C)S2)c3ccccc3)C(=O)C1=O"
JPP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O"
JPP SMILES "OpenEye OEToolkits" 1.7.6 "CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C=O)C3NC(C(S3)(C)C)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
JPP "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,4S)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"
JPP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R,4S)-2-[(1R)-1-[[(2R)-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-phenyl-ethanoyl]amino]-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
JPP "Create component" 2013-07-18 RCSB
JPP "Initial release" 2013-11-06 RCSB
JPP "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id JPP
_pdbx_chem_comp_pcm.modified_residue_id SER
_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 C01
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#