data_PNM
#
_chem_comp.id PNM
_chem_comp.name "OPEN FORM - PENICILLIN G"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H20 N2 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-10-23
_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 336.406
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PNM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1GHP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
PNM O8 O8 O 0 1 N N N N N N 4.891 -10.980 -11.986 -3.127 0.310 -0.385 O8 PNM 1
PNM C7 C7 C 0 1 N N N N N N 3.748 -10.586 -12.111 -2.652 -0.617 0.224 C7 PNM 2
PNM N4 N4 N 0 1 N N N N N N 4.566 -7.897 -11.806 -0.735 0.615 2.210 N4 PNM 3
PNM C3 C3 C 0 1 N N S N N N 4.799 -6.773 -10.861 0.189 0.839 3.325 C3 PNM 4
PNM C11 C11 C 0 1 N N N N N N 6.130 -6.060 -11.134 -0.494 0.438 4.606 C11 PNM 5
PNM O13 O13 O 0 1 N N N N N N 6.847 -5.846 -10.132 -0.158 1.033 5.761 O13 PNM 6
PNM O12 O12 O 0 1 N N N N N N 6.519 -5.845 -12.273 -1.346 -0.418 4.593 O12 PNM 7
PNM C2 C2 C 0 1 N N N N N N 3.563 -5.858 -10.862 1.511 0.048 3.207 C2 PNM 8
PNM C10 C10 C 0 1 N N N N N N 3.566 -4.896 -9.680 1.736 -0.828 4.441 C10 PNM 9
PNM C9 C9 C 0 1 N N N N N N 3.442 -5.073 -12.175 2.696 0.990 2.985 C9 PNM 10
PNM S1 S1 S 0 1 N N N N N N 2.183 -7.039 -10.732 1.200 -0.985 1.712 S1 PNM 11
PNM C5 C5 C 0 1 N N R N N N 3.165 -8.312 -11.626 -0.634 -0.767 1.657 C5 PNM 12
PNM C6 C6 C 0 1 N N R N N N 3.130 -9.712 -11.045 -1.161 -0.835 0.222 C6 PNM 13
PNM N14 N14 N 0 1 N N N N N N 3.797 -9.799 -9.749 -0.516 0.204 -0.584 N14 PNM 14
PNM C15 C15 C 0 1 N N N N N N 3.120 -9.679 -8.599 -0.319 0.008 -1.903 C15 PNM 15
PNM O16 O16 O 0 1 N N N N N N 1.884 -9.599 -8.573 -0.676 -1.028 -2.422 O16 PNM 16
PNM C17 C17 C 0 1 N N N N N N 3.930 -9.701 -7.248 0.342 1.077 -2.732 C17 PNM 17
PNM C18 C18 C 0 1 Y N N N N N 4.652 -8.394 -6.959 0.442 0.614 -4.163 C18 PNM 18
PNM C19 C19 C 0 1 Y N N N N N 3.942 -7.215 -6.738 -0.581 0.885 -5.050 C19 PNM 19
PNM C20 C20 C 0 1 Y N N N N N 4.617 -5.984 -6.571 -0.490 0.459 -6.362 C20 PNM 20
PNM C21 C21 C 0 1 Y N N N N N 6.022 -5.948 -6.620 0.626 -0.236 -6.787 C21 PNM 21
PNM C22 C22 C 0 1 Y N N N N N 6.727 -7.120 -6.823 1.650 -0.506 -5.900 C22 PNM 22
PNM C23 C23 C 0 1 Y N N N N N 6.052 -8.329 -6.992 1.561 -0.077 -4.589 C23 PNM 23
PNM HC7 HC7 H 0 1 N N N N N N 3.330 -10.967 -13.058 -3.295 -1.291 0.770 HC7 PNM 24
PNM H4 H4 H 0 1 N N N N N N 5.231 -8.662 -11.694 -1.667 0.710 2.584 H4 PNM 25
PNM HC3 HC3 H 0 1 N N N N N N 4.917 -7.160 -9.822 0.423 1.903 3.374 HC3 PNM 26
PNM HXT HXT H 0 1 N N N N N N 7.671 -5.404 -10.301 -0.597 0.776 6.583 HXT PNM 27
PNM H101 1H10 H 0 0 N N N N N N 2.669 -4.232 -9.680 2.645 -1.415 4.309 H101 PNM 28
PNM H102 2H10 H 0 0 N N N N N N 3.664 -5.442 -8.713 1.838 -0.195 5.323 H102 PNM 29
PNM H103 3H10 H 0 0 N N N N N N 4.509 -4.302 -9.643 0.886 -1.497 4.571 H103 PNM 30
PNM HC91 1HC9 H 0 0 N N N N N N 2.545 -4.409 -12.175 3.605 0.404 2.851 HC91 PNM 31
PNM HC92 2HC9 H 0 0 N N N N N N 4.373 -4.499 -12.394 2.518 1.593 2.095 HC92 PNM 32
PNM HC93 3HC9 H 0 0 N N N N N N 3.445 -5.753 -13.058 2.808 1.643 3.850 HC93 PNM 33
PNM HC5 HC5 H 0 1 N N N N N N 2.645 -8.378 -12.610 -1.140 -1.490 2.297 HC5 PNM 34
PNM HC6 HC6 H 0 1 N N N N N N 2.092 -10.045 -10.810 -0.937 -1.814 -0.201 HC6 PNM 35
PNM H14 H14 H 0 1 N N N N N N 4.799 -9.953 -9.640 -0.231 1.033 -0.169 H14 PNM 36
PNM H171 1H17 H 0 0 N N N N N N 3.270 -9.986 -6.395 -0.249 1.991 -2.687 H171 PNM 37
PNM H172 2H17 H 0 0 N N N N N N 4.641 -10.559 -7.226 1.342 1.272 -2.343 H172 PNM 38
PNM H19 H19 H 0 1 N N N N N N 2.840 -7.256 -6.695 -1.453 1.429 -4.719 H19 PNM 39
PNM H20 H20 H 0 1 N N N N N N 4.048 -5.053 -6.402 -1.290 0.670 -7.056 H20 PNM 40
PNM H21 H21 H 0 1 N N N N N N 6.571 -4.999 -6.499 0.697 -0.569 -7.812 H21 PNM 41
PNM H22 H22 H 0 1 N N N N N N 7.829 -7.090 -6.850 2.522 -1.051 -6.231 H22 PNM 42
PNM H23 H23 H 0 1 N N N N N N 6.636 -9.250 -7.154 2.362 -0.288 -3.895 H23 PNM 43
#
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
PNM O8 C7 DOUB N N 1
PNM C7 C6 SING N N 2
PNM C7 HC7 SING N N 3
PNM N4 C3 SING N N 4
PNM N4 C5 SING N N 5
PNM N4 H4 SING N N 6
PNM C3 C11 SING N N 7
PNM C3 C2 SING N N 8
PNM C3 HC3 SING N N 9
PNM C11 O13 SING N N 10
PNM C11 O12 DOUB N N 11
PNM O13 HXT SING N N 12
PNM C2 C10 SING N N 13
PNM C2 C9 SING N N 14
PNM C2 S1 SING N N 15
PNM C10 H101 SING N N 16
PNM C10 H102 SING N N 17
PNM C10 H103 SING N N 18
PNM C9 HC91 SING N N 19
PNM C9 HC92 SING N N 20
PNM C9 HC93 SING N N 21
PNM S1 C5 SING N N 22
PNM C5 C6 SING N N 23
PNM C5 HC5 SING N N 24
PNM C6 N14 SING N N 25
PNM C6 HC6 SING N N 26
PNM N14 C15 SING N N 27
PNM N14 H14 SING N N 28
PNM C15 O16 DOUB N N 29
PNM C15 C17 SING N N 30
PNM C17 C18 SING N N 31
PNM C17 H171 SING N N 32
PNM C17 H172 SING N N 33
PNM C18 C19 DOUB Y N 34
PNM C18 C23 SING Y N 35
PNM C19 C20 SING Y N 36
PNM C19 H19 SING N N 37
PNM C20 C21 DOUB Y N 38
PNM C20 H20 SING N N 39
PNM C21 C22 SING Y N 40
PNM C21 H21 SING N N 41
PNM C22 C23 DOUB Y N 42
PNM C22 H22 SING N N 43
PNM C23 H23 SING N N 44
#
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
PNM SMILES ACDLabs 10.04 "O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2"
PNM SMILES_CANONICAL CACTVS 3.341 "CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C=O"
PNM SMILES CACTVS 3.341 "CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C=O"
PNM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2)C(=O)O)C"
PNM SMILES "OpenEye OEToolkits" 1.5.0 "CC1(C(NC(S1)C(C=O)NC(=O)Cc2ccccc2)C(=O)O)C"
PNM InChI InChI 1.03 "InChI=1S/C16H20N2O4S/c1-16(2)13(15(21)22)18-14(23-16)11(9-19)17-12(20)8-10-6-4-3-5-7-10/h3-7,9,11,13-14,18H,8H2,1-2H3,(H,17,20)(H,21,22)/t11-,13+,14-/m1/s1"
PNM InChIKey InChI 1.03 OGFZUTGOGYUTKZ-KWCYVHTRSA-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
PNM "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid"
PNM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-(2-phenylethanoylamino)ethyl]-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
PNM "Create component" 2000-10-23 EBI
PNM "Modify descriptor" 2011-06-04 RCSB
PNM "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PNM
_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 C7
_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 ?
#