data_PEP
#
_chem_comp.id PEP
_chem_comp.name PHOSPHOENOLPYRUVATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C3 H5 O6 P'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 168.042
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PEP
_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 1ONE
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
PEP C1 C1 C 0 1 N N N N N N 47.020 -7.698 24.673 0.334 -0.083 1.960 C1 PEP 1
PEP O1 O1 O 0 1 N N N N N N 47.137 -7.876 25.944 1.524 -0.292 1.834 O1 PEP 2
PEP "O2'" "O2'" O 0 1 N N N N N N 47.971 -7.601 23.936 -0.130 0.515 3.074 "O2'" PEP 3
PEP C2 C2 C 0 1 N N N N N N 45.590 -7.507 24.205 -0.601 -0.484 0.894 C2 PEP 4
PEP C3 C3 C 0 1 N N N N N N 44.434 -7.601 24.906 -1.907 -0.254 1.032 C3 PEP 5
PEP O2 O2 O 0 1 N N N N N N 45.459 -7.359 22.836 -0.131 -1.088 -0.229 O2 PEP 6
PEP P P P 0 1 N N N N N N 45.141 -8.531 21.826 0.110 0.074 -1.316 P PEP 7
PEP O1P O1P O 0 1 N N N N N N 46.445 -9.356 21.756 1.007 1.103 -0.746 O1P PEP 8
PEP O2P O2P O 0 1 N N N N N N 44.787 -7.826 20.552 0.786 -0.555 -2.635 O2P PEP 9
PEP O3P O3P O 0 1 N N N N N N 44.086 -9.381 22.432 -1.299 0.747 -1.705 O3P PEP 10
PEP HO2 HO2 H 0 1 N N N N N N 47.884 -7.469 22.999 0.482 0.779 3.774 HO2 PEP 11
PEP H31 1H3 H 0 1 N N N N N N 44.538 -7.719 25.997 -2.602 -0.622 0.291 H31 PEP 12
PEP H32 2H3 H 0 1 N N N N N N 43.394 -7.462 24.565 -2.271 0.300 1.884 H32 PEP 13
PEP HOP2 2HOP H 0 0 N N N N N N 44.595 -8.530 19.944 0.913 0.172 -3.259 HOP2 PEP 14
PEP HOP3 3HOP H 0 0 N N N N N N 43.894 -10.085 21.824 -1.853 0.044 -2.072 HOP3 PEP 15
#
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
PEP C1 O1 DOUB N N 1
PEP C1 "O2'" SING N N 2
PEP C1 C2 SING N N 3
PEP "O2'" HO2 SING N N 4
PEP C2 C3 DOUB N N 5
PEP C2 O2 SING N N 6
PEP C3 H31 SING N N 7
PEP C3 H32 SING N N 8
PEP O2 P SING N N 9
PEP P O1P DOUB N N 10
PEP P O2P SING N N 11
PEP P O3P SING N N 12
PEP O2P HOP2 SING N N 13
PEP O3P HOP3 SING N N 14
#
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
PEP SMILES ACDLabs 10.04 'O=C(O)C(\OP(=O)(O)O)=C'
PEP SMILES_CANONICAL CACTVS 3.341 'OC(=O)C(=C)O[P](O)(O)=O'
PEP SMILES CACTVS 3.341 'OC(=O)C(=C)O[P](O)(O)=O'
PEP SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C=C(C(=O)O)OP(=O)(O)O'
PEP SMILES 'OpenEye OEToolkits' 1.5.0 'C=C(C(=O)O)OP(=O)(O)O'
PEP InChI InChI 1.03 'InChI=1S/C3H5O6P/c1-2(3(4)5)9-10(6,7)8/h1H2,(H,4,5)(H2,6,7,8)'
PEP InChIKey InChI 1.03 DTBNBXWJWCWCIK-UHFFFAOYSA-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
PEP 'SYSTEMATIC NAME' ACDLabs 10.04 '2-(phosphonooxy)prop-2-enoic acid'
PEP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '2-phosphonooxyprop-2-enoic 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
PEP 'Create component' 1999-07-08 RCSB
PEP 'Modify descriptor' 2011-06-04 RCSB
PEP 'Modify PCM' 2024-09-27 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id PEP
_pdbe_chem_comp_drugbank_details.drugbank_id DB01819
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Phosphoenolpyruvate
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 138-08-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id PEP
_pdbe_chem_comp_synonyms.name Phosphoenolpyruvate
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PEP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01819
_pdbe_chem_comp_drugbank_classification.parent 'Phosphate esters'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organic phosphoric acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as phosphate esters. These are organic compounds containing phosphoric acid ester functional group, with the general structure R1P(=O)(R2)OR3. R1,R2 = O,N,  or halogen atom; R3 = organyl group.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
PEP DB01819 '2-dehydro-3-deoxyphosphooctonate aldolase' 'Shigella flexneri' P0A716 unknown 1
PEP DB01819 Beta-enolase Humans P13929 unknown 2
PEP DB01819 'Phosphoenolpyruvate carboxykinase, cytosolic [GTP]' Humans P35558 unknown 3
PEP DB01819 '2-dehydro-3-deoxyphosphooctonate aldolase' 'Aquifex aeolicus (strain VF5)' O66496 unknown 4
PEP DB01819 'Phospho-2-dehydro-3-deoxyheptonate aldolase' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9WYH8 unknown 5
PEP DB01819 'Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive' 'Escherichia coli (strain K12)' P0AB91 unknown 6
PEP DB01819 'Capsule biosynthesis protein' 'Neisseria meningitidis' Q57265 unknown 7
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
PEP C1 C 9.002 0.465 1
PEP O1 O 10.301 -0.285 2
PEP "O2'" O 9.002 1.965 3
PEP C2 C 7.702 -0.285 4
PEP C3 C 7.702 -1.785 5
PEP O2 O 6.404 0.465 6
PEP P P 5.104 -0.285 7
PEP O1P O 3.805 -1.035 8
PEP O2P O 4.354 1.014 9
PEP O3P O 5.854 -1.584 10
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
PEP C1 O1 DOUBLE NONE 1
PEP C1 "O2'" SINGLE NONE 2
PEP C1 C2 SINGLE NONE 3
PEP C2 C3 DOUBLE NONE 4
PEP C2 O2 SINGLE NONE 5
PEP O2 P SINGLE NONE 6
PEP P O1P DOUBLE NONE 7
PEP P O2P SINGLE NONE 8
PEP P O3P SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id PEP
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PEP O2 F1 1
PEP P F1 1
PEP O1P F1 1
PEP O2P F1 1
PEP O3P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PEP
_pdbe_chem_comp_rdkit_properties.exactmw 167.982
_pdbe_chem_comp_rdkit_properties.amw 168.041
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 63.272
_pdbe_chem_comp_rdkit_properties.tpsa 104.060
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.306
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.905
_pdbe_chem_comp_rdkit_properties.chi0v 5.291
_pdbe_chem_comp_rdkit_properties.chi1v 3.303
_pdbe_chem_comp_rdkit_properties.chi2v 0.795
_pdbe_chem_comp_rdkit_properties.chi3v 0.795
_pdbe_chem_comp_rdkit_properties.chi4v 0.447
_pdbe_chem_comp_rdkit_properties.chi0n 9.397
_pdbe_chem_comp_rdkit_properties.chi1n 4.067
_pdbe_chem_comp_rdkit_properties.chi2n 0.388
_pdbe_chem_comp_rdkit_properties.chi3n 0.388
_pdbe_chem_comp_rdkit_properties.chi4n 0.149
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.840
_pdbe_chem_comp_rdkit_properties.kappa1 3.522
_pdbe_chem_comp_rdkit_properties.kappa2 2.829
_pdbe_chem_comp_rdkit_properties.kappa3 4.080
_pdbe_chem_comp_rdkit_properties.Phi 0.996
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PEP UniChem DrugBank DB01819
PEP UniChem 'Guide to Pharmacology' 4692
PEP UniChem 'KEGG LIGAND' C00074
PEP UniChem ChEBI 44897
PEP UniChem ZINC ZINC000003870145
PEP UniChem fdasrs 545YL308OW
PEP UniChem SureChEMBL SCHEMBL7908
PEP UniChem HMDB HMDB0000263
PEP UniChem PubChem 58114173
PEP UniChem NMRShiftDB 60020995
PEP UniChem 'EPA CompTox Dashboard' DTXSID80861797
PEP UniChem MetaboLights MTBLC44897
PEP UniChem BRENDA 139687
PEP UniChem BRENDA 213707
PEP UniChem BRENDA 3897
PEP UniChem BRENDA 51
PEP UniChem ChemicalBook CB7916207
PEP UniChem 'Probes And Drugs' PD008752
PEP UniChem CCDC VENWUG
PEP UniChem BindingDb 50366413
PEP UniChem 'PubChem TPHARMA' 14772543
PEP UniChem PubChem 1005
PEP UniChem PubChem 59658623
PEP UniChem ACTor 101015-20-7
PEP UniChem ACTor 138-08-9
PEP UniChem Nikkaji J9.706C
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
PEP C1 2.296 0.268 -0.180 ETKDGv3 1
PEP O1 3.287 -0.484 -0.393 ETKDGv3 2
PEP "O2'" 2.496 1.636 -0.023 ETKDGv3 3
PEP C2 0.928 -0.278 -0.096 ETKDGv3 4
PEP C3 0.712 -1.595 -0.245 ETKDGv3 5
PEP O2 -0.112 0.636 0.144 ETKDGv3 6
PEP P -1.782 0.234 0.287 ETKDGv3 7
PEP O1P -1.983 -0.708 1.453 ETKDGv3 8
PEP O2P -2.674 1.648 0.549 ETKDGv3 9
PEP O3P -2.314 -0.503 -1.141 ETKDGv3 10
PEP HO2 3.425 2.035 -0.076 ETKDGv3 11
PEP H31 1.529 -2.280 -0.429 ETKDGv3 12
PEP H32 -0.276 -2.025 -0.188 ETKDGv3 13
PEP HOP2 -2.250 2.070 1.338 ETKDGv3 14
PEP HOP3 -3.283 -0.653 -1.001 ETKDGv3 15
#