data_2PG
#
_chem_comp.id 2PG
_chem_comp.name "2-PHOSPHOGLYCERIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C3 H7 O7 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 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces PAG
_chem_comp.formula_weight 186.057
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2PG
_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 5ENL
_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.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
2PG C1 C1 C 0 1 N N N N N N 96.197 46.232 26.716 -0.731 0.054 -1.975 C1 2PG 1
2PG C2 C2 C 0 1 N N R N N N 95.276 46.832 25.656 0.297 -0.090 -0.883 C2 2PG 2
2PG C3 C3 C 0 1 N N N N N N 95.103 48.315 26.007 1.685 0.219 -1.447 C3 2PG 3
2PG P P P 0 1 N N N N N N 95.045 45.689 23.274 -0.238 -0.064 1.498 P 2PG 4
2PG O1 O1 O 0 1 N N N N N N 95.747 45.099 27.141 -1.627 0.855 -1.858 O1 2PG 5
2PG O2 O2 O 0 1 N N N N N N 97.263 46.851 27.075 -0.651 -0.707 -3.077 O2 2PG 6
2PG O3 O3 O 0 1 N N N N N N 96.030 48.888 26.907 2.661 0.082 -0.411 O3 2PG 7
2PG O1P O1P O 0 1 N N N N N N 95.833 46.582 24.333 -0.000 0.821 0.175 O1P 2PG 8
2PG O2P O2P O 0 1 N N N N N N 95.443 44.281 23.569 0.987 -0.837 1.800 O2P 2PG 9
2PG O3P O3P O 0 1 N N N N N N 93.578 45.907 23.532 -0.580 0.904 2.738 O3P 2PG 10
2PG O4P O4P O 0 1 N N N N N N 95.427 46.067 21.912 -1.465 -1.076 1.254 O4P 2PG 11
2PG H2 H2 H 0 1 N N N N N N 94.263 46.365 25.638 0.279 -1.110 -0.500 H2 2PG 12
2PG H31 1H3 H 0 1 N N N N N N 95.083 48.915 25.067 1.703 1.239 -1.830 H31 2PG 13
2PG H32 2H3 H 0 1 N N N N N N 94.068 48.484 26.386 1.913 -0.476 -2.255 H32 2PG 14
2PG HO2 HO2 H 0 1 N N N N N N 97.836 46.477 27.734 -1.311 -0.614 -3.778 HO2 2PG 15
2PG H3 H3 H 0 1 N N N N N N 95.922 49.806 27.124 3.519 0.285 -0.808 H3 2PG 16
2PG HOP3 3HOP H 0 0 N N N N N N 93.108 45.374 22.900 -0.714 0.335 3.508 HOP3 2PG 17
2PG HOP4 4HOP H 0 0 N N N N N N 94.957 45.534 21.280 -2.241 -0.533 1.060 HOP4 2PG 18
#
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
2PG C1 C2 SING N N 1
2PG C1 O1 DOUB N N 2
2PG C1 O2 SING N N 3
2PG C2 C3 SING N N 4
2PG C2 O1P SING N N 5
2PG C2 H2 SING N N 6
2PG C3 O3 SING N N 7
2PG C3 H31 SING N N 8
2PG C3 H32 SING N N 9
2PG P O1P SING N N 10
2PG P O2P DOUB N N 11
2PG P O3P SING N N 12
2PG P O4P SING N N 13
2PG O2 HO2 SING N N 14
2PG O3 H3 SING N N 15
2PG O3P HOP3 SING N N 16
2PG O4P HOP4 SING N N 17
#
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
2PG SMILES ACDLabs 10.04 O=P(O)(O)OC(C(=O)O)CO
2PG SMILES_CANONICAL CACTVS 3.341 OC[C@@H](O[P](O)(O)=O)C(O)=O
2PG SMILES CACTVS 3.341 OC[CH](O[P](O)(O)=O)C(O)=O
2PG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H](C(=O)O)OP(=O)(O)O)O
2PG SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)OP(=O)(O)O)O
2PG InChI InChI 1.03 InChI=1S/C3H7O7P/c4-1-2(3(5)6)10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
2PG InChIKey InChI 1.03 GXIURPTVHJPJLF-UWTATZPHSA-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
2PG "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-3-hydroxy-2-(phosphonooxy)propanoic acid"
2PG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-3-hydroxy-2-phosphonooxy-propanoic 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
2PG 'Create component' 1999-07-08 RCSB
2PG 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id 2PG
_pdbe_chem_comp_drugbank_details.drugbank_id DB01709
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '2-phospho-D-glyceric acid'
_pdbe_chem_comp_drugbank_details.description
'A 2-phosphoglyceric acid in which the glyceric acid moiety has D (R) configuration.'
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
2PG 2-phospho-D-glycerate DrugBank ?
2PG 'D-glycerate 2-phosphate' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 2PG
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01709
_pdbe_chem_comp_drugbank_classification.parent 'Sugar acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid 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
2PG DB01709 '2-dehydro-3-deoxyphosphooctonate aldolase' 'Aquifex aeolicus (strain VF5)' O66496 unknown 1
2PG DB01709 '2,3-bisphosphoglycerate-independent phosphoglycerate mutase' 'Geobacillus stearothermophilus' Q9X519 unknown 2
2PG DB01709 'Triosephosphate isomerase' 'Plasmodium falciparum' Q07412 unknown 3
2PG DB01709 Beta-enolase Humans P13929 unknown 4
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
2PG C1 C 5.104 1.215 1
2PG C2 C 6.404 0.465 2
2PG C3 C 6.404 -1.035 3
2PG P P 9.002 0.465 4
2PG O1 O 3.805 0.465 5
2PG O2 O 5.104 2.715 6
2PG O3 O 5.104 -1.785 7
2PG O1P O 7.702 1.215 8
2PG O2P O 10.301 -0.285 9
2PG O3P O 9.752 1.764 10
2PG O4P O 8.252 -0.834 11
#
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
2PG C1 C2 SINGLE NONE 1
2PG C1 O1 DOUBLE NONE 2
2PG C1 O2 SINGLE NONE 3
2PG C2 C3 SINGLE BEGINDASH 4
2PG C2 O1P SINGLE NONE 5
2PG C3 O3 SINGLE NONE 6
2PG P O1P SINGLE NONE 7
2PG P O2P DOUBLE NONE 8
2PG P O3P SINGLE NONE 9
2PG P O4P SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id 2PG
_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
2PG O1P F1 1
2PG P F1 1
2PG O2P F1 1
2PG O3P F1 1
2PG O4P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2PG
_pdbe_chem_comp_rdkit_properties.exactmw 185.993
_pdbe_chem_comp_rdkit_properties.amw 186.056
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 71.652
_pdbe_chem_comp_rdkit_properties.tpsa 124.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.459
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.639
_pdbe_chem_comp_rdkit_properties.chi0v 5.699
_pdbe_chem_comp_rdkit_properties.chi1v 3.507
_pdbe_chem_comp_rdkit_properties.chi2v 0.887
_pdbe_chem_comp_rdkit_properties.chi3v 0.887
_pdbe_chem_comp_rdkit_properties.chi4v 0.545
_pdbe_chem_comp_rdkit_properties.chi0n 11.805
_pdbe_chem_comp_rdkit_properties.chi1n 5.180
_pdbe_chem_comp_rdkit_properties.chi2n 0.481
_pdbe_chem_comp_rdkit_properties.chi3n 0.481
_pdbe_chem_comp_rdkit_properties.chi4n 0.209
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.460
_pdbe_chem_comp_rdkit_properties.kappa1 3.506
_pdbe_chem_comp_rdkit_properties.kappa2 3.795
_pdbe_chem_comp_rdkit_properties.kappa3 4.882
_pdbe_chem_comp_rdkit_properties.Phi 1.210
#
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
2PG UniChem DrugBank DB01709
2PG UniChem PDBe 2PG
2PG UniChem 'KEGG LIGAND' C00631
2PG UniChem ChEBI 17835
2PG UniChem ZINC ZINC000003869232
2PG UniChem SureChEMBL SCHEMBL2726719
2PG UniChem HMDB HMDB0003391
2PG UniChem PubChem 439278
2PG UniChem NMRShiftDB 60020595
2PG UniChem MetaboLights MTBLC17835
2PG UniChem BRENDA 10090
2PG UniChem BRENDA 1023
2PG UniChem BRENDA 43990
2PG UniChem BRENDA 68873
2PG UniChem BRENDA 93009
2PG UniChem BRENDA 93049
2PG UniChem 'Probes And Drugs' PD007510
#
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
2PG C1 -1.318 0.719 0.011 ETKDGv3 1
2PG C2 -0.303 -0.390 0.039 ETKDGv3 2
2PG C3 -1.014 -1.745 -0.012 ETKDGv3 3
2PG P 1.889 0.705 -0.712 ETKDGv3 4
2PG O1 -1.895 1.026 -1.066 ETKDGv3 5
2PG O2 -1.643 1.388 1.187 ETKDGv3 6
2PG O3 -1.824 -1.910 1.120 ETKDGv3 7
2PG O1P 0.552 -0.292 -1.084 ETKDGv3 8
2PG O2P 2.646 0.999 -1.987 ETKDGv3 9
2PG O3P 2.921 -0.101 0.364 ETKDGv3 10
2PG O4P 1.370 2.165 -0.029 ETKDGv3 11
2PG H2 0.252 -0.361 1.006 ETKDGv3 12
2PG H31 -0.248 -2.553 -0.039 ETKDGv3 13
2PG H32 -1.632 -1.816 -0.936 ETKDGv3 14
2PG HO2 -2.331 2.132 1.189 ETKDGv3 15
2PG H3 -2.254 -2.799 1.023 ETKDGv3 16
2PG HOP3 2.628 0.186 1.265 ETKDGv3 17
2PG HOP4 2.204 2.648 0.201 ETKDGv3 18
#