data_G3P
#
_chem_comp.id G3P
_chem_comp.name SN-GLYCEROL-3-PHOSPHATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C3 H9 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 172.074
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G3P
_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 2TSY
_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
G3P O1 O1 O 0 1 N Y N N N N 23.851 41.167 10.051 4.379 0.302 -0.314 O1 G3P 1
G3P C1 C1 C 0 1 N N N N N N 24.040 42.479 9.583 3.156 0.705 0.305 C1 G3P 2
G3P C2 C2 C 0 1 N N R N N N 23.888 43.437 10.733 1.997 -0.105 -0.279 C2 G3P 3
G3P O2 O2 O 0 1 N Y N N N N 25.185 43.823 11.072 2.159 -1.483 0.064 O2 G3P 4
G3P C3 C3 C 0 1 N N N N N N 23.164 44.727 10.244 0.675 0.410 0.291 C3 G3P 5
G3P O1P O1P O 0 1 N N N N N N 23.315 45.812 11.199 -0.413 -0.267 -0.341 O1P G3P 6
G3P O4P O4P O 0 1 N N N N N N 22.855 48.218 12.132 -2.898 -1.003 -0.786 O4P G3P 7
G3P O2P O2P O 0 1 N N N N N N 22.816 47.876 9.719 -2.166 -0.144 1.472 O2P G3P 8
G3P O3P O3P O 0 1 N N N N N N 20.943 46.985 11.184 -2.326 1.535 -0.406 O3P G3P 9
G3P P P P 0 1 N N N N N N 22.447 47.228 11.041 -1.955 0.027 0.016 P G3P 10
G3P HO1 HO1 H 0 1 N N N N N N 23.946 40.556 9.330 5.158 0.776 0.009 HO1 G3P 11
G3P H11 H11 H 0 1 N N N N N N 25.048 42.576 9.154 3.217 0.529 1.379 H11 G3P 12
G3P H12 H12 H 0 1 N N N N N N 23.290 42.707 8.812 2.987 1.766 0.120 H12 G3P 13
G3P H2 H2 H 0 1 N N N N N N 23.340 42.978 11.569 1.991 0.000 -1.364 H2 G3P 14
G3P HO2 HO2 H 0 1 N N N N N N 25.154 44.434 11.799 2.174 -1.652 1.016 HO2 G3P 15
G3P H31 H31 H 0 1 N N N N N N 23.594 45.036 9.280 0.645 0.224 1.365 H31 G3P 16
G3P H32 H32 H 0 1 N N N N N N 22.093 44.510 10.115 0.593 1.482 0.106 H32 G3P 17
G3P HOP3 HOP3 H 0 0 N N N N N N 20.497 47.290 10.403 -2.212 1.719 -1.349 HOP3 G3P 18
G3P HOP4 HOP4 H 0 0 N N N N N N 23.236 48.991 11.732 -3.842 -0.884 -0.619 HOP4 G3P 19
#
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
G3P O1 C1 SING N N 1
G3P C1 C2 SING N N 2
G3P C2 O2 SING N N 3
G3P C2 C3 SING N N 4
G3P C3 O1P SING N N 5
G3P O1P P SING N N 6
G3P O4P P SING N N 7
G3P O2P P DOUB N N 8
G3P O3P P SING N N 9
G3P O1 HO1 SING N N 10
G3P C1 H11 SING N N 11
G3P C1 H12 SING N N 12
G3P C2 H2 SING N N 13
G3P O2 HO2 SING N N 14
G3P C3 H31 SING N N 15
G3P C3 H32 SING N N 16
G3P O3P HOP3 SING N N 17
G3P O4P HOP4 SING N N 18
#
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
G3P SMILES ACDLabs 12.01 'O=P(OCC(O)CO)(O)O'
G3P InChI InChI 1.03 'InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m1/s1'
G3P InChIKey InChI 1.03 AWUCVROLDVIAJX-GSVOUGTGSA-N
G3P SMILES_CANONICAL CACTVS 3.385 'OC[C@@H](O)CO[P](O)(O)=O'
G3P SMILES CACTVS 3.385 'OC[CH](O)CO[P](O)(O)=O'
G3P SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'C([C@H](COP(=O)(O)O)O)O'
G3P SMILES 'OpenEye OEToolkits' 1.7.6 'C(C(COP(=O)(O)O)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
G3P 'SYSTEMATIC NAME' ACDLabs 12.01 '(2R)-2,3-dihydroxypropyl dihydrogen phosphate'
G3P 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '[(2R)-2,3-bis(oxidanyl)propyl] dihydrogen phosphate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
G3P 'Create component' 1999-07-08 RCSB
G3P 'Modify leaving atom flag' 2011-01-19 RCSB
G3P 'Modify descriptor' 2011-06-04 RCSB
G3P 'Modify leaving atom flag' 2016-02-24 RCSB
G3P 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 G3P CYS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C1 SG ? ?
2 G3P GLU None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C1 OE2 ? ?
3 G3P LYS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C2 NZ ? ?
4 G3P SER None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' O4P CB ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id G3P
_pdbe_chem_comp_drugbank_details.drugbank_id DB02515
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'sn-glycerol 3-phosphate'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 17989-41-2
_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
G3P '(R)-glycerol 1-phosphate' DrugBank ?
G3P 'D-(glycerol 1-phosphate)' DrugBank ?
G3P 'D-Glycerol 1-phosphate' DrugBank ?
G3P Glycerol-3-phosphate DrugBank ?
G3P 'Glycerophosphoric acid' DrugBank ?
G3P 'L-(glycerol 3-phosphate)' DrugBank ?
G3P 'Phosphoric acid mono-((R)-2,3-dihydroxy-propyl) ester' DrugBank ?
G3P 'sn-Glycerol 3-phosphate' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id G3P
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02515
_pdbe_chem_comp_drugbank_classification.parent Glycerophosphates
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Glycerophospholipids
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as glycerophosphates. These are compounds containing a glycerol linked to a phosphate 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
G3P DB02515 'Fructose-bisphosphate aldolase B' Humans P05062 unknown 1
G3P DB02515 "Pyridoxine 5'-phosphate synthase" 'Escherichia coli (strain K12)' P0A794 unknown 2
G3P DB02515 'Triosephosphate isomerase' 'Plasmodium falciparum' Q07412 unknown 3
G3P DB02515 '6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1' Humans P16118 unknown 4
#
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
G3P O1 O 11.600 0.042 1
G3P C1 C 10.301 -0.708 2
G3P C2 C 9.002 0.042 3
G3P O2 O 9.002 1.542 4
G3P C3 C 7.702 -0.708 5
G3P O1P O 6.404 0.042 6
G3P O4P O 3.805 -1.458 7
G3P O2P O 4.354 0.591 8
G3P O3P O 5.854 -2.007 9
G3P P P 5.104 -0.708 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
G3P O1 C1 SINGLE NONE 1
G3P C1 C2 SINGLE NONE 2
G3P C2 O2 SINGLE BEGINDASH 3
G3P C2 C3 SINGLE NONE 4
G3P C3 O1P SINGLE NONE 5
G3P O1P P SINGLE NONE 6
G3P O4P P SINGLE NONE 7
G3P O2P P DOUBLE NONE 8
G3P O3P P SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id G3P
_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
G3P O1P F1 1
G3P P F1 1
G3P O2P F1 1
G3P O4P F1 1
G3P O3P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G3P
_pdbe_chem_comp_rdkit_properties.exactmw 172.014
_pdbe_chem_comp_rdkit_properties.amw 172.073
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 70.301
_pdbe_chem_comp_rdkit_properties.tpsa 107.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.551
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.089
_pdbe_chem_comp_rdkit_properties.chi0v 5.291
_pdbe_chem_comp_rdkit_properties.chi1v 3.303
_pdbe_chem_comp_rdkit_properties.chi2v 0.658
_pdbe_chem_comp_rdkit_properties.chi3v 0.658
_pdbe_chem_comp_rdkit_properties.chi4v 0.313
_pdbe_chem_comp_rdkit_properties.chi0n 13.397
_pdbe_chem_comp_rdkit_properties.chi1n 5.976
_pdbe_chem_comp_rdkit_properties.chi2n 0.343
_pdbe_chem_comp_rdkit_properties.chi3n 0.343
_pdbe_chem_comp_rdkit_properties.chi4n 0.118
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.516
_pdbe_chem_comp_rdkit_properties.kappa2 4.023
_pdbe_chem_comp_rdkit_properties.kappa3 6.155
_pdbe_chem_comp_rdkit_properties.Phi 1.012
#
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
G3P UniChem DrugBank DB02515
G3P UniChem 'KEGG LIGAND' C00093
G3P UniChem ChEBI 15978
G3P UniChem ZINC ZINC000003830896
G3P UniChem fdasrs 370V52HE4B
G3P UniChem SureChEMBL SCHEMBL213379
G3P UniChem HMDB HMDB0000126
G3P UniChem 'PubChem TPHARMA' 16154514
G3P UniChem NMRShiftDB 60020021
G3P UniChem 'EPA CompTox Dashboard' DTXSID5048346
G3P UniChem MetaboLights MTBLC15978
G3P UniChem BRENDA 100784
G3P UniChem BRENDA 102080
G3P UniChem BRENDA 195020
G3P UniChem BRENDA 198542
G3P UniChem BRENDA 20212
G3P UniChem BRENDA 217351
G3P UniChem BRENDA 228531
G3P UniChem BRENDA 249020
G3P UniChem BRENDA 5652
G3P UniChem BRENDA 7332
G3P UniChem BRENDA 9436
G3P UniChem MedChemExpress HY-113128
G3P UniChem 'Probes And Drugs' PD007905
G3P UniChem Nikkaji J4.456C
G3P UniChem PubChem 439162
G3P UniChem ACTor 17989-41-2
#
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
G3P O1 -3.483 -0.094 0.576 ETKDGv3 1
G3P C1 -2.102 -0.298 0.706 ETKDGv3 2
G3P C2 -1.396 -0.071 -0.643 ETKDGv3 3
G3P O2 -1.652 1.220 -1.138 ETKDGv3 4
G3P C3 0.116 -0.330 -0.551 ETKDGv3 5
G3P O1P 0.705 0.553 0.376 ETKDGv3 6
G3P O4P 3.084 1.226 1.612 ETKDGv3 7
G3P O2P 3.009 0.552 -0.912 ETKDGv3 8
G3P O3P 2.661 -1.381 0.825 ETKDGv3 9
G3P P 2.381 0.242 0.429 ETKDGv3 10
G3P HO1 -3.846 -0.895 0.116 ETKDGv3 11
G3P H11 -1.711 0.414 1.465 ETKDGv3 12
G3P H12 -1.901 -1.329 1.076 ETKDGv3 13
G3P H2 -1.813 -0.800 -1.372 ETKDGv3 14
G3P HO2 -1.333 1.873 -0.462 ETKDGv3 15
G3P H31 0.270 -1.389 -0.242 ETKDGv3 16
G3P H32 0.550 -0.183 -1.567 ETKDGv3 17
G3P HOP3 3.646 -1.456 0.900 ETKDGv3 18
G3P HOP4 2.813 2.146 1.368 ETKDGv3 19
#