data_GSE
#
_chem_comp.id GSE
_chem_comp.name L-ALPHA-GLYCEROPHOSPHORYLSERINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C6 H14 N O8 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 259.151
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GSE
_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 1A8A
_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
GSE C1 C1 C 0 1 N N N N N N 20.084 46.898 17.532 -0.229 -0.322 -2.653 C1 GSE 1
GSE O11 O11 O 0 1 N N N N N N 19.501 47.820 16.574 0.518 0.243 -1.575 O11 GSE 2
GSE O12 O12 O 0 1 N N N N N N 18.232 48.984 14.988 0.573 0.410 1.047 O12 GSE 3
GSE C2 C2 C 0 1 N N R N N N 20.318 47.710 18.809 0.423 0.059 -3.983 C2 GSE 4
GSE C3 C3 C 0 1 N N N N N N 21.617 48.531 18.815 -0.377 -0.546 -5.137 C3 GSE 5
GSE O31 O31 O 0 1 N N N N N N 21.608 49.557 17.822 0.232 -0.189 -6.379 O31 GSE 6
GSE P P P 0 1 N N R N N N 18.876 47.590 15.205 -0.220 -0.196 -0.214 P GSE 7
GSE O14 O14 O 0 1 N N N N N N 19.907 47.328 14.169 -1.730 0.362 -0.218 O14 GSE 8
GSE O13 O13 O 0 1 N N N N N N 17.947 46.481 15.134 -0.241 -1.673 -0.120 O13 GSE 9
GSE O21 O21 O 0 1 N N N N N N 19.214 48.622 18.962 0.441 1.482 -4.112 O21 GSE 10
GSE C11 C11 C 0 1 N N N N N N 18.268 49.967 16.125 -0.127 -0.013 2.218 C11 GSE 11
GSE CA C12 C 0 1 N N S Y N N 18.237 51.477 15.771 0.578 0.533 3.461 C12 GSE 12
GSE N N N 0 1 N N N Y Y N 17.404 51.290 14.648 1.956 0.025 3.504 N GSE 13
GSE C C13 C 0 1 N N N Y N Y 19.549 52.335 15.908 -0.160 0.086 4.696 C13 GSE 14
GSE OXT O16 O 0 1 N N N Y N Y 20.069 53.085 15.062 -1.147 0.844 5.199 O16 GSE 15
GSE O O15 O 0 1 N N N Y N Y 20.124 52.432 16.966 0.135 -0.954 5.233 O15 GSE 16
GSE H11 H11 H 0 1 N N N N N N 19.473 45.979 17.694 -0.243 -1.408 -2.554 H11 GSE 17
GSE H12A H12A H 0 0 N N N N N N 21.000 46.385 17.156 -1.250 0.057 -2.626 H12A GSE 18
GSE H21 H2 H 0 1 N N N N N N 20.403 46.975 19.643 1.444 -0.320 -4.009 H2 GSE 19
GSE H31 H31 H 0 1 N N N N N N 21.825 48.949 19.827 -0.391 -1.632 -5.038 H31 GSE 20
GSE H32 H32 H 0 1 N N N N N N 22.511 47.873 18.708 -1.398 -0.166 -5.111 H32 GSE 21
GSE HO1 HO1 H 0 1 N N N N N N 22.411 50.064 17.825 -0.302 -0.590 -7.078 HO1 GSE 22
GSE HO4 HO4 H 0 1 N N N N N N 19.517 47.184 13.314 -1.671 1.325 -0.281 HO4 GSE 23
GSE HO2 HO2 H 0 1 N N N N N N 19.359 49.125 19.754 -0.478 1.778 -4.084 HO2 GSE 24
GSE H111 H111 H 0 0 N N N N N N 17.439 49.738 16.835 -0.143 -1.102 2.259 H111 GSE 25
GSE H112 H112 H 0 0 N N N N N N 19.156 49.757 16.764 -1.149 0.363 2.186 H112 GSE 26
GSE HA H12 H 0 1 N N N Y N N 17.862 52.274 16.454 0.594 1.622 3.421 H12 GSE 27
GSE H2 HN1 H 0 1 N N N Y Y N 17.383 52.282 14.415 1.893 -0.981 3.540 HN1 GSE 28
GSE H HN2 H 0 1 N N N Y Y N 16.517 50.803 14.777 2.378 0.257 2.618 HN2 GSE 29
GSE HXT HO6 H 0 1 N N N Y N Y 20.861 53.603 15.144 -1.621 0.558 5.991 HO6 GSE 30
#
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
GSE C1 O11 SING N N 1
GSE C1 C2 SING N N 2
GSE C1 H11 SING N N 3
GSE C1 H12A SING N N 4
GSE O11 P SING N N 5
GSE O12 P SING N N 6
GSE O12 C11 SING N N 7
GSE C2 C3 SING N N 8
GSE C2 O21 SING N N 9
GSE C2 H21 SING N N 10
GSE C3 O31 SING N N 11
GSE C3 H31 SING N N 12
GSE C3 H32 SING N N 13
GSE O31 HO1 SING N N 14
GSE P O14 SING N N 15
GSE P O13 DOUB N N 16
GSE O14 HO4 SING N N 17
GSE O21 HO2 SING N N 18
GSE C11 CA SING N N 19
GSE C11 H111 SING N N 20
GSE C11 H112 SING N N 21
GSE CA N SING N N 22
GSE CA C SING N N 23
GSE CA HA SING N N 24
GSE N H2 SING N N 25
GSE N H SING N N 26
GSE C OXT SING N N 27
GSE C O DOUB N N 28
GSE OXT HXT SING N N 29
#
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
GSE SMILES ACDLabs 10.04 'O=C(O)C(N)COP(=O)(OCC(O)CO)O'
GSE SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CO[P@](O)(=O)OC[C@H](O)CO)C(O)=O'
GSE SMILES CACTVS 3.341 'N[CH](CO[P](O)(=O)OC[CH](O)CO)C(O)=O'
GSE SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@H](CO[P@](=O)(O)OC[C@@H](C(=O)O)N)O)O'
GSE SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(COP(=O)(O)OCC(C(=O)O)N)O)O'
GSE InChI InChI 1.03 'InChI=1S/C6H14NO8P/c7-5(6(10)11)3-15-16(12,13)14-2-4(9)1-8/h4-5,8-9H,1-3,7H2,(H,10,11)(H,12,13)/t4-,5+/m1/s1'
GSE InChIKey InChI 1.03 ZWZWYGMENQVNFU-UHNVWZDZSA-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
GSE 'SYSTEMATIC NAME' ACDLabs 10.04 'O-[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]-L-serine'
GSE 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-3-[[(2R)-2,3-dihydroxypropoxy]-hydroxy-phosphoryl]oxy-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
GSE 'Create component' 1999-07-08 RCSB
GSE 'Modify descriptor' 2011-06-04 RCSB
GSE 'Modify backbone' 2023-11-03 PDBE
GSE 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id GSE
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type Glycerophosphorylation
_pdbx_chem_comp_pcm.category 'Named protein 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 ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0230
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id GSE
_pdbe_chem_comp_drugbank_details.drugbank_id DB02497
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name L-Alpha-Glycerophosphorylserine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GSE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02497
_pdbe_chem_comp_drugbank_classification.parent Glycerophosphoserines
_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 glycerophosphoserines. These are lipids containing a glycerol moiety carrying a phosphoserine at the 3-position.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GSE
_pdbe_chem_comp_drugbank_targets.drugbank_id DB02497
_pdbe_chem_comp_drugbank_targets.name 'Annexin A5'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P08758
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
GSE C1 C 7.702 0.000 1
GSE O11 O 9.002 -0.750 2
GSE O12 O 11.600 0.750 3
GSE C2 C 6.404 -0.750 4
GSE C3 C 5.104 0.000 5
GSE O31 O 3.805 -0.750 6
GSE P P 10.301 0.000 7
GSE O14 O 9.551 1.299 8
GSE O13 O 11.051 -1.299 9
GSE O21 O 6.404 -2.250 10
GSE C11 C 12.899 0.000 11
GSE CA C 14.198 0.750 12
GSE N N 14.198 2.250 13
GSE C C 15.497 0.000 14
GSE OXT O 16.796 0.750 15
GSE O O 15.497 -1.500 16
#
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
GSE C1 O11 SINGLE NONE 1
GSE C1 C2 SINGLE NONE 2
GSE O11 P SINGLE NONE 3
GSE O12 P SINGLE NONE 4
GSE O12 C11 SINGLE NONE 5
GSE C2 C3 SINGLE NONE 6
GSE C2 O21 SINGLE BEGINDASH 7
GSE C3 O31 SINGLE NONE 8
GSE P O14 SINGLE BEGINWEDGE 9
GSE P O13 DOUBLE NONE 10
GSE C11 CA SINGLE NONE 11
GSE CA N SINGLE BEGINDASH 12
GSE CA C SINGLE NONE 13
GSE C OXT SINGLE NONE 14
GSE C O DOUBLE NONE 15
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
GSE peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
GSE phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) 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
GSE O F1 1
GSE C F1 1
GSE CA F1 1
GSE N F1 1
GSE O11 F2 1
GSE P F2 1
GSE O13 F2 1
GSE O12 F2 1
GSE O14 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GSE
_pdbe_chem_comp_rdkit_properties.exactmw 259.046
_pdbe_chem_comp_rdkit_properties.amw 259.151
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 111.151
_pdbe_chem_comp_rdkit_properties.tpsa 159.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.115
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.433
_pdbe_chem_comp_rdkit_properties.chi0v 8.055
_pdbe_chem_comp_rdkit_properties.chi1v 4.639
_pdbe_chem_comp_rdkit_properties.chi2v 1.420
_pdbe_chem_comp_rdkit_properties.chi3v 1.420
_pdbe_chem_comp_rdkit_properties.chi4v 0.708
_pdbe_chem_comp_rdkit_properties.chi0n 21.160
_pdbe_chem_comp_rdkit_properties.chi1n 9.706
_pdbe_chem_comp_rdkit_properties.chi2n 0.790
_pdbe_chem_comp_rdkit_properties.chi3n 0.790
_pdbe_chem_comp_rdkit_properties.chi4n 0.278
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.540
_pdbe_chem_comp_rdkit_properties.kappa1 3.991
_pdbe_chem_comp_rdkit_properties.kappa2 6.918
_pdbe_chem_comp_rdkit_properties.kappa3 6.855
_pdbe_chem_comp_rdkit_properties.Phi 1.726
#
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
GSE UniChem DrugBank DB02497
GSE UniChem ChEBI 64945
GSE UniChem SureChEMBL SCHEMBL13863415
GSE UniChem MetaboLights MTBLC64945
GSE UniChem BRENDA 120877
GSE UniChem BRENDA 198964
GSE UniChem BRENDA 198967
GSE UniChem BRENDA 249021
GSE UniChem 'Probes And Drugs' PD059944
GSE UniChem Nikkaji J641.596B
GSE UniChem PubChem 444182
#
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
GSE C1 -2.083 -0.898 0.043 ETKDGv3 1
GSE O11 -1.516 -0.514 1.275 ETKDGv3 2
GSE O12 0.920 -0.263 -0.060 ETKDGv3 3
GSE C2 -3.562 -0.483 0.004 ETKDGv3 4
GSE C3 -3.734 1.041 0.120 ETKDGv3 5
GSE O31 -3.080 1.708 -0.927 ETKDGv3 6
GSE P 0.127 -0.968 1.278 ETKDGv3 7
GSE O14 0.831 -0.420 2.716 ETKDGv3 8
GSE O13 0.237 -2.476 1.217 ETKDGv3 9
GSE O21 -4.152 -0.926 -1.191 ETKDGv3 10
GSE C11 2.284 -0.612 -0.006 ETKDGv3 11
GSE CA 3.022 0.033 -1.187 ETKDGv3 12
GSE N 4.432 -0.360 -1.173 ETKDGv3 13
GSE C 2.914 1.530 -1.111 ETKDGv3 14
GSE OXT 3.603 2.230 -0.125 ETKDGv3 15
GSE O 2.180 2.152 -1.925 ETKDGv3 16
GSE H11 -2.034 -2.004 -0.075 ETKDGv3 17
GSE H12A -1.554 -0.419 -0.811 ETKDGv3 18
GSE H21 -4.086 -0.948 0.872 ETKDGv3 19
GSE H31 -4.819 1.296 0.124 ETKDGv3 20
GSE H32 -3.313 1.394 1.085 ETKDGv3 21
GSE HO1 -3.671 1.641 -1.722 ETKDGv3 22
GSE HO4 0.731 0.565 2.685 ETKDGv3 23
GSE HO2 -4.304 -1.902 -1.092 ETKDGv3 24
GSE H111 2.402 -1.717 -0.084 ETKDGv3 25
GSE H112 2.751 -0.259 0.942 ETKDGv3 26
GSE HA 2.556 -0.323 -2.135 ETKDGv3 27
GSE H2 4.898 0.059 -2.011 ETKDGv3 28
GSE H 4.488 -1.396 -1.303 ETKDGv3 29
GSE HXT 3.531 3.238 -0.056 ETKDGv3 30
#