data_SEP
#
_chem_comp.id SEP
_chem_comp.name PHOSPHOSERINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C3 H8 N O6 P"
_chem_comp.mon_nstd_parent_comp_id SER
_chem_comp.pdbx_synonyms PHOSPHONOSERINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2025-08-24
_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 185.072
_chem_comp.one_letter_code S
_chem_comp.three_letter_code SEP
_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 1BX6
_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
SEP N N N 0 1 N N N Y Y N 12.751 44.134 -4.949 1.855 0.421 1.751 N SEP 1
SEP CA CA C 0 1 N N S Y N N 12.373 44.600 -6.265 0.401 0.620 1.687 CA SEP 2
SEP CB CB C 0 1 N N N N N N 11.077 45.353 -6.305 -0.139 0.015 0.391 CB SEP 3
SEP OG OG O 0 1 N N N N N N 10.895 45.809 -7.608 0.477 0.655 -0.727 OG SEP 4
SEP C C C 0 1 N N N Y N Y 13.435 45.364 -6.941 -0.249 -0.053 2.867 C SEP 5
SEP O O O 0 1 N N N Y N Y 14.373 45.871 -6.303 0.254 -1.038 3.354 O SEP 6
SEP OXT OXT O 0 1 N Y N Y N Y 13.281 45.410 -8.244 -1.389 0.439 3.377 OXT SEP 7
SEP P P P 0 1 N N N N N N 9.607 45.328 -8.384 -0.135 -0.027 -2.050 P SEP 8
SEP O1P O1P O 0 1 N N N N N N 9.500 46.086 -9.633 -1.601 0.172 -2.074 O1P SEP 9
SEP O2P O2P O 0 1 N N N N N N 9.829 43.907 -8.669 0.520 0.649 -3.356 O2P SEP 10
SEP O3P O3P O 0 1 N N N N N N 8.402 45.541 -7.535 0.191 -1.603 -2.041 O3P SEP 11
SEP H H H 0 1 N N N Y Y N 13.632 43.621 -4.921 2.237 0.796 0.895 H SEP 12
SEP H2 2HN H 0 1 N Y N Y Y N 12.001 43.575 -4.540 2.013 -0.574 1.727 H2 SEP 13
SEP HA HA H 0 1 N N N Y N N 12.213 43.656 -6.837 0.179 1.687 1.711 HA SEP 14
SEP HB2 1HB H 0 1 N N N N N N 10.214 44.753 -5.930 0.082 -1.051 0.367 HB2 SEP 15
SEP HB3 2HB H 0 1 N N N N N N 11.026 46.170 -5.548 -1.218 0.163 0.344 HB3 SEP 16
SEP HXT HXT H 0 1 N Y N Y N Y 13.966 45.902 -8.680 -1.807 0.006 4.134 HXT SEP 17
SEP HOP2 2HOP H 0 0 N N N N N N 9.054 43.617 -9.135 0.127 0.212 -4.124 HOP2 SEP 18
SEP HOP3 3HOP H 0 0 N N N N N N 7.627 45.251 -8.001 1.154 -1.689 -2.025 HOP3 SEP 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
SEP N CA SING N N 1
SEP N H SING N N 2
SEP N H2 SING N N 3
SEP CA CB SING N N 4
SEP CA C SING N N 5
SEP CA HA SING N N 6
SEP CB OG SING N N 7
SEP CB HB2 SING N N 8
SEP CB HB3 SING N N 9
SEP OG P SING N N 10
SEP C O DOUB N N 11
SEP C OXT SING N N 12
SEP OXT HXT SING N N 13
SEP P O1P DOUB N N 14
SEP P O2P SING N N 15
SEP P O3P SING N N 16
SEP O2P HOP2 SING N N 17
SEP O3P HOP3 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
SEP SMILES ACDLabs 10.04 O=P(O)(O)OCC(C(=O)O)N
SEP SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO[P](O)(O)=O)C(O)=O
SEP SMILES CACTVS 3.341 N[CH](CO[P](O)(O)=O)C(O)=O
SEP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)OP(=O)(O)O
SEP SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)OP(=O)(O)O
SEP InChI InChI 1.03 InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m0/s1
SEP InChIKey InChI 1.03 BZQFBWGGLXLEPQ-REOHCLBHSA-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
SEP "SYSTEMATIC NAME" ACDLabs 10.04 O-phosphono-L-serine
SEP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-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
SEP 'Create component' 1999-07-08 RCSB
SEP 'Modify descriptor' 2011-06-04 RCSB
SEP 'Modify synonyms' 2021-03-01 PDBE
SEP 'Modify backbone' 2023-11-03 PDBE
SEP 'Modify PCM' 2024-09-27 PDBE
SEP 'Modify PCM' 2025-08-24 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SEP
_pdbx_chem_comp_synonyms.name PHOSPHONOSERINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SEP
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type Phosphorylation
_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-0253
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id SEP
_pdbe_chem_comp_drugbank_details.drugbank_id DB04522
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Dexfosfoserine
_pdbe_chem_comp_drugbank_details.description 'The phosphoric acid ester of serine.'
_pdbe_chem_comp_drugbank_details.cas_number 407-41-0
_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
SEP PHOSPHONOSERINE wwPDB ?
SEP Dexfosfoserine DrugBank ?
SEP Phosphoserine DrugBank ?
SEP 'Serine phosphate' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SEP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04522
_pdbe_chem_comp_drugbank_classification.parent 'L-alpha-amino acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic 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 l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.'
#
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
SEP DB04522 'Glycogen phosphorylase, muscle form' Humans P11217 yes 1
SEP DB04522 'Protein kinase C theta type' Humans Q04759 unknown 2
SEP DB04522 '3-phosphoinositide-dependent protein kinase 1' Humans O15530 unknown 3
SEP DB04522 'Serine/threonine-protein kinase pim-1' Humans P11309 unknown 4
SEP DB04522 'Glycogen phosphorylase, liver form' Humans P06737 unknown 5
SEP DB04522 Phosphomannomutase/phosphoglucomutase 'Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)' P26276 unknown 6
SEP DB04522 'cAMP-dependent protein kinase catalytic subunit alpha' Humans P17612 unknown 7
SEP DB04522 'Anti-sigma F factor antagonist' 'Lysinibacillus sphaericus' O32723 unknown 8
SEP DB04522 'Type IV major pilin protein PilE1' 'Neisseria gonorrhoeae' P02974 unknown 9
SEP DB04522 'Alkaline phosphatase' 'Escherichia coli (strain K12)' P00634 unknown 10
SEP DB04522 Rhodopsin Humans P08100 unknown 11
SEP DB04522 'Serpin B3' Humans P29508 unknown 12
SEP DB04522 'Endo-1,4-beta-xylanase Y' 'Clostridium thermocellum' P51584 unknown 13
SEP DB04522 'Serine/threonine-protein kinase TAO2' Humans Q9UL54 unknown 14
SEP DB04522 'Voltage-gated potassium channel KCNC4' Humans Q03721 unknown 15
SEP DB04522 Lithostathine-1-alpha Humans P05451 unknown 16
SEP DB04522 'SMAD family member 2' Humans Q15796 unknown 17
SEP DB04522 'Glutaminase 1' 'Bacillus subtilis (strain 168)' O31465 unknown 18
SEP DB04522 'Siroheme synthase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P25924 unknown 19
SEP DB04522 'Phosphocarrier protein HPr' 'Enterococcus faecalis (strain ATCC 700802 / V583)' P07515 unknown 20
SEP DB04522 'Cystic fibrosis transmembrane conductance regulator' Humans P13569 unknown 21
#
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
SEP N N 9.002 1.643 1
SEP CA C 9.002 0.142 2
SEP CB C 7.702 -0.608 3
SEP OG O 6.404 0.142 4
SEP C C 10.301 -0.608 5
SEP O O 11.600 0.142 6
SEP OXT O 10.301 -2.107 7
SEP P P 5.104 -0.608 8
SEP O1P O 3.805 -1.357 9
SEP O2P O 4.354 0.692 10
SEP O3P O 5.854 -1.907 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
SEP CA N SINGLE BEGINDASH 1
SEP CA CB SINGLE NONE 2
SEP CA C SINGLE NONE 3
SEP CB OG SINGLE NONE 4
SEP OG P SINGLE NONE 5
SEP C O DOUBLE NONE 6
SEP C OXT SINGLE NONE 7
SEP P O1P DOUBLE NONE 8
SEP P O2P SINGLE NONE 9
SEP P O3P SINGLE NONE 10
#
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
SEP peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
SEP 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
SEP O F1 1
SEP C F1 1
SEP CA F1 1
SEP N F1 1
SEP OG F2 1
SEP P F2 1
SEP O1P F2 1
SEP O2P F2 1
SEP O3P F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SEP
_pdbe_chem_comp_rdkit_properties.exactmw 185.009
_pdbe_chem_comp_rdkit_properties.amw 185.072
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_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 19
_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 73.632
_pdbe_chem_comp_rdkit_properties.tpsa 130.080
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.492
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.607
_pdbe_chem_comp_rdkit_properties.chi0v 5.738
_pdbe_chem_comp_rdkit_properties.chi1v 3.527
_pdbe_chem_comp_rdkit_properties.chi2v 0.762
_pdbe_chem_comp_rdkit_properties.chi3v 0.762
_pdbe_chem_comp_rdkit_properties.chi4v 0.339
_pdbe_chem_comp_rdkit_properties.chi0n 12.844
_pdbe_chem_comp_rdkit_properties.chi1n 5.685
_pdbe_chem_comp_rdkit_properties.chi2n 0.447
_pdbe_chem_comp_rdkit_properties.chi3n 0.447
_pdbe_chem_comp_rdkit_properties.chi4n 0.141
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.460
_pdbe_chem_comp_rdkit_properties.kappa1 3.118
_pdbe_chem_comp_rdkit_properties.kappa2 3.795
_pdbe_chem_comp_rdkit_properties.kappa3 5.959
_pdbe_chem_comp_rdkit_properties.Phi 1.076
#
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
SEP UniChem DrugBank DB04522
SEP UniChem 'Guide to Pharmacology' 1411
SEP UniChem 'KEGG LIGAND' C01005
SEP UniChem ChEBI 15811
SEP UniChem ZINC ZINC000003869280
SEP UniChem eMolecules 29542138
SEP UniChem fdasrs VI4F0K069V
SEP UniChem HMDB HMDB0000272
SEP UniChem NMRShiftDB 80004315
SEP UniChem Nikkaji J136.545B
SEP UniChem 'EPA CompTox Dashboard' DTXSID1046348
SEP UniChem DrugCentral 4120
SEP UniChem MetaboLights MTBLC15811
SEP UniChem BRENDA 100780
SEP UniChem BRENDA 113733
SEP UniChem BRENDA 1189
SEP UniChem BRENDA 127904
SEP UniChem BRENDA 130033
SEP UniChem BRENDA 133508
SEP UniChem BRENDA 19742
SEP UniChem BRENDA 224856
SEP UniChem BRENDA 229591
SEP UniChem BRENDA 257921
SEP UniChem BRENDA 2994
SEP UniChem BRENDA 30850
SEP UniChem BRENDA 44708
SEP UniChem BRENDA 47300
SEP UniChem BRENDA 47421
SEP UniChem BRENDA 69436
SEP UniChem BRENDA 8160
SEP UniChem BRENDA 91544
SEP UniChem BRENDA 9243
SEP UniChem BRENDA 97368
SEP UniChem ChemicalBook CB0456205
SEP UniChem ClinicalTrials PHOSPHOSERINE
SEP UniChem MedChemExpress HY-15129
SEP UniChem 'Probes And Drugs' PD002659
SEP UniChem CCDC SERPOP
SEP UniChem BindingDb 17664
SEP UniChem SureChEMBL SCHEMBL6846
SEP UniChem 'PubChem TPHARMA' 15340053
SEP UniChem PubChem 57689797
SEP UniChem PubChem 68841
SEP UniChem ACTor 407-41-0
SEP UniChem ACTor 68762-59-4
#
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
SEP N 1.656 -1.575 -0.370 ETKDGv3 1
SEP CA 1.298 -0.204 -0.738 ETKDGv3 2
SEP CB -0.210 0.023 -0.564 ETKDGv3 3
SEP OG -0.586 -0.247 0.767 ETKDGv3 4
SEP C 2.076 0.779 0.092 ETKDGv3 5
SEP O 2.235 0.586 1.328 ETKDGv3 6
SEP OXT 2.587 1.930 -0.500 ETKDGv3 7
SEP P -2.272 -0.032 0.906 ETKDGv3 8
SEP O1P -2.683 -0.306 2.334 ETKDGv3 9
SEP O2P -2.694 1.559 0.511 ETKDGv3 10
SEP O3P -3.084 -1.110 -0.118 ETKDGv3 11
SEP H 1.151 -2.230 -1.011 ETKDGv3 12
SEP H2 2.675 -1.711 -0.564 ETKDGv3 13
SEP HA 1.554 -0.038 -1.810 ETKDGv3 14
SEP HB2 -0.439 1.080 -0.833 ETKDGv3 15
SEP HB3 -0.744 -0.651 -1.271 ETKDGv3 16
SEP HXT 3.101 2.611 0.046 ETKDGv3 17
SEP HOP2 -2.893 1.538 -0.459 ETKDGv3 18
SEP HOP3 -2.726 -2.003 0.121 ETKDGv3 19
#