data_DSN
#
_chem_comp.id DSN
_chem_comp.name D-SERINE
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C3 H7 N O3"
_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 2023-11-03
_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 105.093
_chem_comp.one_letter_code S
_chem_comp.three_letter_code DSN
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1BFW
_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
DSN N N N 0 1 N N N Y Y N 2.939 10.455 -1.900 -0.787 -0.923 0.538 N DSN 1
DSN CA CA C 0 1 N N R Y N N 2.468 11.798 -2.190 -0.469 -2.117 -0.207 CA DSN 2
DSN C C C 0 1 N N N Y N Y 1.876 11.853 -3.600 -1.299 -2.093 -1.474 C DSN 3
DSN O O O 0 1 N N N Y N Y 0.872 11.200 -3.881 -1.583 -1.087 -2.112 O DSN 4
DSN OXT OXT O 0 1 N Y N Y N Y ? ? ? -1.749 -3.331 -1.808 OXT DSN 5
DSN CB CB C 0 1 N N N N N N 1.430 12.251 -1.161 1.014 -2.190 -0.542 CB DSN 6
DSN OG OG O 0 1 N N N N N N 1.463 11.453 0.019 1.271 -3.390 -1.262 OG DSN 7
DSN H H H 0 1 N N N Y Y N 3.333 10.418 -0.960 -1.409 -0.247 0.132 H DSN 8
DSN H2 HN2 H 0 1 N Y N Y Y N 3.597 10.120 -2.604 -0.233 -0.692 1.345 H2 DSN 9
DSN HA HA H 0 1 N N N Y N N 3.337 12.493 -2.132 -0.782 -2.950 0.431 HA DSN 10
DSN HXT HXT H 0 1 N Y N Y N Y -0.367 0.034 -0.875 -2.322 -3.366 -2.604 HXT DSN 11
DSN HB2 1HB H 0 1 N N N N N N 1.545 13.333 -0.920 1.622 -2.208 0.368 HB2 DSN 12
DSN HB3 2HB H 0 1 N N N N N N 0.406 12.276 -1.603 1.331 -1.339 -1.154 HB3 DSN 13
DSN HG HOG H 0 1 N N N N N N 0.818 11.734 0.657 1.917 -3.168 -1.952 HG DSN 14
#
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
DSN N CA SING N N 1
DSN N H SING N N 2
DSN N H2 SING N N 3
DSN CA C SING N N 4
DSN CA CB SING N N 5
DSN CA HA SING N N 6
DSN C O DOUB N N 7
DSN C OXT SING N N 8
DSN OXT HXT SING N N 9
DSN CB OG SING N N 10
DSN CB HB2 SING N N 11
DSN CB HB3 SING N N 12
DSN OG HG SING N N 13
#
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
DSN SMILES ACDLabs 10.04 O=C(O)C(N)CO
DSN SMILES_CANONICAL CACTVS 3.341 N[C@H](CO)C(O)=O
DSN SMILES CACTVS 3.341 N[CH](CO)C(O)=O
DSN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H](C(=O)O)N)O
DSN SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O
DSN InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
DSN InChIKey InChI 1.03 MTCFGRXMJLQNBG-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
DSN "SYSTEMATIC NAME" ACDLabs 10.04 D-serine
DSN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-3-hydroxy-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
DSN 'Create component' 1999-07-08 RCSB
DSN 'Modify descriptor' 2011-06-04 RCSB
DSN 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id DSN
_pdbe_chem_comp_drugbank_details.drugbank_id DB03929
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name D-Serine
_pdbe_chem_comp_drugbank_details.description
'A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids. [PubChem]'
_pdbe_chem_comp_drugbank_details.cas_number 312-84-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DSN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03929
_pdbe_chem_comp_drugbank_classification.parent 'Serine and derivatives'
_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 serine and derivatives. These are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
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
DSN DB03929 'Glutamate receptor ionotropic, NMDA 1' Humans Q05586 yes 1
DSN DB03929 'Glycine receptor subunit alpha-1' Humans P23415 yes 2
DSN DB03929 'Serpin B3' Humans P29508 unknown 3
DSN DB03929 'Head decoration protein' 'Bacteriophage 21' P36275 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
DSN N N 3.805 1.215 1
DSN CA C 5.104 0.465 2
DSN C C 6.404 1.215 3
DSN O O 7.702 0.465 4
DSN OXT O 6.404 2.715 5
DSN CB C 5.104 -1.035 6
DSN OG O 6.404 -1.785 7
#
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
DSN CA N SINGLE BEGINWEDGE 1
DSN CA C SINGLE NONE 2
DSN CA CB SINGLE NONE 3
DSN C O DOUBLE NONE 4
DSN C OXT SINGLE NONE 5
DSN CB OG SINGLE NONE 6
#
_pdbe_chem_comp_substructure.comp_id DSN
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
DSN O F1 1
DSN C F1 1
DSN CA F1 1
DSN N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DSN
_pdbe_chem_comp_rdkit_properties.exactmw 105.043
_pdbe_chem_comp_rdkit_properties.amw 105.093
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 50.683
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.609
_pdbe_chem_comp_rdkit_properties.CrippenMR 22.697
_pdbe_chem_comp_rdkit_properties.chi0v 3.172
_pdbe_chem_comp_rdkit_properties.chi1v 1.336
_pdbe_chem_comp_rdkit_properties.chi2v 0.290
_pdbe_chem_comp_rdkit_properties.chi3v 0.290
_pdbe_chem_comp_rdkit_properties.chi4v 0.042
_pdbe_chem_comp_rdkit_properties.chi0n 10.172
_pdbe_chem_comp_rdkit_properties.chi1n 4.547
_pdbe_chem_comp_rdkit_properties.chi2n 0.290
_pdbe_chem_comp_rdkit_properties.chi3n 0.290
_pdbe_chem_comp_rdkit_properties.chi4n 0.042
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.209
_pdbe_chem_comp_rdkit_properties.kappa2 2.544
_pdbe_chem_comp_rdkit_properties.kappa3 2.132
_pdbe_chem_comp_rdkit_properties.Phi 0.439
#
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
DSN UniChem DrugBank DB03929
DSN UniChem 'Guide to Pharmacology' 4171
DSN UniChem 'KEGG LIGAND' C00740
DSN UniChem ChEBI 16523
DSN UniChem ChEBI 35247
DSN UniChem ZINC ZINC000000895342
DSN UniChem atlas D-serine
DSN UniChem fdasrs 1K77H2Z9B1
DSN UniChem SureChEMBL SCHEMBL43094
DSN UniChem HMDB HMDB0003406
DSN UniChem NMRShiftDB 60020761
DSN UniChem LINCS LSM-45895
DSN UniChem Recon 'ser_D'
DSN UniChem BindingDb 23167
DSN UniChem 'EPA CompTox Dashboard' DTXSID9041021
DSN UniChem MetaboLights MTBLC16523
DSN UniChem MetaboLights MTBLC35247
DSN UniChem BRENDA 481
DSN UniChem BRENDA 972
DSN UniChem Rhea 35247
DSN UniChem ChemicalBook CB0747387
DSN UniChem ClinicalTrials CTP-692
DSN UniChem rxnorm 'SERINE, D-'
DSN UniChem MedChemExpress HY-100808
DSN UniChem 'Probes And Drugs' PD002617
DSN UniChem CCDC ZUTRIR
DSN UniChem Nikkaji J1.196G
DSN UniChem eMolecules 531444
DSN UniChem 'PubChem TPHARMA' 14747454
DSN UniChem 'PubChem TPHARMA' 15146420
DSN UniChem PubChem 6857549
DSN UniChem PubChem 71077
DSN UniChem Mcule MCULE-3271603208
DSN UniChem Mcule MCULE-8560981570
DSN UniChem ACTor 62595-04-4
#
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
DSN N -0.401 -1.693 0.144 ETKDGv3 1
DSN CA -0.166 -0.286 0.475 ETKDGv3 2
DSN C 1.309 0.000 0.439 ETKDGv3 3
DSN O 1.884 0.474 1.454 ETKDGv3 4
DSN OXT 2.040 -0.245 -0.720 ETKDGv3 5
DSN CB -0.927 0.643 -0.489 ETKDGv3 6
DSN OG -0.748 1.987 -0.130 ETKDGv3 7
DSN H -1.416 -1.904 0.285 ETKDGv3 8
DSN H2 -0.188 -1.855 -0.867 ETKDGv3 9
DSN HA -0.541 -0.104 1.507 ETKDGv3 10
DSN HXT 3.033 -0.052 -0.759 ETKDGv3 11
DSN HB2 -2.012 0.390 -0.484 ETKDGv3 12
DSN HB3 -0.556 0.501 -1.527 ETKDGv3 13
DSN HG -1.311 2.144 0.673 ETKDGv3 14
#