data_5CS
#
_chem_comp.id 5CS
_chem_comp.name '2-AMINO-3-(CYSTEIN-S-YL)-ISOXAZOLIDIN-5-YL-ACETIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C8 H15 N3 O5 S'
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-04-10
_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 265.287
_chem_comp.one_letter_code C
_chem_comp.three_letter_code 5CS
_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 1OX5
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
5CS N N N 0 1 N N N N N N 68.387 89.778 5.381 -2.119 3.671 3.207 N 5CS 1
5CS CA CA C 0 1 N N R N N N 67.918 88.753 4.432 -1.330 3.511 2.011 CA 5CS 2
5CS CB CB C 0 1 N N N N N N 67.318 87.611 5.260 -1.158 2.038 1.632 CB 5CS 3
5CS SG SG S 0 1 N N N N N N 66.281 86.343 4.563 -2.694 1.235 1.113 SG 5CS 4
5CS C C C 0 1 N N N N N N 66.962 89.359 3.399 -1.867 4.346 0.861 C 5CS 5
5CS O O O 0 1 N N N N N N 67.410 90.097 2.524 -2.909 4.987 0.914 O 5CS 6
5CS CI CI C 0 1 N N S N N N 65.860 84.798 -0.148 -0.446 -1.985 -2.207 CI 5CS 7
5CS NI NI N 0 1 N N N N N N 64.539 85.439 -0.281 0.958 -1.527 -2.298 NI 5CS 8
5CS CJ CJ C 0 1 N N N N N N 65.865 83.436 -0.835 -1.249 -1.179 -3.197 CJ 5CS 9
5CS OJ1 OJ1 O 0 1 N N N N N N 66.820 83.276 -1.619 -2.534 -1.616 -3.234 OJ1 5CS 10
5CS OJ2 OJ2 O 0 1 N N N N N N 64.997 82.564 -0.568 -0.829 -0.266 -3.895 OJ2 5CS 11
5CS CF CF C 0 1 N N R N N N 66.506 84.900 1.219 -0.945 -1.794 -0.787 CF 5CS 12
5CS OF OF O 0 1 N N N N N N 66.533 83.828 2.089 -2.298 -2.248 -0.681 OF 5CS 13
5CS NX NX N 0 1 N N N N N N 66.789 84.306 3.442 -3.031 -1.308 0.172 NX 5CS 14
5CS CD CD C 0 1 N N R N N N 67.243 85.631 3.246 -2.026 -0.401 0.726 CD 5CS 15
5CS CE CE C 0 1 N N N N N N 66.962 86.186 1.851 -0.976 -0.346 -0.355 CE 5CS 16
5CS OXT OXT O 0 1 N Y N N N N ? ? ? -1.085 4.301 -0.244 OXT 5CS 17
5CS H H H 0 1 N N N N N N 68.786 90.537 4.830 -1.687 3.513 4.102 H 5CS 18
5CS H2 HN2 H 0 1 N Y N N N N 69.031 89.410 6.080 -3.119 3.735 3.126 H2 5CS 19
5CS HA HA H 0 1 N N N N N N 68.753 88.338 3.820 -0.346 3.929 2.257 HA 5CS 20
5CS HB2 1HB H 0 1 N N N N N N 68.160 87.101 5.782 -0.771 1.476 2.488 HB2 5CS 21
5CS HB3 2HB H 0 1 N N N N N N 66.756 88.072 6.105 -0.438 1.935 0.813 HB3 5CS 22
5CS HI HI H 0 1 N N N N N N 66.594 85.413 -0.717 -0.475 -3.040 -2.503 HI 5CS 23
5CS HN1 1HN H 0 1 N N N N N N 64.535 86.349 0.178 1.662 -2.198 -2.128 HN1 5CS 24
5CS HN2A 2HN H 0 0 N N N N N N 63.789 84.838 0.062 1.112 -0.551 -2.320 HN2A 5CS 25
5CS HJ1 HJ1 H 0 1 N N N N N N 66.823 82.427 -2.046 -3.073 -1.113 -3.882 HJ1 5CS 26
5CS HF HF H 0 1 N N N N N N 67.142 84.828 0.306 -0.337 -2.395 -0.101 HF 5CS 27
5CS HX HX H 0 1 N N N N N N 67.422 83.718 3.984 -3.368 -1.930 0.906 HX 5CS 28
5CS HD HD H 0 1 N N N N N N 68.342 85.813 3.282 -1.607 -0.830 1.644 HD 5CS 29
5CS HE3 1HE H 0 1 N N N N N N 67.795 86.728 1.346 0.000 0.001 -0.001 HE3 5CS 30
5CS HE2 2HE H 0 1 N N N N N N 66.266 87.055 1.784 -1.288 0.294 -1.192 HE2 5CS 31
5CS HXT HXT H 0 1 N Y N N N N -0.592 0.375 -0.640 -1.455 4.837 -0.977 HXT 5CS 32
#
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
5CS N CA SING N N 1
5CS N H SING N N 2
5CS N H2 SING N N 3
5CS CA CB SING N N 4
5CS CA C SING N N 5
5CS CA HA SING N N 6
5CS CB SG SING N N 7
5CS CB HB2 SING N N 8
5CS CB HB3 SING N N 9
5CS SG CD SING N N 10
5CS C O DOUB N N 11
5CS C OXT SING N N 12
5CS CI NI SING N N 13
5CS CI CJ SING N N 14
5CS CI CF SING N N 15
5CS CI HI SING N N 16
5CS NI HN1 SING N N 17
5CS NI HN2A SING N N 18
5CS CJ OJ1 SING N N 19
5CS CJ OJ2 DOUB N N 20
5CS OJ1 HJ1 SING N N 21
5CS CF OF SING N N 22
5CS CF CE SING N N 23
5CS CF HF SING N N 24
5CS OF NX SING N N 25
5CS NX CD SING N N 26
5CS NX HX SING N N 27
5CS CD CE SING N N 28
5CS CD HD SING N N 29
5CS CE HE3 SING N N 30
5CS CE HE2 SING N N 31
5CS OXT HXT SING N N 32
#
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
5CS SMILES ACDLabs 10.04 'O=C(O)C(N)C1ONC(SCC(N)C(=O)O)C1'
5CS SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CS[C@@H]1C[C@@H](ON1)[C@H](N)C(O)=O)C(O)=O'
5CS SMILES CACTVS 3.341 'N[CH](CS[CH]1C[CH](ON1)[CH](N)C(O)=O)C(O)=O'
5CS SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1C(ON[C@@H]1SC[C@@H](C(=O)O)N)[C@@H](C(=O)O)N'
5CS SMILES 'OpenEye OEToolkits' 1.5.0 'C1C(ONC1SCC(C(=O)O)N)C(C(=O)O)N'
5CS InChI InChI 1.03 'InChI=1S/C8H15N3O5S/c9-3(7(12)13)2-17-5-1-4(16-11-5)6(10)8(14)15/h3-6,11H,1-2,9-10H2,(H,12,13)(H,14,15)/t3-,4+,5+,6-/m0/s1'
5CS InChIKey InChI 1.03 YLODKYYPRFTBNK-KCDKBNATSA-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
5CS 'SYSTEMATIC NAME' ACDLabs 10.04 'S-{(3R,5R)-5-[(S)-amino(carboxy)methyl]isoxazolidin-3-yl}-L-cysteine'
5CS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-amino-3-[[(3R)-5-[(1S)-1-amino-2-hydroxy-2-oxo-ethyl]-1,2-oxazolidin-3-yl]sulfanyl]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
5CS 'Create component' 2003-04-10 RCSB
5CS 'Modify descriptor' 2011-06-04 RCSB
5CS 'Modify PCM' 2024-09-27 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id 5CS
_pdbe_chem_comp_drugbank_details.drugbank_id DB04323
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '2-Amino-3-(Cystein-S-Yl)-Isoxazolidin-5-Yl-Acetic Acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id 5CS
_pdbe_chem_comp_synonyms.name '2-Amino-3-(Cystein-S-Yl)-Isoxazolidin-5-Yl-Acetic Acid'
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 5CS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04323
_pdbe_chem_comp_drugbank_classification.parent L-cysteine-S-conjugates
_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-cysteine-s-conjugates. These are compounds containing L-cysteine where the thio-group is conjugated.'
#
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
5CS N N 5.920 -3.421 1
5CS CA C 6.232 -1.954 2
5CS CB C 7.659 -1.490 3
5CS SG S 8.774 -2.494 4
5CS C C 5.118 -0.950 5
5CS O O 3.691 -1.414 6
5CS CI C 13.046 0.610 7
5CS NI N 14.537 0.453 8
5CS CJ C 12.435 1.980 9
5CS OJ1 O 13.317 3.194 10
5CS OJ2 O 10.944 2.137 11
5CS CF C 12.164 -0.604 12
5CS OF O 12.627 -2.030 13
5CS NX N 11.414 -2.912 14
5CS CD C 10.200 -2.030 15
5CS CE C 10.664 -0.604 16
5CS OXT O 5.429 0.517 17
#
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
5CS CA N SINGLE BEGINDASH 1
5CS CA CB SINGLE NONE 2
5CS CA C SINGLE NONE 3
5CS CB SG SINGLE NONE 4
5CS CD SG SINGLE BEGINDASH 5
5CS C O DOUBLE NONE 6
5CS C OXT SINGLE NONE 7
5CS CI NI SINGLE BEGINWEDGE 8
5CS CI CJ SINGLE NONE 9
5CS CI CF SINGLE NONE 10
5CS CJ OJ1 SINGLE NONE 11
5CS CJ OJ2 DOUBLE NONE 12
5CS CF OF SINGLE NONE 13
5CS CF CE SINGLE BEGINDASH 14
5CS OF NX SINGLE NONE 15
5CS NX CD SINGLE NONE 16
5CS CD CE SINGLE NONE 17
#
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
5CS MurckoScaffold S1 scaffold C1CNOC1 InChI=1S/C3H7NO/c1-2-4-5-3-1/h4H,1-3H2 CIISBYKBBMFLEZ-UHFFFAOYSA-N
5CS peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
5CS CF S1 1
5CS OF S1 1
5CS NX S1 1
5CS CD S1 1
5CS CE S1 1
5CS O F1 1
5CS C F1 1
5CS CA F1 1
5CS N F1 1
5CS OJ2 F1 2
5CS CJ F1 2
5CS CI F1 2
5CS NI F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 5CS
_pdbe_chem_comp_rdkit_properties.exactmw 265.073
_pdbe_chem_comp_rdkit_properties.amw 265.291
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 123.158
_pdbe_chem_comp_rdkit_properties.tpsa 147.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.837
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.094
_pdbe_chem_comp_rdkit_properties.chi0v 8.608
_pdbe_chem_comp_rdkit_properties.chi1v 4.599
_pdbe_chem_comp_rdkit_properties.chi2v 1.952
_pdbe_chem_comp_rdkit_properties.chi3v 1.952
_pdbe_chem_comp_rdkit_properties.chi4v 1.102
_pdbe_chem_comp_rdkit_properties.chi0n 22.791
_pdbe_chem_comp_rdkit_properties.chi1n 10.835
_pdbe_chem_comp_rdkit_properties.chi2n 1.286
_pdbe_chem_comp_rdkit_properties.chi3n 1.286
_pdbe_chem_comp_rdkit_properties.chi4n 0.607
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.870
_pdbe_chem_comp_rdkit_properties.kappa1 3.810
_pdbe_chem_comp_rdkit_properties.kappa2 6.168
_pdbe_chem_comp_rdkit_properties.kappa3 4.130
_pdbe_chem_comp_rdkit_properties.Phi 1.383
#
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
5CS UniChem DrugBank DB04323
5CS UniChem ZINC ZINC000006361516
5CS UniChem PubChem 17753793
5CS UniChem 'Probes And Drugs' PD059319
#
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
5CS N 4.639 0.235 1.184 ETKDGv3 1
5CS CA 3.717 -0.692 0.525 ETKDGv3 2
5CS CB 2.407 0.017 0.139 ETKDGv3 3
5CS SG 1.177 -1.187 -0.483 ETKDGv3 4
5CS C 4.388 -1.286 -0.682 ETKDGv3 5
5CS O 4.549 -2.533 -0.764 ETKDGv3 6
5CS CI -3.286 0.252 0.867 ETKDGv3 7
5CS NI -3.367 -1.213 0.898 ETKDGv3 8
5CS CJ -4.635 0.822 0.530 ETKDGv3 9
5CS OJ1 -5.226 1.751 1.381 ETKDGv3 10
5CS OJ2 -5.227 0.476 -0.528 ETKDGv3 11
5CS CF -2.211 0.775 -0.123 ETKDGv3 12
5CS OF -2.343 0.164 -1.393 ETKDGv3 13
5CS NX -1.194 -0.535 -1.647 ETKDGv3 14
5CS CD -0.120 0.055 -0.861 ETKDGv3 15
5CS CE -0.787 0.580 0.371 ETKDGv3 16
5CS OXT 4.829 -0.460 -1.713 ETKDGv3 17
5CS H 4.212 0.547 2.087 ETKDGv3 18
5CS H2 4.764 1.087 0.589 ETKDGv3 19
5CS HA 3.476 -1.509 1.242 ETKDGv3 20
5CS HB2 1.988 0.519 1.036 ETKDGv3 21
5CS HB3 2.604 0.788 -0.637 ETKDGv3 22
5CS HI -3.022 0.607 1.888 ETKDGv3 23
5CS HN1 -2.455 -1.612 1.214 ETKDGv3 24
5CS HN2A -3.561 -1.585 -0.060 ETKDGv3 25
5CS HJ1 -6.131 2.151 1.165 ETKDGv3 26
5CS HF -2.366 1.869 -0.261 ETKDGv3 27
5CS HX -1.362 -1.520 -1.332 ETKDGv3 28
5CS HD 0.319 0.894 -1.445 ETKDGv3 29
5CS HE3 -0.725 -0.152 1.204 ETKDGv3 30
5CS HE2 -0.332 1.541 0.697 ETKDGv3 31
5CS HXT 5.280 -0.849 -2.533 ETKDGv3 32
#