data_CME
#
_chem_comp.id CME
_chem_comp.name 'S,S-(2-HYDROXYETHYL)THIOCYSTEINE'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H11 N O3 S2'
_chem_comp.mon_nstd_parent_comp_id CYS
_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 197.276
_chem_comp.one_letter_code C
_chem_comp.three_letter_code CME
_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 1A2T
_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
CME N N N 0 1 N N N Y Y N 12.745 20.633 16.161 1.971 -0.433 -2.743 N CME 1
CME CA CA C 0 1 N N R Y N N 13.954 21.227 15.576 0.756 -0.389 -1.917 CA CME 2
CME CB CB C 0 1 N N N N N N 13.574 22.221 14.477 0.972 0.568 -0.744 CB CME 3
CME SG SG S 0 1 N N N N N N 12.498 23.604 15.025 -0.538 0.649 0.255 SG CME 4
CME SD SD S 0 1 N N N N N N 11.608 24.197 13.291 -0.423 -1.155 1.221 SD CME 5
CME CE CE C 0 1 N N N N N N 10.047 23.245 13.216 0.512 -0.664 2.695 CE CME 6
CME CZ CZ C 0 1 N N N N N N 10.187 21.756 13.485 -0.268 0.403 3.463 CZ CME 7
CME OH OH O 0 1 N N N N N N 11.163 21.073 12.700 0.468 0.790 4.625 OH CME 8
CME C C C 0 1 N N N Y N Y 14.755 21.991 16.621 -0.401 0.091 -2.753 C CME 9
CME O O O 0 1 N N N Y N Y 14.227 22.357 17.675 -0.208 0.851 -3.672 O CME 10
CME OXT OXT O 0 1 N Y N Y N Y 16.026 22.236 16.327 -1.647 -0.324 -2.476 OXT CME 11
CME H 1HN H 0 1 N N N Y Y N 12.359 21.073 16.951 2.718 -0.749 -2.143 H CME 12
CME H2 2HN H 0 1 N Y N Y Y N 12.147 20.207 15.452 2.185 0.519 -2.995 H2 CME 13
CME HA HA H 0 1 N N N Y N N 14.565 20.389 15.165 0.540 -1.387 -1.536 HA CME 14
CME HB2 1HB H 0 1 N N N N N N 14.490 22.618 13.982 1.796 0.209 -0.128 HB2 CME 15
CME HB3 2HB H 0 1 N N N N N N 13.106 21.685 13.617 1.209 1.562 -1.125 HB3 CME 16
CME HE2 1HE H 0 1 N N N N N N 9.291 23.690 13.904 0.665 -1.533 3.335 HE2 CME 17
CME HE3 2HE H 0 1 N N N N N N 9.541 23.412 12.236 1.479 -0.260 2.394 HE3 CME 18
CME HZ2 1HZ H 0 1 N N N N N N 10.382 21.582 14.569 -0.421 1.272 2.824 HZ2 CME 19
CME HZ3 2HZ H 0 1 N N N N N N 9.196 21.255 13.378 -1.235 -0.000 3.765 HZ3 CME 20
CME HH HO H 0 1 N N N N N N 11.250 20.142 12.868 -0.057 1.462 5.079 HH CME 21
CME HXT HXT H 0 1 N Y N Y N Y 16.525 22.712 16.979 -2.390 -0.015 -3.012 HXT CME 22
#
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
CME N CA SING N N 1
CME N H SING N N 2
CME N H2 SING N N 3
CME CA CB SING N N 4
CME CA C SING N N 5
CME CA HA SING N N 6
CME CB SG SING N N 7
CME CB HB2 SING N N 8
CME CB HB3 SING N N 9
CME SG SD SING N N 10
CME SD CE SING N N 11
CME CE CZ SING N N 12
CME CE HE2 SING N N 13
CME CE HE3 SING N N 14
CME CZ OH SING N N 15
CME CZ HZ2 SING N N 16
CME CZ HZ3 SING N N 17
CME OH HH SING N N 18
CME C O DOUB N N 19
CME C OXT SING N N 20
CME OXT HXT SING N N 21
#
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
CME SMILES ACDLabs 10.04 'O=C(O)C(N)CSSCCO'
CME SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CSSCCO)C(O)=O'
CME SMILES CACTVS 3.341 'N[CH](CSSCCO)C(O)=O'
CME SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(CSSC[C@@H](C(=O)O)N)O'
CME SMILES 'OpenEye OEToolkits' 1.5.0 'C(CSSCC(C(=O)O)N)O'
CME InChI InChI 1.03 'InChI=1S/C5H11NO3S2/c6-4(5(8)9)3-11-10-2-1-7/h4,7H,1-3,6H2,(H,8,9)/t4-/m0/s1'
CME InChIKey InChI 1.03 YPUBRSXDQSFQBA-BYPYZUCNSA-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
CME 'SYSTEMATIC NAME' ACDLabs 10.04 '3-[(2-hydroxyethyl)disulfanyl]-L-alanine'
CME 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-amino-3-(2-hydroxyethyldisulfanyl)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
CME 'Create component' 1999-07-08 RCSB
CME 'Modify descriptor' 2011-06-04 RCSB
CME 'Modify backbone' 2023-11-03 PDBE
CME 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CME
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type Beta-mercaptoethanol
_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 ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1A2T
#
_pdbe_chem_comp_drugbank_details.comp_id CME
_pdbe_chem_comp_drugbank_details.drugbank_id DB04530
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name S,S-(2-Hydroxyethyl)Thiocysteine
_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 CME
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04530
_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_
_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
CME DB04530 'Thymidylate synthase' 'Escherichia coli (strain K12)' P0A884 unknown 1
CME DB04530 "cAMP-specific 3',5'-cyclic phosphodiesterase 4B" Humans Q07343 unknown 2
CME DB04530 'Thymidylate synthase' Humans P04818 unknown 3
CME DB04530 'cAMP-dependent protein kinase catalytic subunit alpha' Humans P17612 unknown 4
CME DB04530 'Serine/threonine-protein kinase pim-1' Humans P11309 unknown 5
CME DB04530 Arginase-1 Humans P05089 unknown 6
CME DB04530 Beta-galactosidase 'Escherichia coli (strain K12)' P00722 unknown 7
CME DB04530 'Isocitrate dehydrogenase [NADP]' 'Bacillus subtilis (strain 168)' P39126 unknown 8
CME DB04530 'Serpin B5' Humans P36952 unknown 9
CME DB04530 'Maltose-binding periplasmic protein' 'Escherichia coli (strain K12)' P0AEX9 unknown 10
CME DB04530 'Delta-aminolevulinic acid dehydratase' 'Escherichia coli (strain K12)' P0ACB2 unknown 11
CME DB04530 'dTDP-4-dehydrorhamnose 3,5-epimerase' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WH11 unknown 12
CME DB04530 "Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B" Humans Q01064 unknown 13
CME DB04530 'Sorting nexin-3' Humans O60493 unknown 14
CME DB04530 'Transcription antiterminator LicT' 'Bacillus subtilis (strain 168)' P39805 unknown 15
CME DB04530 Cytohesin-2 Humans Q99418 unknown 16
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
CME N N 5.598 3.465 1
CME CA C 6.897 2.715 2
CME CB C 6.897 1.215 3
CME SG S 5.598 0.465 4
CME SD S 5.598 -1.035 5
CME CE C 4.299 -1.785 6
CME CZ C 4.299 -3.285 7
CME OH O 3.000 -4.035 8
CME C C 8.196 3.465 9
CME O O 9.495 2.715 10
CME OXT O 8.196 4.965 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
CME CA N SINGLE BEGINDASH 1
CME CA CB SINGLE NONE 2
CME CA C SINGLE NONE 3
CME CB SG SINGLE NONE 4
CME SG SD SINGLE NONE 5
CME SD CE SINGLE NONE 6
CME CE CZ SINGLE NONE 7
CME CZ OH SINGLE NONE 8
CME C O DOUBLE NONE 9
CME C OXT SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id CME
_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
CME O F1 1
CME C F1 1
CME CA F1 1
CME N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CME
_pdbe_chem_comp_rdkit_properties.exactmw 197.018
_pdbe_chem_comp_rdkit_properties.amw 197.281
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 88.679
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.228
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.613
_pdbe_chem_comp_rdkit_properties.chi0v 6.621
_pdbe_chem_comp_rdkit_properties.chi1v 4.311
_pdbe_chem_comp_rdkit_properties.chi2v 1.733
_pdbe_chem_comp_rdkit_properties.chi3v 1.733
_pdbe_chem_comp_rdkit_properties.chi4v 1.008
_pdbe_chem_comp_rdkit_properties.chi0n 15.988
_pdbe_chem_comp_rdkit_properties.chi1n 7.372
_pdbe_chem_comp_rdkit_properties.chi2n 0.457
_pdbe_chem_comp_rdkit_properties.chi3n 0.457
_pdbe_chem_comp_rdkit_properties.chi4n 0.140
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.090
_pdbe_chem_comp_rdkit_properties.kappa1 2.538
_pdbe_chem_comp_rdkit_properties.kappa2 6.779
_pdbe_chem_comp_rdkit_properties.kappa3 6.486
_pdbe_chem_comp_rdkit_properties.Phi 1.564
#
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
CME UniChem DrugBank DB04530
CME UniChem PDBe CME
CME UniChem ChEBI 74104
CME UniChem fdasrs 7N9D5X3NW4
CME UniChem 'PubChem TPHARMA' 14968822
CME UniChem NMRShiftDB 60023639
CME UniChem ACTor 38254-63-6
CME UniChem MetaboLights MTBLC74104
CME UniChem 'Probes And Drugs' PD006026
CME UniChem PubChem 170018
CME UniChem SureChEMBL SCHEMBL177692
#
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
CME N -3.430 -0.815 0.422 ETKDGv3 1
CME CA -2.436 0.173 0.847 ETKDGv3 2
CME CB -1.084 -0.515 1.080 ETKDGv3 3
CME SG 0.111 0.638 1.840 ETKDGv3 4
CME SD 1.696 -0.791 1.829 ETKDGv3 5
CME CE 2.388 -0.174 0.261 ETKDGv3 6
CME CZ 3.619 -0.991 -0.122 ETKDGv3 7
CME OH 4.139 -0.542 -1.344 ETKDGv3 8
CME C -2.321 1.284 -0.165 ETKDGv3 9
CME O -1.954 1.036 -1.346 ETKDGv3 10
CME OXT -2.621 2.590 0.206 ETKDGv3 11
CME H -4.355 -0.336 0.317 ETKDGv3 12
CME H2 -3.167 -1.195 -0.517 ETKDGv3 13
CME HA -2.774 0.606 1.815 ETKDGv3 14
CME HB2 -1.226 -1.376 1.768 ETKDGv3 15
CME HB3 -0.681 -0.899 0.118 ETKDGv3 16
CME HE2 1.625 -0.258 -0.543 ETKDGv3 17
CME HE3 2.673 0.893 0.381 ETKDGv3 18
CME HZ2 3.332 -2.058 -0.232 ETKDGv3 19
CME HZ3 4.391 -0.921 0.677 ETKDGv3 20
CME HH 4.624 0.303 -1.152 ETKDGv3 21
CME HXT -2.547 3.350 -0.460 ETKDGv3 22
#