data_OSS
#
_chem_comp.id OSS
_chem_comp.name "6-(HYDROXYETHYLDITHIO)-8-(AMINOMETHYLTHIO)OCTANOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H23 N O3 S3"
_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 2011-06-04
_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 313.500
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OSS
_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 1HTP
_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
OSS C1 C1 C 0 1 N N N N N N -6.708 26.046 -4.312 0.569 -0.341 -6.068 C1 OSS 1
OSS O1 O1 O 0 1 N N N N N N -5.738 26.217 -5.054 -0.207 0.552 -6.307 O1 OSS 2
OSS O2 O2 O 0 1 N Y N N N N -7.921 26.437 -4.667 1.164 -1.000 -7.075 O2 OSS 3
OSS C2 C2 C 0 1 N N N N N N -6.618 25.389 -2.933 0.870 -0.716 -4.640 C2 OSS 4
OSS C3 C3 C 0 1 N N N N N N -5.886 24.049 -2.827 0.067 0.181 -3.697 C3 OSS 5
OSS C4 C4 C 0 1 N N N N N N -6.597 23.197 -1.790 0.373 -0.199 -2.247 C4 OSS 6
OSS C5 C5 C 0 1 N N N N N N -6.077 23.494 -0.403 -0.429 0.699 -1.304 C5 OSS 7
OSS C6 C6 C 0 1 N N S N N N -6.846 22.832 0.738 -0.224 0.235 0.139 C6 OSS 8
OSS C7 C7 C 0 1 N N N N N N -6.734 21.316 0.666 1.237 0.447 0.539 C7 OSS 9
OSS C8 C8 C 0 1 N N N N N N -7.432 20.491 1.760 1.443 -0.015 1.983 C8 OSS 10
OSS S9 S9 S 0 1 N N N N N N -7.540 18.685 1.471 3.175 0.235 2.457 S9 OSS 11
OSS C10 C10 C 0 1 N N N N N N -6.820 18.077 3.013 3.128 -0.382 4.162 C10 OSS 12
OSS N11 N11 N 0 1 N N N N N N -5.443 17.639 2.874 4.465 -0.271 4.761 N11 OSS 13
OSS S12 S12 S 0 1 N N N N N N -6.194 23.374 2.326 -1.298 1.196 1.241 S12 OSS 14
OSS S13 S13 S 0 1 N N N N N N -5.644 25.328 2.465 -3.123 0.420 0.724 S13 OSS 15
OSS C14 C14 C 0 1 N N N N N N -3.885 25.384 2.089 -3.229 -0.951 1.907 C14 OSS 16
OSS C15 C15 C 0 1 N N N N N N -3.077 24.399 2.923 -3.168 -0.400 3.333 C15 OSS 17
OSS O16 O16 O 0 1 N N N N N N -3.246 24.582 4.328 -3.251 -1.481 4.265 O16 OSS 18
OSS HO2 HO2 H 0 1 N N N N N N -8.668 26.305 -4.095 0.971 -0.760 -7.991 HO2 OSS 19
OSS H21 1H2 H 0 1 N N N N N N -6.168 26.110 -2.211 1.935 -0.586 -4.447 H21 OSS 20
OSS H22 2H2 H 0 1 N N N N N N -7.644 25.280 -2.510 0.595 -1.757 -4.472 H22 OSS 21
OSS H31 1H3 H 0 1 N N N N N N -5.788 23.534 -3.811 -0.997 0.051 -3.890 H31 OSS 22
OSS H32 2H3 H 0 1 N N N N N N -4.798 24.169 -2.610 0.342 1.222 -3.865 H32 OSS 23
OSS H41 1H4 H 0 1 N N N N N N -7.704 23.313 -1.849 1.438 -0.068 -2.054 H41 OSS 24
OSS H42 2H4 H 0 1 N N N N N N -6.529 22.110 -2.032 0.098 -1.240 -2.079 H42 OSS 25
OSS H51 1H5 H 0 1 N N N N N N -4.994 23.234 -0.336 -1.488 0.638 -1.557 H51 OSS 26
OSS H52 2H5 H 0 1 N N N N N N -6.025 24.596 -0.241 -0.090 1.729 -1.406 H52 OSS 27
OSS H6 H6 H 0 1 N N N N N N -7.915 23.129 0.638 -0.473 -0.822 0.220 H6 OSS 28
OSS H71 1H7 H 0 1 N N N N N N -7.085 20.969 -0.334 1.486 1.505 0.458 H71 OSS 29
OSS H72 2H7 H 0 1 N N N N N N -5.657 21.029 0.622 1.882 -0.129 -0.122 H72 OSS 30
OSS H81 1H8 H 0 1 N N N N N N -6.947 20.686 2.745 1.193 -1.073 2.064 H81 OSS 31
OSS H82 2H8 H 0 1 N N N N N N -8.450 20.903 1.950 0.797 0.561 2.645 H82 OSS 32
OSS H101 1H10 H 0 0 N N N N N N -6.912 18.840 3.820 2.815 -1.426 4.162 H101 OSS 33
OSS H102 2H10 H 0 0 N N N N N N -7.449 17.267 3.451 2.419 0.208 4.743 H102 OSS 34
OSS HN11 1HN1 H 0 0 N N N N N N -5.036 17.295 3.744 4.391 -0.624 5.703 HN11 OSS 35
OSS HN12 2HN1 H 0 0 N N N N N N -4.866 18.379 2.473 5.061 -0.910 4.258 HN12 OSS 36
OSS H141 1H14 H 0 0 N N N N N N -3.703 25.230 0.999 -4.168 -1.484 1.763 H141 OSS 37
OSS H142 2H14 H 0 0 N N N N N N -3.485 26.419 2.193 -2.395 -1.634 1.746 H142 OSS 38
OSS H151 1H15 H 0 0 N N N N N N -3.306 23.348 2.629 -2.228 0.132 3.478 H151 OSS 39
OSS H152 2H15 H 0 0 N N N N N N -1.997 24.435 2.645 -4.002 0.282 3.494 H152 OSS 40
OSS HO6 HO6 H 0 1 N N N N N N -2.741 23.967 4.848 -3.210 -1.091 5.149 HO6 OSS 41
#
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
OSS C1 O1 DOUB N N 1
OSS C1 O2 SING N N 2
OSS C1 C2 SING N N 3
OSS O2 HO2 SING N N 4
OSS C2 C3 SING N N 5
OSS C2 H21 SING N N 6
OSS C2 H22 SING N N 7
OSS C3 C4 SING N N 8
OSS C3 H31 SING N N 9
OSS C3 H32 SING N N 10
OSS C4 C5 SING N N 11
OSS C4 H41 SING N N 12
OSS C4 H42 SING N N 13
OSS C5 C6 SING N N 14
OSS C5 H51 SING N N 15
OSS C5 H52 SING N N 16
OSS C6 C7 SING N N 17
OSS C6 S12 SING N N 18
OSS C6 H6 SING N N 19
OSS C7 C8 SING N N 20
OSS C7 H71 SING N N 21
OSS C7 H72 SING N N 22
OSS C8 S9 SING N N 23
OSS C8 H81 SING N N 24
OSS C8 H82 SING N N 25
OSS S9 C10 SING N N 26
OSS C10 N11 SING N N 27
OSS C10 H101 SING N N 28
OSS C10 H102 SING N N 29
OSS N11 HN11 SING N N 30
OSS N11 HN12 SING N N 31
OSS S12 S13 SING N N 32
OSS S13 C14 SING N N 33
OSS C14 C15 SING N N 34
OSS C14 H141 SING N N 35
OSS C14 H142 SING N N 36
OSS C15 O16 SING N N 37
OSS C15 H151 SING N N 38
OSS C15 H152 SING N N 39
OSS O16 HO6 SING N N 40
#
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
OSS SMILES ACDLabs 10.04 O=C(O)CCCCC(SSCCO)CCSCN
OSS SMILES_CANONICAL CACTVS 3.341 NCSCC[C@H](CCCCC(O)=O)SSCCO
OSS SMILES CACTVS 3.341 NCSCC[CH](CCCCC(O)=O)SSCCO
OSS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CCC(=O)O)C[C@@H](CCSCN)SSCCO
OSS SMILES "OpenEye OEToolkits" 1.5.0 C(CCC(=O)O)CC(CCSCN)SSCCO
OSS InChI InChI 1.03 InChI=1S/C11H23NO3S3/c12-9-16-7-5-10(18-17-8-6-13)3-1-2-4-11(14)15/h10,13H,1-9,12H2,(H,14,15)/t10-/m0/s1
OSS InChIKey InChI 1.03 BFRWEULQQALYNZ-JTQLQIEISA-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
OSS "SYSTEMATIC NAME" ACDLabs 10.04 "(6S)-8-[(aminomethyl)sulfanyl]-6-[(2-hydroxyethyl)disulfanyl]octanoic acid"
OSS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(6S)-8-(aminomethylsulfanyl)-6-(2-hydroxyethyldisulfanyl)octanoic 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
OSS 'Create component' 1999-07-08 RCSB
OSS 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id OSS
_pdbe_chem_comp_drugbank_details.drugbank_id DB03187
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '6-(Hydroxyethyldithio)-8-(Aminomethylthio)Octanoic 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_drugbank_classification.comp_id OSS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03187
_pdbe_chem_comp_drugbank_classification.parent 'Medium-chain fatty acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Fatty Acyls'
_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 medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id OSS
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03187
_pdbe_chem_comp_drugbank_targets.name 'Glycine cleavage system H protein, mitochondrial'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P23434
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
OSS C1 C 16.796 2.857 1
OSS O1 O 18.095 2.107 2
OSS O2 O 16.796 4.357 3
OSS C2 C 15.497 2.107 4
OSS C3 C 14.198 2.857 5
OSS C4 C 12.899 2.107 6
OSS C5 C 11.600 2.857 7
OSS C6 C 10.301 2.107 8
OSS C7 C 10.301 0.608 9
OSS C8 C 9.002 -0.142 10
OSS S9 S 9.002 -1.643 11
OSS C10 C 7.702 -2.393 12
OSS N11 N 7.702 -3.893 13
OSS S12 S 9.002 2.857 14
OSS S13 S 7.702 2.107 15
OSS C14 C 6.404 2.857 16
OSS C15 C 5.104 2.107 17
OSS O16 O 3.805 2.857 18
#
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
OSS C1 O1 DOUBLE NONE 1
OSS C1 O2 SINGLE NONE 2
OSS C1 C2 SINGLE NONE 3
OSS C2 C3 SINGLE NONE 4
OSS C3 C4 SINGLE NONE 5
OSS C4 C5 SINGLE NONE 6
OSS C6 C5 SINGLE BEGINWEDGE 7
OSS C6 C7 SINGLE NONE 8
OSS C6 S12 SINGLE NONE 9
OSS C7 C8 SINGLE NONE 10
OSS C8 S9 SINGLE NONE 11
OSS S9 C10 SINGLE NONE 12
OSS C10 N11 SINGLE NONE 13
OSS S12 S13 SINGLE NONE 14
OSS S13 C14 SINGLE NONE 15
OSS C14 C15 SINGLE NONE 16
OSS C15 O16 SINGLE NONE 17
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id OSS
_pdbe_chem_comp_rdkit_properties.exactmw 313.084
_pdbe_chem_comp_rdkit_properties.amw 313.510
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 15
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 41
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.909
_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 153.852
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.413
_pdbe_chem_comp_rdkit_properties.CrippenMR 83.156
_pdbe_chem_comp_rdkit_properties.chi0v 10.846
_pdbe_chem_comp_rdkit_properties.chi1v 6.785
_pdbe_chem_comp_rdkit_properties.chi2v 2.789
_pdbe_chem_comp_rdkit_properties.chi3v 2.789
_pdbe_chem_comp_rdkit_properties.chi4v 1.752
_pdbe_chem_comp_rdkit_properties.chi0n 31.397
_pdbe_chem_comp_rdkit_properties.chi1n 15.030
_pdbe_chem_comp_rdkit_properties.chi2n 0.873
_pdbe_chem_comp_rdkit_properties.chi3n 0.873
_pdbe_chem_comp_rdkit_properties.chi4n 0.417
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.440
_pdbe_chem_comp_rdkit_properties.kappa1 3.430
_pdbe_chem_comp_rdkit_properties.kappa2 13.862
_pdbe_chem_comp_rdkit_properties.kappa3 12.886
_pdbe_chem_comp_rdkit_properties.Phi 2.641
#
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
OSS UniChem DrugBank DB03187
OSS UniChem PDBe OSS
OSS UniChem ZINC ZINC000005975463
OSS UniChem PubChem 5289084
OSS UniChem 'Probes And Drugs' PD059964
#
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
OSS C1 5.070 -0.732 0.275 ETKDGv3 1
OSS O1 5.886 -1.258 -0.529 ETKDGv3 2
OSS O2 5.538 -0.046 1.391 ETKDGv3 3
OSS C2 3.601 -0.805 0.007 ETKDGv3 4
OSS C3 3.142 0.422 -0.792 ETKDGv3 5
OSS C4 1.665 0.337 -1.206 ETKDGv3 6
OSS C5 0.706 0.475 -0.010 ETKDGv3 7
OSS C6 -0.765 0.649 -0.438 ETKDGv3 8
OSS C7 -1.327 -0.528 -1.272 ETKDGv3 9
OSS C8 -1.210 -1.896 -0.589 ETKDGv3 10
OSS S9 -2.057 -3.160 -1.599 ETKDGv3 11
OSS C10 -1.737 -4.562 -0.465 ETKDGv3 12
OSS N11 -2.796 -4.679 0.532 ETKDGv3 13
OSS S12 -1.787 0.928 1.060 ETKDGv3 14
OSS S13 -3.328 2.004 0.038 ETKDGv3 15
OSS C14 -2.606 3.646 0.377 ETKDGv3 16
OSS C15 -2.941 4.101 1.797 ETKDGv3 17
OSS O16 -2.445 5.392 2.021 ETKDGv3 18
OSS HO2 6.531 0.026 1.578 ETKDGv3 19
OSS H21 3.374 -1.735 -0.559 ETKDGv3 20
OSS H22 3.067 -0.851 0.980 ETKDGv3 21
OSS H31 3.316 1.347 -0.200 ETKDGv3 22
OSS H32 3.754 0.496 -1.719 ETKDGv3 23
OSS H41 1.462 1.159 -1.927 ETKDGv3 24
OSS H42 1.489 -0.626 -1.732 ETKDGv3 25
OSS H51 1.001 1.373 0.577 ETKDGv3 26
OSS H52 0.802 -0.402 0.664 ETKDGv3 27
OSS H6 -0.818 1.564 -1.066 ETKDGv3 28
OSS H71 -0.809 -0.566 -2.254 ETKDGv3 29
OSS H72 -2.398 -0.328 -1.490 ETKDGv3 30
OSS H81 -1.673 -1.859 0.418 ETKDGv3 31
OSS H82 -0.142 -2.181 -0.492 ETKDGv3 32
OSS H101 -1.706 -5.495 -1.065 ETKDGv3 33
OSS H102 -0.754 -4.456 0.041 ETKDGv3 34
OSS HN11 -3.713 -4.751 0.034 ETKDGv3 35
OSS HN12 -2.818 -3.805 1.104 ETKDGv3 36
OSS H141 -1.505 3.624 0.229 ETKDGv3 37
OSS H142 -3.037 4.369 -0.347 ETKDGv3 38
OSS H151 -2.520 3.391 2.544 ETKDGv3 39
OSS H152 -4.044 4.120 1.925 ETKDGv3 40
OSS HO6 -1.466 5.300 2.159 ETKDGv3 41
#