data_GEM
#
_chem_comp.id GEM
_chem_comp.name "(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H13 N3 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "2-GUANIDINOETHYLTHIO)SUCCINIC ACID; GUANIDINOETHYL MERCAPTOSUCCINIC ACID; GEMSA"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-02-12
_chem_comp.pdbx_modified_date 2020-06-17
_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 235.261
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GEM
_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 1H8L
_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
GEM C8 C8 C 0 1 N N S N N N 7.010 32.256 20.766 -0.546 0.368 -1.805 C8 GEM 1
GEM S7 S7 S 0 1 N N N N N N 7.536 33.222 19.333 0.462 -0.445 -0.537 S7 GEM 2
GEM C6 C6 C 0 1 N N N N N N 9.318 33.225 19.550 -0.240 0.307 0.955 C6 GEM 3
GEM C5 C5 C 0 1 N N N N N N 9.974 32.223 18.611 0.475 -0.243 2.190 C5 GEM 4
GEM N3 N3 N 0 1 N N N N N N 10.142 30.916 19.230 -0.092 0.364 3.396 N3 GEM 5
GEM C1 C1 C 0 1 N N N N N N 10.299 29.781 18.556 0.395 0.019 4.634 C1 GEM 6
GEM N4 N4 N 0 1 N N N N N N 10.299 29.775 17.232 -0.137 0.590 5.766 N4 GEM 7
GEM N2 N2 N 0 1 N N N N N N 10.484 28.650 19.214 1.362 -0.847 4.736 N2 GEM 8
GEM C9 C9 C 0 1 N N N N N N 5.525 31.902 20.656 -1.999 0.038 -1.579 C9 GEM 9
GEM O14 O14 O 0 1 N N N N N N 4.987 31.771 19.546 -2.410 -1.238 -1.609 O14 GEM 10
GEM O15 O15 O 0 1 N N N N N N 4.889 31.788 21.714 -2.795 0.924 -1.372 O15 GEM 11
GEM C10 C10 C 0 1 N N N N N N 7.294 32.938 22.123 -0.121 -0.124 -3.190 C10 GEM 12
GEM C11 C11 C 0 1 N N N N N N 6.348 34.076 22.423 1.331 0.205 -3.416 C11 GEM 13
GEM O12 O12 O 0 1 N N N N N N 6.852 35.111 22.866 1.962 0.776 -2.558 O12 GEM 14
GEM O13 O13 O 0 1 N N N N N N 5.110 33.924 22.349 1.925 -0.135 -4.571 O13 GEM 15
GEM HC8 8HC H 0 1 N N N N N N 7.582 31.299 20.749 -0.405 1.447 -1.745 HC8 GEM 16
GEM HC61 1HC6 H 0 0 N N N N N N 9.606 33.046 20.612 -1.302 0.071 1.016 HC61 GEM 17
GEM HC62 2HC6 H 0 0 N N N N N N 9.748 34.247 19.430 -0.110 1.388 0.913 HC62 GEM 18
GEM HC51 1HC5 H 0 0 N N N N N N 10.943 32.612 18.220 1.537 -0.007 2.130 HC51 GEM 19
GEM HC52 2HC5 H 0 0 N N N N N N 9.414 32.145 17.650 0.345 -1.325 2.233 HC52 GEM 20
GEM HN3 3HN H 0 1 N N N N N N 10.139 30.868 20.249 -0.812 1.009 3.320 HN3 GEM 21
GEM HN41 1HN4 H 0 0 N N N N N N 10.429 28.833 16.673 0.206 0.347 6.640 HN41 GEM 22
GEM HN42 2HN4 H 0 0 N N N N N N 10.145 30.719 16.683 -0.855 1.239 5.690 HN42 GEM 23
GEM HN21 1HN2 H 0 0 N N N N N N 9.799 28.089 18.706 1.738 -1.250 3.937 HN21 GEM 24
GEM HO41 1HO4 H 0 0 N N N N N N 4.065 31.551 19.477 -3.342 -1.450 -1.464 HO41 GEM 25
GEM H101 1H10 H 0 0 N N N N N N 8.355 33.276 22.184 -0.262 -1.203 -3.250 H101 GEM 26
GEM H102 2H10 H 0 0 N N N N N N 7.293 32.191 22.951 -0.727 0.364 -3.952 H102 GEM 27
GEM HO31 1HO3 H 0 0 N N N N N N 4.514 34.640 22.537 2.857 0.076 -4.716 HO31 GEM 28
#
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
GEM C8 S7 SING N N 1
GEM C8 C9 SING N N 2
GEM C8 C10 SING N N 3
GEM C8 HC8 SING N N 4
GEM S7 C6 SING N N 5
GEM C6 C5 SING N N 6
GEM C6 HC61 SING N N 7
GEM C6 HC62 SING N N 8
GEM C5 N3 SING N N 9
GEM C5 HC51 SING N N 10
GEM C5 HC52 SING N N 11
GEM N3 C1 SING N N 12
GEM N3 HN3 SING N N 13
GEM C1 N4 SING N N 14
GEM C1 N2 DOUB N N 15
GEM N4 HN41 SING N N 16
GEM N4 HN42 SING N N 17
GEM N2 HN21 SING N N 18
GEM C9 O14 SING N N 19
GEM C9 O15 DOUB N N 20
GEM O14 HO41 SING N N 21
GEM C10 C11 SING N N 22
GEM C10 H101 SING N N 23
GEM C10 H102 SING N N 24
GEM C11 O12 DOUB N N 25
GEM C11 O13 SING N N 26
GEM O13 HO31 SING N N 27
#
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
GEM SMILES ACDLabs 10.04 O=C(O)C(SCCNC(=[N@H])N)CC(=O)O
GEM SMILES_CANONICAL CACTVS 3.341 NC(=N)NCCS[C@@H](CC(O)=O)C(O)=O
GEM SMILES CACTVS 3.341 NC(=N)NCCS[CH](CC(O)=O)C(O)=O
GEM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CS[C@@H](CC(=O)O)C(=O)O)NC(=N)N
GEM SMILES "OpenEye OEToolkits" 1.5.0 C(CSC(CC(=O)O)C(=O)O)NC(=N)N
GEM InChI InChI 1.03 InChI=1S/C7H13N3O4S/c8-7(9)10-1-2-15-4(6(13)14)3-5(11)12/h4H,1-3H2,(H,11,12)(H,13,14)(H4,8,9,10)/t4-/m0/s1
GEM InChIKey InChI 1.03 VKVCLXDFOQQABP-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
GEM "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-[(2-carbamimidamidoethyl)sulfanyl]butanedioic acid"
GEM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-(2-carbamimidamidoethylsulfanyl)butanedioic 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
GEM 'Create component' 2001-02-12 RCSB
GEM 'Modify descriptor' 2011-06-04 RCSB
GEM 'Modify synonyms' 2020-06-05 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 GEM "2-GUANIDINOETHYLTHIO)SUCCINIC ACID" ? ?
2 GEM "GUANIDINOETHYL MERCAPTOSUCCINIC ACID" ? ?
3 GEM GEMSA ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id GEM
_pdbe_chem_comp_drugbank_details.drugbank_id DB04489
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Guanidinoethylmercaptosuccinic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 77482-44-1
_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
GEM '2-GUANIDINOETHYLTHIO)SUCCINIC ACID' wwPDB ?
GEM 'GUANIDINOETHYL MERCAPTOSUCCINIC ACID' wwPDB ?
GEM GEMSA wwPDB ?
GEM GEMSA DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GEM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04489
_pdbe_chem_comp_drugbank_classification.parent 'Thia 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 thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GEM
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04489
_pdbe_chem_comp_drugbank_targets.name 'Carboxypeptidase D'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id O75976
_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
GEM C8 C 7.702 2.715 1
GEM S7 S 7.702 1.215 2
GEM C6 C 6.404 0.465 3
GEM C5 C 6.404 -1.035 4
GEM N3 N 5.104 -1.785 5
GEM C1 C 5.104 -3.285 6
GEM N4 N 3.805 -4.035 7
GEM N2 N 6.404 -4.035 8
GEM C9 C 9.002 3.465 9
GEM O14 O 10.301 2.715 10
GEM O15 O 9.002 4.965 11
GEM C10 C 6.404 3.465 12
GEM C11 C 5.104 2.715 13
GEM O12 O 3.805 3.465 14
GEM O13 O 5.104 1.215 15
GEM HN21 H 7.703 -3.285 16
#
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
GEM C8 S7 SINGLE NONE 1
GEM C8 C9 SINGLE NONE 2
GEM C8 C10 SINGLE BEGINWEDGE 3
GEM S7 C6 SINGLE NONE 4
GEM C6 C5 SINGLE NONE 5
GEM C5 N3 SINGLE NONE 6
GEM N3 C1 SINGLE ENDUPRIGHT 7
GEM C1 N4 SINGLE ENDUPRIGHT 8
GEM C1 N2 DOUBLE NONE 9
GEM C9 O14 SINGLE NONE 10
GEM C9 O15 DOUBLE NONE 11
GEM C10 C11 SINGLE NONE 12
GEM C11 O12 DOUBLE NONE 13
GEM C11 O13 SINGLE NONE 14
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id GEM
_pdbe_chem_comp_rdkit_properties.exactmw 235.063
_pdbe_chem_comp_rdkit_properties.amw 235.265
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.571
_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 109.209
_pdbe_chem_comp_rdkit_properties.tpsa 136.500
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.869
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.051
_pdbe_chem_comp_rdkit_properties.chi0v 7.699
_pdbe_chem_comp_rdkit_properties.chi1v 3.936
_pdbe_chem_comp_rdkit_properties.chi2v 1.422
_pdbe_chem_comp_rdkit_properties.chi3v 1.422
_pdbe_chem_comp_rdkit_properties.chi4v 0.769
_pdbe_chem_comp_rdkit_properties.chi0n 19.883
_pdbe_chem_comp_rdkit_properties.chi1n 9.225
_pdbe_chem_comp_rdkit_properties.chi2n 0.756
_pdbe_chem_comp_rdkit_properties.chi3n 0.756
_pdbe_chem_comp_rdkit_properties.chi4n 0.358
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.440
_pdbe_chem_comp_rdkit_properties.kappa1 3.274
_pdbe_chem_comp_rdkit_properties.kappa2 6.932
_pdbe_chem_comp_rdkit_properties.kappa3 7.617
_pdbe_chem_comp_rdkit_properties.Phi 1.513
#
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
GEM UniChem DrugBank DB04489
GEM UniChem PDBe GEM
GEM UniChem ZINC ZINC000002384679
GEM UniChem SureChEMBL SCHEMBL601714
GEM UniChem 'Probes And Drugs' PD006185
GEM UniChem PubChem 446018
#
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
GEM C8 -1.907 0.232 -0.473 ETKDGv3 1
GEM S7 -0.245 0.987 -0.326 ETKDGv3 2
GEM C6 0.175 0.207 1.275 ETKDGv3 3
GEM C5 1.592 0.589 1.701 ETKDGv3 4
GEM N3 2.595 0.013 0.802 ETKDGv3 5
GEM C1 3.998 0.246 0.983 ETKDGv3 6
GEM N4 4.936 -0.340 0.077 ETKDGv3 7
GEM N2 4.417 0.984 1.963 ETKDGv3 8
GEM C9 -1.779 -1.215 -0.861 ETKDGv3 9
GEM O14 -2.372 -2.196 -0.072 ETKDGv3 10
GEM O15 -1.147 -1.543 -1.902 ETKDGv3 11
GEM C10 -2.728 1.013 -1.510 ETKDGv3 12
GEM C11 -4.146 0.532 -1.567 ETKDGv3 13
GEM O12 -4.991 0.955 -0.734 ETKDGv3 14
GEM O13 -4.519 -0.414 -2.517 ETKDGv3 15
GEM HC8 -2.422 0.308 0.510 ETKDGv3 16
GEM HC61 0.095 -0.898 1.199 ETKDGv3 17
GEM HC62 -0.540 0.562 2.048 ETKDGv3 18
GEM HC51 1.769 0.212 2.732 ETKDGv3 19
GEM HC52 1.690 1.696 1.711 ETKDGv3 20
GEM HN3 2.293 -0.592 0.005 ETKDGv3 21
GEM HN41 4.605 -0.935 -0.715 ETKDGv3 22
GEM HN42 5.962 -0.183 0.190 ETKDGv3 23
GEM HN21 5.434 1.169 2.116 ETKDGv3 24
GEM HO41 -2.299 -3.176 -0.320 ETKDGv3 25
GEM H101 -2.731 2.092 -1.240 ETKDGv3 26
GEM H102 -2.264 0.922 -2.517 ETKDGv3 27
GEM HO31 -5.470 -0.762 -2.558 ETKDGv3 28
#