data_4GJ
#
_chem_comp.id 4GJ
_chem_comp.name 3-(pyridin-4-yldisulfanyl)-L-alanine
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C8 H10 N2 O2 S2"
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-03-17
_chem_comp.pdbx_modified_date 2015-07-10
_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 230.307
_chem_comp.one_letter_code C
_chem_comp.three_letter_code 4GJ
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4YT9
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
4GJ N5 N5 N 0 1 Y N N N N N 11.834 37.485 26.506 -4.105 1.490 -0.262 N5 4GJ 1
4GJ C1 C1 C 0 1 Y N N N N N 11.320 35.600 27.875 -3.072 -0.023 1.206 C1 4GJ 2
4GJ C2 C2 C 0 1 Y N N N N N 12.144 34.825 27.055 -2.082 -0.276 0.256 C2 4GJ 3
4GJ C3 C3 C 0 1 Y N N N N N 12.792 35.376 25.948 -2.151 0.396 -0.966 C3 4GJ 4
4GJ C4 C4 C 0 1 Y N N N N N 12.636 36.743 25.712 -3.187 1.278 -1.187 C4 4GJ 5
4GJ C6 C6 C 0 1 Y N N N N N 11.183 36.957 27.581 -4.075 0.874 0.905 C6 4GJ 6
4GJ S2 S2 S 0 1 N N N N N N 12.328 33.161 27.391 -0.778 -1.413 0.589 S2 4GJ 7
4GJ N N N 0 1 N N N N N N 15.311 33.167 31.561 2.000 -0.640 1.403 N 4GJ 8
4GJ CA CA C 0 1 N N R N N N 14.483 32.537 30.538 2.558 -0.335 0.079 CA 4GJ 9
4GJ C C C 0 1 N N N N N N 15.240 32.554 29.209 3.537 0.805 0.196 C 4GJ 10
4GJ O O O 0 1 N N N N N N 14.908 31.763 28.317 3.495 1.541 1.153 O 4GJ 11
4GJ CB CB C 0 1 N N N N N N 13.147 33.272 30.428 1.426 0.061 -0.872 CB 4GJ 12
4GJ SG SG S 0 1 N N N N N N 11.956 32.503 29.298 0.331 -1.361 -1.134 SG 4GJ 13
4GJ H1 H1 H 0 1 N N N N N N 10.803 35.160 28.715 -3.054 -0.524 2.162 H1 4GJ 14
4GJ H3 H3 H 0 1 N Y N N N N 13.395 34.764 25.294 -1.403 0.227 -1.727 H3 4GJ 15
4GJ H4 H4 H 0 1 N N N N N N 13.159 37.210 24.890 -3.249 1.803 -2.129 H4 4GJ 16
4GJ H6 H6 H 0 1 N N N N N N 10.564 37.587 28.203 -4.845 1.076 1.635 H6 4GJ 17
4GJ H H H 0 1 N N N N N N 14.824 33.161 32.435 1.410 0.111 1.729 H 4GJ 18
4GJ H2 H2 H 0 1 N Y N N N N 16.169 32.661 31.654 1.498 -1.515 1.392 H2 4GJ 19
4GJ HA HA H 0 1 N N N N N N 14.286 31.491 30.817 3.069 -1.215 -0.312 HA 4GJ 20
4GJ HB2 HB2 H 0 1 N N N N N N 13.346 34.294 30.074 0.857 0.882 -0.437 HB2 4GJ 21
4GJ HB3 HB3 H 0 1 N N N N N N 12.694 33.312 31.429 1.847 0.376 -1.827 HB3 4GJ 22
4GJ OXT OXT O 0 1 N Y N N N N 16.221 33.481 29.050 4.456 1.001 -0.763 OXT 4GJ 23
4GJ HXT HXT H 0 1 N Y N N N N 16.584 33.412 28.175 5.063 1.745 -0.643 HXT 4GJ 24
#
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
4GJ C4 C3 DOUB Y N 1
4GJ C4 N5 SING Y N 2
4GJ C3 C2 SING Y N 3
4GJ N5 C6 DOUB Y N 4
4GJ C2 S2 SING N N 5
4GJ C2 C1 DOUB Y N 6
4GJ S2 SG SING N N 7
4GJ C6 C1 SING Y N 8
4GJ O C DOUB N N 9
4GJ C CA SING N N 10
4GJ SG CB SING N N 11
4GJ CB CA SING N N 12
4GJ CA N SING N N 13
4GJ C1 H1 SING N N 14
4GJ C3 H3 SING N N 15
4GJ C4 H4 SING N N 16
4GJ C6 H6 SING N N 17
4GJ N H SING N N 18
4GJ N H2 SING N N 19
4GJ CA HA SING N N 20
4GJ CB HB2 SING N N 21
4GJ CB HB3 SING N N 22
4GJ C OXT SING N N 23
4GJ OXT HXT SING N N 24
#
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
4GJ SMILES ACDLabs 12.01 n1ccc(SSCC(N)C(O)=O)cc1
4GJ InChI InChI 1.03 InChI=1S/C8H10N2O2S2/c9-7(8(11)12)5-13-14-6-1-3-10-4-2-6/h1-4,7H,5,9H2,(H,11,12)/t7-/m0/s1
4GJ InChIKey InChI 1.03 KKZLPOFNAGBKFL-ZETCQYMHSA-N
4GJ SMILES_CANONICAL CACTVS 3.385 N[C@@H](CSSc1ccncc1)C(O)=O
4GJ SMILES CACTVS 3.385 N[CH](CSSc1ccncc1)C(O)=O
4GJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cnccc1SSC[C@@H](C(=O)O)N
4GJ SMILES "OpenEye OEToolkits" 1.7.6 c1cnccc1SSCC(C(=O)O)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
4GJ "SYSTEMATIC NAME" ACDLabs 12.01 3-(pyridin-4-yldisulfanyl)-L-alanine
4GJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-2-azanyl-3-(pyridin-4-yldisulfanyl)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
4GJ 'Create component' 2015-03-17 EBI
4GJ 'Other modification' 2015-03-18 EBI
4GJ 'Initial release' 2015-07-15 RCSB
#
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
4GJ N5 N 4.299 -5.340 1
4GJ C1 C 3.000 -3.090 2
4GJ C2 C 4.299 -2.340 3
4GJ C3 C 5.598 -3.090 4
4GJ C4 C 5.598 -4.590 5
4GJ C6 C 3.000 -4.590 6
4GJ S2 S 4.299 -0.840 7
4GJ N N 8.196 1.410 8
4GJ CA C 6.897 2.160 9
4GJ C C 6.897 3.660 10
4GJ O O 8.196 4.410 11
4GJ CB C 5.598 1.410 12
4GJ SG S 5.598 -0.090 13
4GJ OXT O 5.598 4.410 14
#
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
4GJ C4 C3 SINGLE NONE 1
4GJ C4 N5 DOUBLE NONE 2
4GJ C3 C2 DOUBLE NONE 3
4GJ N5 C6 SINGLE NONE 4
4GJ C2 S2 SINGLE NONE 5
4GJ C2 C1 SINGLE NONE 6
4GJ S2 SG SINGLE NONE 7
4GJ C6 C1 DOUBLE NONE 8
4GJ O C DOUBLE NONE 9
4GJ C CA SINGLE NONE 10
4GJ SG CB SINGLE NONE 11
4GJ CB CA SINGLE NONE 12
4GJ CA N SINGLE BEGINWEDGE 13
4GJ C OXT SINGLE NONE 14
#
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
4GJ MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
4GJ peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
4GJ pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
4GJ N5 S1 1
4GJ C1 S1 1
4GJ C2 S1 1
4GJ C3 S1 1
4GJ C4 S1 1
4GJ C6 S1 1
4GJ O F1 1
4GJ C F1 1
4GJ CA F1 1
4GJ N F1 1
4GJ C4 F2 1
4GJ C3 F2 1
4GJ C2 F2 1
4GJ C1 F2 1
4GJ C6 F2 1
4GJ N5 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4GJ
_pdbe_chem_comp_rdkit_properties.exactmw 230.018
_pdbe_chem_comp_rdkit_properties.amw 230.314
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 103.940
_pdbe_chem_comp_rdkit_properties.tpsa 76.210
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.126
_pdbe_chem_comp_rdkit_properties.CrippenMR 58.733
_pdbe_chem_comp_rdkit_properties.chi0v 8.160
_pdbe_chem_comp_rdkit_properties.chi1v 5.304
_pdbe_chem_comp_rdkit_properties.chi2v 2.638
_pdbe_chem_comp_rdkit_properties.chi3v 2.638
_pdbe_chem_comp_rdkit_properties.chi4v 1.726
_pdbe_chem_comp_rdkit_properties.chi0n 16.527
_pdbe_chem_comp_rdkit_properties.chi1n 7.957
_pdbe_chem_comp_rdkit_properties.chi2n 0.907
_pdbe_chem_comp_rdkit_properties.chi3n 0.907
_pdbe_chem_comp_rdkit_properties.chi4n 0.402
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.720
_pdbe_chem_comp_rdkit_properties.kappa1 3.695
_pdbe_chem_comp_rdkit_properties.kappa2 5.895
_pdbe_chem_comp_rdkit_properties.kappa3 3.992
_pdbe_chem_comp_rdkit_properties.Phi 1.556
#
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
4GJ UniChem PDBe 4GJ
4GJ UniChem ZINC ZINC000263620650
4GJ UniChem PubChem 137348240
#
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
4GJ N5 4.106 1.240 -0.318 ETKDGv3 1
4GJ C1 3.388 -1.053 -0.194 ETKDGv3 2
4GJ C2 2.180 -0.668 -0.953 ETKDGv3 3
4GJ C3 2.022 0.603 -1.345 ETKDGv3 4
4GJ C4 3.053 1.600 -0.994 ETKDGv3 5
4GJ C6 4.301 -0.121 0.104 ETKDGv3 6
4GJ S2 0.953 -1.906 -1.367 ETKDGv3 7
4GJ N -3.040 -1.395 1.398 ETKDGv3 8
4GJ CA -2.306 -0.202 0.968 ETKDGv3 9
4GJ C -3.254 0.864 0.486 ETKDGv3 10
4GJ O -4.014 0.646 -0.496 ETKDGv3 11
4GJ CB -1.294 -0.559 -0.128 ETKDGv3 12
4GJ SG -0.036 -1.713 0.514 ETKDGv3 13
4GJ H1 3.531 -2.078 0.123 ETKDGv3 14
4GJ H3 1.154 0.905 -1.917 ETKDGv3 15
4GJ H4 2.935 2.631 -1.299 ETKDGv3 16
4GJ H6 5.188 -0.388 0.662 ETKDGv3 17
4GJ H -3.687 -1.128 2.176 ETKDGv3 18
4GJ H2 -3.628 -1.749 0.608 ETKDGv3 19
4GJ HA -1.744 0.200 1.840 ETKDGv3 20
4GJ HB2 -1.815 -1.024 -0.992 ETKDGv3 21
4GJ HB3 -0.786 0.367 -0.473 ETKDGv3 22
4GJ OXT -3.288 2.099 1.127 ETKDGv3 23
4GJ HXT -3.918 2.829 0.815 ETKDGv3 24
#