data_GDS
#
_chem_comp.id GDS
_chem_comp.name 'OXIDIZED GLUTATHIONE DISULFIDE'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C20 H32 N6 O12 S2'
_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 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 612.631
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GDS
_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 2GRT
_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
GDS N1 N1 N 0 1 N N N N N N 65.119 36.708 23.105 -1.103 2.393 6.466 N1 GDS 1
GDS CA1 CA1 C 0 1 N N S N N N 65.667 37.980 22.521 -2.373 1.986 5.848 CA1 GDS 2
GDS C1 C1 C 0 1 N N N N N N 65.429 39.221 23.442 -3.436 1.876 6.911 C1 GDS 3
GDS OE1 OE1 O 0 1 N N N N N N 66.154 40.250 23.268 -3.132 1.571 8.040 OE1 GDS 4
GDS OE2 OE2 O 0 1 N N N N N N 64.524 39.129 24.338 -4.720 2.116 6.602 OE2 GDS 5
GDS CB1 CB1 C 0 1 N N N N N N 65.152 38.194 21.062 -2.195 0.631 5.162 CB1 GDS 6
GDS CG1 CG1 C 0 1 N N N N N N 63.701 37.681 20.780 -1.115 0.743 4.083 CG1 GDS 7
GDS CD1 CD1 C 0 1 N N N N N N 62.672 38.814 20.543 -0.940 -0.592 3.407 CD1 GDS 8
GDS O1 O1 O 0 1 N N N N N N 61.452 38.541 20.487 -1.612 -1.540 3.754 O1 GDS 9
GDS N2 N2 N 0 1 N N N N N N 63.212 39.959 20.100 -0.036 -0.733 2.417 N2 GDS 10
GDS CA2 CA2 C 0 1 N N R N N N 62.490 41.218 19.758 0.133 -2.031 1.760 CA2 GDS 11
GDS C2 C2 C 0 1 N N N N N N 61.339 41.758 20.630 1.182 -2.829 2.490 C2 GDS 12
GDS O2 O2 O 0 1 N N N N N N 60.812 42.848 20.327 1.122 -4.040 2.504 O2 GDS 13
GDS CB2 CB2 C 0 1 N N N N N N 61.997 41.201 18.290 0.573 -1.815 0.311 CB2 GDS 14
GDS SG2 SG2 S 0 1 N N N N N N 63.198 40.881 16.938 -0.689 -0.853 -0.567 SG2 GDS 15
GDS N3 N3 N 0 1 N N N N N N 60.817 40.917 21.525 2.189 -2.197 3.126 N3 GDS 16
GDS CA3 CA3 C 0 1 N N N N N N 59.709 41.310 22.385 3.209 -2.974 3.836 CA3 GDS 17
GDS C3 C3 C 0 1 N N N N N N 59.731 40.644 23.753 4.212 -2.036 4.456 C3 GDS 18
GDS OE3 OE3 O 0 1 N N N N N N 59.572 41.388 24.733 4.088 -0.842 4.320 OE3 GDS 19
GDS OE4 OE4 O 0 1 N N N N N N 59.911 39.405 23.856 5.244 -2.528 5.161 OE4 GDS 20
GDS N4 N4 N 0 1 N N N N N N 61.155 35.599 17.354 2.189 2.197 -3.126 N4 GDS 21
GDS CA4 CA4 C 0 1 N N N N N N 59.895 34.914 17.230 3.210 2.973 -3.835 CA4 GDS 22
GDS C4 C4 C 0 1 N N N N N N 59.646 34.251 18.564 4.213 2.035 -4.456 C4 GDS 23
GDS OE5 OE5 O 0 1 N N N N N N 59.569 32.999 18.602 4.088 0.841 -4.320 OE5 GDS 24
GDS OE6 OE6 O 0 1 N N N N N N 59.570 34.989 19.579 5.245 2.527 -5.160 OE6 GDS 25
GDS C5 C5 C 0 1 N N N N N N 62.004 35.659 16.340 1.183 2.829 -2.490 C5 GDS 26
GDS O5 O5 O 0 1 N N N N N N 62.042 34.825 15.428 1.123 4.040 -2.504 O5 GDS 27
GDS CA5 CA5 C 0 1 N N R N N N 63.252 36.404 16.720 0.134 2.031 -1.760 CA5 GDS 28
GDS N5 N5 N 0 1 N N N N N N 64.415 35.560 16.378 -0.036 0.733 -2.417 N5 GDS 29
GDS CB5 CB5 C 0 1 N N N N N N 63.267 37.846 16.128 0.573 1.815 -0.311 CB5 GDS 30
GDS SG5 SG5 S 0 1 N N N N N N 64.005 39.032 17.314 -0.689 0.854 0.566 SG5 GDS 31
GDS CA6 CA6 C 0 1 N N S N N N 68.697 35.063 17.021 -2.372 -1.986 -5.849 CA6 GDS 32
GDS C6 C6 C 0 1 N N N N N N 69.028 36.118 16.011 -3.435 -1.875 -6.911 C6 GDS 33
GDS OE7 OE7 O 0 1 N N N N N N 68.869 37.303 16.346 -3.132 -1.571 -8.040 OE7 GDS 34
GDS OE8 OE8 O 0 1 N N N N N N 69.480 35.752 14.916 -4.720 -2.115 -6.603 OE8 GDS 35
GDS N6 N6 N 0 1 N N N N N N 68.896 35.694 18.337 -1.103 -2.392 -6.466 N6 GDS 36
GDS CB6 CB6 C 0 1 N N N N N N 67.260 34.523 16.880 -2.194 -0.630 -5.162 CB6 GDS 37
GDS CG6 CG6 C 0 1 N N N N N N 66.533 34.794 15.556 -1.115 -0.742 -4.084 CG6 GDS 38
GDS CD6 CD6 C 0 1 N N N N N N 65.502 35.930 15.696 -0.940 0.592 -3.407 CD6 GDS 39
GDS O6 O6 O 0 1 N N N N N N 65.612 37.031 15.078 -1.612 1.540 -3.754 O6 GDS 40
GDS HN11 1HN1 H 0 0 N N N N N N 65.274 35.898 22.504 -0.402 2.353 5.742 HN11 GDS 41
GDS HN12 2HN1 H 0 0 N N N N N N 64.130 36.807 23.335 -0.866 1.678 7.138 HN12 GDS 42
GDS HA1 HA1 H 0 1 N N N N N N 66.775 37.869 22.464 -2.672 2.731 5.110 HA1 GDS 43
GDS HO2 HO2 H 0 1 N N N N N N 64.379 39.883 24.897 -5.402 2.045 7.284 HO2 GDS 44
GDS HB11 1HB1 H 0 0 N N N N N N 65.238 39.269 20.779 -1.895 -0.113 5.900 HB11 GDS 45
GDS HB12 2HB1 H 0 0 N N N N N N 65.865 37.741 20.334 -3.137 0.329 4.703 HB12 GDS 46
GDS HG11 1HG1 H 0 0 N N N N N N 63.697 36.962 19.927 -1.415 1.487 3.346 HG11 GDS 47
GDS HG12 2HG1 H 0 0 N N N N N N 63.358 37.003 21.596 -0.174 1.044 4.542 HG12 GDS 48
GDS HN2 HN2 H 0 1 N N N N N N 64.224 39.867 20.019 0.500 0.025 2.140 HN2 GDS 49
GDS HA2 HA2 H 0 1 N N N N N N 63.315 41.935 19.975 -0.811 -2.573 1.776 HA2 GDS 50
GDS HB21 1HB2 H 0 0 N N N N N N 61.160 40.469 18.203 1.518 -1.273 0.295 HB21 GDS 51
GDS HB22 2HB2 H 0 0 N N N N N N 61.471 42.161 18.079 0.700 -2.781 -0.177 HB22 GDS 52
GDS HN3 HN3 H 0 1 N N N N N N 61.254 39.995 21.551 2.237 -1.229 3.115 HN3 GDS 53
GDS HA31 1HA3 H 0 0 N N N N N N 59.665 42.419 22.488 2.735 -3.568 4.617 HA31 GDS 54
GDS HA32 2HA3 H 0 0 N N N N N N 58.733 41.131 21.876 3.716 -3.635 3.133 HA32 GDS 55
GDS HO4 HO4 H 0 1 N N N N N N 59.924 38.989 24.710 5.887 -1.926 5.559 HO4 GDS 56
GDS HN4 HN4 H 0 1 N N N N N N 61.462 36.067 18.206 2.238 1.228 -3.115 HN4 GDS 57
GDS HA41 1HA4 H 0 0 N N N N N N 59.060 35.575 16.900 2.736 3.568 -4.616 HA41 GDS 58
GDS HA42 2HA4 H 0 0 N N N N N N 59.856 34.207 16.368 3.717 3.634 -3.133 HA42 GDS 59
GDS HO6 HO6 H 0 1 N N N N N N 59.413 34.572 20.418 5.888 1.925 -5.558 HO6 GDS 60
GDS HA5 HA5 H 0 1 N N N N N N 63.294 36.585 17.819 -0.811 2.573 -1.776 HA5 GDS 61
GDS HN5 HN5 H 0 1 N N N N N N 64.476 34.579 16.652 0.501 -0.025 -2.140 HN5 GDS 62
GDS HB51 1HB5 H 0 0 N N N N N N 63.780 37.879 15.138 0.700 2.780 0.177 HB51 GDS 63
GDS HB52 2HB5 H 0 0 N N N N N N 62.250 38.168 15.802 1.519 1.272 -0.295 HB52 GDS 64
GDS HA6 HA6 H 0 1 N N N N N N 69.352 34.172 16.875 -2.672 -2.730 -5.111 HA6 GDS 65
GDS HO8 HO8 H 0 1 N N N N N N 69.690 36.421 14.275 -5.402 -2.044 -7.285 HO8 GDS 66
GDS HN61 1HN6 H 0 0 N N N N N N 68.670 34.975 19.024 -0.866 -1.678 -7.139 HN61 GDS 67
GDS HN62 2HN6 H 0 0 N N N N N N 68.367 36.557 18.460 -0.402 -2.353 -5.742 HN62 GDS 68
GDS HB61 1HB6 H 0 0 N N N N N N 67.254 33.427 17.087 -3.136 -0.328 -4.704 HB61 GDS 69
GDS HB62 2HB6 H 0 0 N N N N N N 66.639 34.898 17.726 -1.894 0.113 -5.900 HB62 GDS 70
GDS HG61 1HG6 H 0 0 N N N N N N 67.253 34.998 14.730 -0.173 -1.044 -4.542 HG61 GDS 71
GDS HG62 2HG6 H 0 0 N N N N N N 66.064 33.866 15.151 -1.415 -1.487 -3.346 HG62 GDS 72
#
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
GDS N1 CA1 SING N N 1
GDS N1 HN11 SING N N 2
GDS N1 HN12 SING N N 3
GDS CA1 C1 SING N N 4
GDS CA1 CB1 SING N N 5
GDS CA1 HA1 SING N N 6
GDS C1 OE1 DOUB N N 7
GDS C1 OE2 SING N N 8
GDS OE2 HO2 SING N N 9
GDS CB1 CG1 SING N N 10
GDS CB1 HB11 SING N N 11
GDS CB1 HB12 SING N N 12
GDS CG1 CD1 SING N N 13
GDS CG1 HG11 SING N N 14
GDS CG1 HG12 SING N N 15
GDS CD1 O1 DOUB N N 16
GDS CD1 N2 SING N N 17
GDS N2 CA2 SING N N 18
GDS N2 HN2 SING N N 19
GDS CA2 C2 SING N N 20
GDS CA2 CB2 SING N N 21
GDS CA2 HA2 SING N N 22
GDS C2 O2 DOUB N N 23
GDS C2 N3 SING N N 24
GDS CB2 SG2 SING N N 25
GDS CB2 HB21 SING N N 26
GDS CB2 HB22 SING N N 27
GDS SG2 SG5 SING N N 28
GDS N3 CA3 SING N N 29
GDS N3 HN3 SING N N 30
GDS CA3 C3 SING N N 31
GDS CA3 HA31 SING N N 32
GDS CA3 HA32 SING N N 33
GDS C3 OE3 DOUB N N 34
GDS C3 OE4 SING N N 35
GDS OE4 HO4 SING N N 36
GDS N4 CA4 SING N N 37
GDS N4 C5 SING N N 38
GDS N4 HN4 SING N N 39
GDS CA4 C4 SING N N 40
GDS CA4 HA41 SING N N 41
GDS CA4 HA42 SING N N 42
GDS C4 OE5 DOUB N N 43
GDS C4 OE6 SING N N 44
GDS OE6 HO6 SING N N 45
GDS C5 O5 DOUB N N 46
GDS C5 CA5 SING N N 47
GDS CA5 N5 SING N N 48
GDS CA5 CB5 SING N N 49
GDS CA5 HA5 SING N N 50
GDS N5 CD6 SING N N 51
GDS N5 HN5 SING N N 52
GDS CB5 SG5 SING N N 53
GDS CB5 HB51 SING N N 54
GDS CB5 HB52 SING N N 55
GDS CA6 C6 SING N N 56
GDS CA6 N6 SING N N 57
GDS CA6 CB6 SING N N 58
GDS CA6 HA6 SING N N 59
GDS C6 OE7 DOUB N N 60
GDS C6 OE8 SING N N 61
GDS OE8 HO8 SING N N 62
GDS N6 HN61 SING N N 63
GDS N6 HN62 SING N N 64
GDS CB6 CG6 SING N N 65
GDS CB6 HB61 SING N N 66
GDS CB6 HB62 SING N N 67
GDS CG6 CD6 SING N N 68
GDS CG6 HG61 SING N N 69
GDS CG6 HG62 SING N N 70
GDS CD6 O6 DOUB N N 71
#
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
GDS SMILES ACDLabs 10.04 'O=C(NC(C(=O)NCC(=O)O)CSSCC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N)CCC(C(=O)O)N'
GDS SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CCC(=O)N[C@@H](CSSC[C@H](NC(=O)CC[C@H](N)C(O)=O)C(=O)NCC(O)=O)C(=O)NCC(O)=O)C(O)=O'
GDS SMILES CACTVS 3.341 'N[CH](CCC(=O)N[CH](CSSC[CH](NC(=O)CC[CH](N)C(O)=O)C(=O)NCC(O)=O)C(=O)NCC(O)=O)C(O)=O'
GDS SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(=O)O)N)C(=O)NCC(=O)O)[C@@H](C(=O)O)N'
GDS SMILES 'OpenEye OEToolkits' 1.5.0 'C(CC(=O)NC(CSSCC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N)C(=O)NCC(=O)O)C(C(=O)O)N'
GDS InChI InChI 1.03 'InChI=1S/C20H32N6O12S2/c21-9(19(35)36)1-3-13(27)25-11(17(33)23-5-15(29)30)7-39-40-8-12(18(34)24-6-16(31)32)26-14(28)4-2-10(22)20(37)38/h9-12H,1-8,21-22H2,(H,23,33)(H,24,34)(H,25,27)(H,26,28)(H,29,30)(H,31,32)(H,35,36)(H,37,38)/t9-,10-,11-,12-/m0/s1'
GDS InChIKey InChI 1.03 YPZRWBKMTBYPTK-BJDJZHNGSA-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
GDS 'SYSTEMATIC NAME' ACDLabs 10.04
;(2S,2'S)-5,5'-[disulfanediylbis({(2R)-3-[(carboxymethyl)amino]-3-oxopropane-1,2-diyl}imino)]bis(2-amino-5-oxopentanoic acid) (non-preferred name)
;
GDS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-5-[[(2R)-3-[(2R)-2-[[(4S)-4-amino-5-hydroxy-5-oxo-pentanoyl]amino]-3-(carboxymethylamino)-3-oxo-propyl]disulfanyl-1-(carboxymethylamino)-1-oxo-propan-2-yl]amino]-5-oxo-pentanoic 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
GDS 'Create component' 1999-07-08 RCSB
GDS 'Modify descriptor' 2011-06-04 RCSB
GDS 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id GDS
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical 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 C2
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id GDS
_pdbe_chem_comp_drugbank_details.drugbank_id DB03310
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Glutathione disulfide'
_pdbe_chem_comp_drugbank_details.description
'A GLUTATHIONE dimer formed by a disulfide bond between the cysteine sulfhydryl side chains during the course of being oxidized.'
_pdbe_chem_comp_drugbank_details.cas_number 27025-41-8
_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
GDS 'Glutathione disulfide' DrugBank ?
GDS 'Glutathione disulphide' DrugBank ?
GDS GSSG DrugBank ?
GDS 'Oxidized glutathione' DrugBank ?
GDS Oxiglutatione DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GDS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03310
_pdbe_chem_comp_drugbank_classification.parent Peptides
_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 peptides. These are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.'
#
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
GDS DB03310 'Epididymal secretory glutathione peroxidase' Humans O75715 unknown 1
GDS DB03310 'Glutathione peroxidase 1' Humans P07203 unknown 2
GDS DB03310 'Glutathione peroxidase 2' Humans P18283 unknown 3
GDS DB03310 'Glutathione peroxidase 3' Humans P22352 unknown 4
GDS DB03310 'Glutathione peroxidase 6' Humans P59796 unknown 5
GDS DB03310 'Glutathione peroxidase 7' Humans Q96SL4 unknown 6
GDS DB03310 'Phospholipid hydroperoxide glutathione peroxidase GPX4' Humans P36969 unknown 7
GDS DB03310 'Probable glutathione peroxidase 8' Humans Q8TED1 unknown 8
GDS DB03310 'Microsomal glutathione S-transferase 1' Humans P10620 unknown 9
GDS DB03310 'Glutathione S-transferase A1' Humans P08263 unknown 10
GDS DB03310 'Glutathione S-transferase A2' Humans P09210 unknown 11
GDS DB03310 'Glutathione S-transferase Mu 1' Humans P09488 unknown 12
GDS DB03310 'Glutathione S-transferase Mu 2' Humans P28161 unknown 13
GDS DB03310 'Glutathione S-transferase Mu 3' Humans P21266 unknown 14
GDS DB03310 'Glutathione S-transferase Mu 4' Humans Q03013 unknown 15
GDS DB03310 'Glutathione S-transferase Mu 5' Humans P46439 unknown 16
GDS DB03310 'Glutathione S-transferase P' Humans P09211 unknown 17
GDS DB03310 'Glutathione S-transferase theta-1' Humans P30711 unknown 18
GDS DB03310 'Glutathione S-transferase theta-2' Humans P0CG29 unknown 19
GDS DB03310 'Glutathione S-transferase theta-2B' Humans P0CG30 unknown 20
GDS DB03310 'Hematopoietic prostaglandin D synthase' Humans O60760 unknown 21
GDS DB03310 'Glutathione S-transferase Mu 2' Humans P28161 unknown 22
GDS DB03310 'Glutathione reductase, mitochondrial' Humans P00390 unknown 23
#
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
GDS N1 N 6.404 8.107 1
GDS CA1 C 6.404 6.607 2
GDS C1 C 5.104 5.857 3
GDS OE1 O 3.805 6.607 4
GDS OE2 O 5.104 4.357 5
GDS CB1 C 7.702 5.857 6
GDS CG1 C 9.002 6.607 7
GDS CD1 C 10.301 5.857 8
GDS O1 O 10.301 4.357 9
GDS N2 N 11.600 6.607 10
GDS CA2 C 12.899 5.857 11
GDS C2 C 14.198 6.607 12
GDS O2 O 14.198 8.107 13
GDS CB2 C 12.899 4.357 14
GDS SG2 S 11.600 3.607 15
GDS N3 N 15.497 5.857 16
GDS CA3 C 16.796 6.607 17
GDS C3 C 18.095 5.857 18
GDS OE3 O 19.394 6.607 19
GDS OE4 O 18.095 4.357 20
GDS N4 N 7.702 -0.142 21
GDS CA4 C 6.404 -0.892 22
GDS C4 C 5.104 -0.142 23
GDS OE5 O 3.805 -0.892 24
GDS OE6 O 5.104 1.357 25
GDS C5 C 9.002 -0.892 26
GDS O5 O 9.002 -2.393 27
GDS CA5 C 10.301 -0.142 28
GDS N5 N 11.600 -0.892 29
GDS CB5 C 10.301 1.357 30
GDS SG5 S 11.600 2.107 31
GDS CA6 C 14.198 -5.393 32
GDS C6 C 14.198 -6.893 33
GDS OE7 O 15.497 -7.643 34
GDS OE8 O 12.899 -7.643 35
GDS N6 N 15.497 -4.643 36
GDS CB6 C 12.899 -4.643 37
GDS CG6 C 12.899 -3.143 38
GDS CD6 C 11.600 -2.393 39
GDS O6 O 10.301 -3.143 40
#
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
GDS CA1 N1 SINGLE BEGINWEDGE 1
GDS CA1 C1 SINGLE NONE 2
GDS CA1 CB1 SINGLE NONE 3
GDS C1 OE1 DOUBLE NONE 4
GDS C1 OE2 SINGLE NONE 5
GDS CB1 CG1 SINGLE NONE 6
GDS CG1 CD1 SINGLE NONE 7
GDS CD1 O1 DOUBLE NONE 8
GDS CD1 N2 SINGLE NONE 9
GDS N2 CA2 SINGLE NONE 10
GDS CA2 C2 SINGLE NONE 11
GDS CA2 CB2 SINGLE BEGINDASH 12
GDS C2 O2 DOUBLE NONE 13
GDS C2 N3 SINGLE NONE 14
GDS CB2 SG2 SINGLE NONE 15
GDS SG2 SG5 SINGLE NONE 16
GDS N3 CA3 SINGLE NONE 17
GDS CA3 C3 SINGLE NONE 18
GDS C3 OE3 DOUBLE NONE 19
GDS C3 OE4 SINGLE NONE 20
GDS N4 CA4 SINGLE NONE 21
GDS N4 C5 SINGLE NONE 22
GDS CA4 C4 SINGLE NONE 23
GDS C4 OE5 DOUBLE NONE 24
GDS C4 OE6 SINGLE NONE 25
GDS C5 O5 DOUBLE NONE 26
GDS C5 CA5 SINGLE NONE 27
GDS CA5 N5 SINGLE NONE 28
GDS CA5 CB5 SINGLE BEGINDASH 29
GDS N5 CD6 SINGLE NONE 30
GDS CB5 SG5 SINGLE NONE 31
GDS CA6 C6 SINGLE NONE 32
GDS CA6 N6 SINGLE BEGINDASH 33
GDS CA6 CB6 SINGLE NONE 34
GDS C6 OE7 DOUBLE NONE 35
GDS C6 OE8 SINGLE NONE 36
GDS CB6 CG6 SINGLE NONE 37
GDS CG6 CD6 SINGLE NONE 38
GDS CD6 O6 DOUBLE NONE 39
#
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
GDS amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GDS peptide F2 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
GDS N2 F1 1
GDS CD1 F1 1
GDS O1 F1 1
GDS CG1 F1 1
GDS N3 F1 2
GDS C2 F1 2
GDS O2 F1 2
GDS CA2 F1 2
GDS N4 F1 3
GDS C5 F1 3
GDS O5 F1 3
GDS CA5 F1 3
GDS N5 F1 4
GDS CD6 F1 4
GDS O6 F1 4
GDS CG6 F1 4
GDS OE1 F2 1
GDS C1 F2 1
GDS CA1 F2 1
GDS N1 F2 1
GDS O2 F2 2
GDS C2 F2 2
GDS CA2 F2 2
GDS N2 F2 2
GDS OE3 F2 3
GDS C3 F2 3
GDS CA3 F2 3
GDS N3 F2 3
GDS OE5 F2 4
GDS C4 F2 4
GDS CA4 F2 4
GDS N4 F2 4
GDS O5 F2 5
GDS C5 F2 5
GDS CA5 F2 5
GDS N5 F2 5
GDS OE7 F2 6
GDS C6 F2 6
GDS CA6 F2 6
GDS N6 F2 6
#
_pdbe_chem_comp_rdkit_properties.comp_id GDS
_pdbe_chem_comp_rdkit_properties.exactmw 612.152
_pdbe_chem_comp_rdkit_properties.amw 612.640
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 12
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 23
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 16
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 72
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 20
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 4
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 280.438
_pdbe_chem_comp_rdkit_properties.tpsa 317.640
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.877
_pdbe_chem_comp_rdkit_properties.CrippenMR 139.759
_pdbe_chem_comp_rdkit_properties.chi0v 20.032
_pdbe_chem_comp_rdkit_properties.chi1v 10.910
_pdbe_chem_comp_rdkit_properties.chi2v 3.997
_pdbe_chem_comp_rdkit_properties.chi3v 3.997
_pdbe_chem_comp_rdkit_properties.chi4v 2.465
_pdbe_chem_comp_rdkit_properties.chi0n 50.399
_pdbe_chem_comp_rdkit_properties.chi1n 23.971
_pdbe_chem_comp_rdkit_properties.chi2n 2.610
_pdbe_chem_comp_rdkit_properties.chi3n 2.610
_pdbe_chem_comp_rdkit_properties.chi4n 1.234
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.620
_pdbe_chem_comp_rdkit_properties.kappa1 10.030
_pdbe_chem_comp_rdkit_properties.kappa2 19.441
_pdbe_chem_comp_rdkit_properties.kappa3 17.064
_pdbe_chem_comp_rdkit_properties.Phi 4.875
#
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
GDS UniChem DrugBank DB03310
GDS UniChem 'Guide to Pharmacology' 6835
GDS UniChem 'KEGG LIGAND' C00127
GDS UniChem ChEBI 17858
GDS UniChem ZINC ZINC000003870129
GDS UniChem eMolecules 482701
GDS UniChem fdasrs ULW86O013H
GDS UniChem SureChEMBL SCHEMBL138746
GDS UniChem HMDB HMDB0003337
GDS UniChem PubChem 11215652
GDS UniChem NMRShiftDB 60020944
GDS UniChem ACTor 10421-65-5
GDS UniChem BindingDb 225231
GDS UniChem DrugCentral 5130
GDS UniChem MetaboLights MTBLC17858
GDS UniChem BRENDA 162154
GDS UniChem BRENDA 164360
GDS UniChem BRENDA 1794
GDS UniChem BRENDA 229482
GDS UniChem BRENDA 229483
GDS UniChem BRENDA 229502
GDS UniChem BRENDA 229503
GDS UniChem BRENDA 229675
GDS UniChem BRENDA 32241
GDS UniChem BRENDA 330
GDS UniChem BRENDA 973
GDS UniChem ChemicalBook CB8200802
GDS UniChem DailyMed OXIGLUTATIONE
GDS UniChem ClinicalTrials 'GLUTATHIONE DISULFIDE'
GDS UniChem ClinicalTrials OXIGLUTATIONE
GDS UniChem rxnorm 'GLUTATHIONE DISULFIDE'
GDS UniChem MedChemExpress HY-D0844
GDS UniChem 'Probes And Drugs' PD002533
GDS UniChem CCDC BERLOZ
GDS UniChem 'EPA CompTox Dashboard' DTXSID5048972
GDS UniChem 'PubChem TPHARMA' 14789556
GDS UniChem 'PubChem TPHARMA' 14838688
GDS UniChem 'PubChem TPHARMA' 16298175
GDS UniChem PubChem 65359
GDS UniChem ACTor 27025-41-8
GDS UniChem Nikkaji J415.688I
#
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
GDS N1 -3.647 3.747 0.829 ETKDGv3 1
GDS CA1 -4.153 2.931 -0.279 ETKDGv3 2
GDS C1 -3.959 3.675 -1.568 ETKDGv3 3
GDS OE1 -4.453 4.825 -1.720 ETKDGv3 4
GDS OE2 -3.242 3.086 -2.605 ETKDGv3 5
GDS CB1 -5.646 2.558 -0.098 ETKDGv3 6
GDS CG1 -5.922 1.657 1.117 ETKDGv3 7
GDS CD1 -5.238 0.327 0.987 ETKDGv3 8
GDS O1 -5.735 -0.555 0.236 ETKDGv3 9
GDS N2 -3.998 0.085 1.666 ETKDGv3 10
GDS CA2 -3.143 -1.058 1.335 ETKDGv3 11
GDS C2 -3.636 -2.289 2.046 ETKDGv3 12
GDS O2 -3.978 -2.215 3.258 ETKDGv3 13
GDS CB2 -1.682 -0.779 1.722 ETKDGv3 14
GDS SG2 -1.042 0.712 0.879 ETKDGv3 15
GDS N3 -3.677 -3.548 1.360 ETKDGv3 16
GDS CA3 -4.197 -4.761 1.984 ETKDGv3 17
GDS C3 -5.684 -4.677 2.113 ETKDGv3 18
GDS OE3 -6.214 -4.524 3.246 ETKDGv3 19
GDS OE4 -6.481 -4.741 0.975 ETKDGv3 20
GDS N4 2.216 1.898 0.671 ETKDGv3 21
GDS CA4 2.013 3.168 1.366 ETKDGv3 22
GDS C4 2.489 3.076 2.780 ETKDGv3 23
GDS OE5 1.710 2.666 3.682 ETKDGv3 24
GDS OE6 3.807 3.396 3.090 ETKDGv3 25
GDS C5 1.784 1.710 -0.683 ETKDGv3 26
GDS O5 1.260 2.665 -1.318 ETKDGv3 27
GDS CA5 1.930 0.369 -1.353 ETKDGv3 28
GDS N5 3.323 -0.079 -1.261 ETKDGv3 29
GDS CB5 0.992 -0.672 -0.719 ETKDGv3 30
GDS SG5 -0.766 -0.256 -1.009 ETKDGv3 31
GDS CA6 7.414 -1.796 -2.572 ETKDGv3 32
GDS C6 7.520 -3.079 -3.343 ETKDGv3 33
GDS OE7 7.563 -3.063 -4.603 ETKDGv3 34
GDS OE8 7.548 -4.294 -2.665 ETKDGv3 35
GDS N6 8.495 -0.893 -2.981 ETKDGv3 36
GDS CB6 6.018 -1.168 -2.778 ETKDGv3 37
GDS CG6 5.786 0.053 -1.879 ETKDGv3 38
GDS CD6 4.375 0.542 -2.015 ETKDGv3 39
GDS O6 4.116 1.473 -2.824 ETKDGv3 40
GDS HN11 -3.518 3.142 1.671 ETKDGv3 41
GDS HN12 -4.342 4.490 1.071 ETKDGv3 42
GDS HA1 -3.550 2.000 -0.341 ETKDGv3 43
GDS HO2 -3.104 3.572 -3.483 ETKDGv3 44
GDS HB11 -6.005 2.036 -1.013 ETKDGv3 45
GDS HB12 -6.251 3.485 0.006 ETKDGv3 46
GDS HG11 -5.614 2.164 2.055 ETKDGv3 47
GDS HG12 -7.018 1.486 1.190 ETKDGv3 48
GDS HN2 -3.685 0.766 2.395 ETKDGv3 49
GDS HA2 -3.181 -1.232 0.238 ETKDGv3 50
GDS HB21 -1.610 -0.611 2.818 ETKDGv3 51
GDS HB22 -1.044 -1.653 1.471 ETKDGv3 52
GDS HN3 -3.317 -3.608 0.381 ETKDGv3 53
GDS HA31 -3.946 -5.639 1.351 ETKDGv3 54
GDS HA32 -3.721 -4.911 2.978 ETKDGv3 55
GDS HO4 -7.490 -4.674 1.043 ETKDGv3 56
GDS HN4 2.666 1.096 1.171 ETKDGv3 57
GDS HA41 0.932 3.428 1.357 ETKDGv3 58
GDS HA42 2.573 3.970 0.841 ETKDGv3 59
GDS HO6 4.150 3.321 4.041 ETKDGv3 60
GDS HA5 1.658 0.458 -2.429 ETKDGv3 61
GDS HN5 3.570 -0.870 -0.624 ETKDGv3 62
GDS HB51 1.205 -0.794 0.365 ETKDGv3 63
GDS HB52 1.178 -1.655 -1.200 ETKDGv3 64
GDS HA6 7.541 -2.037 -1.492 ETKDGv3 65
GDS HO8 7.610 -5.170 -3.170 ETKDGv3 66
GDS HN61 8.595 -0.134 -2.270 ETKDGv3 67
GDS HN62 8.258 -0.446 -3.897 ETKDGv3 68
GDS HB61 5.886 -0.873 -3.843 ETKDGv3 69
GDS HB62 5.247 -1.935 -2.541 ETKDGv3 70
GDS HG61 5.978 -0.215 -0.817 ETKDGv3 71
GDS HG62 6.481 0.872 -2.159 ETKDGv3 72
#