data_32S
#
_chem_comp.id 32S
_chem_comp.name "(S)-2-AMINO-3-(4H-SELENOLO[3,2-B]-PYRROL-6-YL)-PROPIONIC ACID"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C9 H10 N2 O2 Se"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-12-30
_chem_comp.pdbx_modified_date 2023-11-03
_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 257.148
_chem_comp.one_letter_code X
_chem_comp.three_letter_code 32S
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1RMM
_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
32S N N N 0 1 N N N Y Y N 23.385 36.512 27.790 1.647 0.963 1.070 N 32S 1
32S CA CA C 0 1 N N S Y N N 23.471 35.125 28.295 2.400 -0.147 0.470 CA 32S 2
32S CB CB C 0 1 N N N N N N 23.683 34.155 27.124 1.669 -0.643 -0.779 CB 32S 3
32S CG CG C 0 1 Y N N N N N 22.439 33.868 26.333 0.340 -1.233 -0.382 CG 32S 4
32S CD2 CD2 C 0 1 Y N N N N N 21.367 33.009 26.716 -0.843 -0.537 -0.190 CD2 32S 5
32S CE2 CE2 C 0 1 Y N N N N N 20.437 33.003 25.693 -1.842 -1.411 0.165 CE2 32S 6
32S SEL SEL SE 0 0 Y N N N N N 20.773 31.906 28.078 -1.748 1.216 -0.202 SEL 32S 7
32S CD1 CD1 C 0 1 Y N N N N N 22.113 34.349 25.104 0.079 -2.539 -0.153 CD1 32S 8
32S NE1 NE1 N 0 1 Y N N N N N 20.900 33.829 24.706 -1.231 -2.665 0.183 NE1 32S 9
32S CZ2 CZ2 C 0 1 Y N N N N N 19.285 32.247 25.785 -3.177 -0.878 0.416 CZ2 32S 10
32S CZ3 CZ3 C 0 1 Y N N N N N 19.243 31.556 27.018 -3.481 0.411 0.320 CZ3 32S 11
32S C C C 0 1 N N N Y N Y 24.592 34.919 29.320 3.778 0.330 0.089 C 32S 12
32S O O O 0 1 N N N Y N Y 24.411 34.211 30.318 3.992 1.511 -0.049 O 32S 13
32S OXT OXT O 0 1 N Y N Y N Y ? ? ? 4.768 -0.557 -0.097 OXT 32S 14
32S H H H 0 1 N N N Y Y N 23.366 37.148 28.562 1.556 1.730 0.421 H 32S 15
32S H2 HN2 H 0 1 N Y N Y Y N 24.181 36.708 27.217 0.742 0.653 1.392 HN2 32S 16
32S HA HA H 0 1 N N N Y N N 22.518 34.923 28.807 2.483 -0.961 1.190 HA 32S 17
32S HB1 HB1 H 0 1 N N N N N N 24.422 34.602 26.443 1.507 0.191 -1.461 HB1 32S 18
32S HB2 HB2 H 0 1 N N N N N N 24.015 33.199 27.556 2.271 -1.405 -1.274 HB2 32S 19
32S HD1 HD1 H 0 1 N N N N N N 22.714 35.035 24.526 0.793 -3.347 -0.224 HD1 32S 20
32S HE1 HE1 H 0 1 N N N N N N 20.437 34.023 23.841 -1.675 -3.500 0.399 HE1 32S 21
32S HZ2 HZ2 H 0 1 N N N N N N 18.523 32.191 25.022 -3.960 -1.569 0.695 HZ2 32S 22
32S HZ3 HZ3 H 0 1 N N N N N N 18.435 30.906 27.319 -4.431 0.897 0.484 HZ3 32S 23
32S HXT HXT H 0 1 N Y N Y N Y ? ? ? 5.634 -0.204 -0.340 HXT 32S 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
32S N CA SING N N 1
32S N H SING N N 2
32S N H2 SING N N 3
32S CA CB SING N N 4
32S CA C SING N N 5
32S CA HA SING N N 6
32S CB CG SING N N 7
32S CB HB1 SING N N 8
32S CB HB2 SING N N 9
32S CG CD2 SING Y N 10
32S CG CD1 DOUB Y N 11
32S CD2 CE2 DOUB Y N 12
32S CD2 SEL SING Y N 13
32S CE2 NE1 SING Y N 14
32S CE2 CZ2 SING Y N 15
32S SEL CZ3 SING Y N 16
32S CD1 NE1 SING Y N 17
32S CD1 HD1 SING N N 18
32S NE1 HE1 SING N N 19
32S CZ2 CZ3 DOUB Y N 20
32S CZ2 HZ2 SING N N 21
32S CZ3 HZ3 SING N N 22
32S C O DOUB N N 23
32S C OXT SING N N 24
32S OXT HXT SING N N 25
#
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
32S SMILES ACDLabs 10.04 O=C(O)C(N)Cc2c1[se]ccc1nc2
32S SMILES_CANONICAL CACTVS 3.341 N[C@@H](Cc1c[nH]c2cc[se]c12)C(O)=O
32S SMILES CACTVS 3.341 N[CH](Cc1c[nH]c2cc[se]c12)C(O)=O
32S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1c[se]c2c1[nH]cc2C[C@@H](C(=O)O)N
32S SMILES "OpenEye OEToolkits" 1.5.0 c1c[se]c2c1[nH]cc2CC(C(=O)O)N
32S InChI InChI 1.03 InChI=1S/C9H10N2O2Se/c10-6(9(12)13)3-5-4-11-7-1-2-14-8(5)7/h1-2,4,6,11H,3,10H2,(H,12,13)/t6-/m0/s1
32S InChIKey InChI 1.03 RKIAGDNYTCWCNV-LURJTMIESA-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
32S "SYSTEMATIC NAME" ACDLabs 10.04 3-(4H-selenopheno[3,2-b]pyrrol-6-yl)-L-alanine
32S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-(4H-selenopheno[2,3-d]pyrrol-6-yl)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
32S 'Create component' 2003-12-30 RCSB
32S 'Modify descriptor' 2011-06-04 RCSB
32S 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id 32S
_pdbe_chem_comp_drugbank_details.drugbank_id DB03513
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '(S)-2-Amino-3-(4h-Selenolo[3,2-B]-Pyrrol-6-Yl)-Propionic 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 32S
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03513
_pdbe_chem_comp_drugbank_classification.parent 'L-alpha-amino acids'
_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-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.'
#
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
32S N N 4.214 0.099 1
32S CA C 5.218 1.214 2
32S CB C 6.685 0.902 3
32S CG C 7.149 -0.525 4
32S CD2 C 8.575 -0.989 5
32S CE2 C 8.575 -2.489 6
32S SEL Se 9.995 -0.531 7
32S CD1 C 6.267 -1.738 8
32S NE1 N 7.149 -2.952 9
32S CZ2 C 9.995 -2.946 10
32S CZ3 C 10.870 -1.738 11
32S C C 4.755 2.640 12
32S O O 3.287 2.952 13
32S OXT O 5.758 3.755 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
32S CA N SINGLE BEGINDASH 1
32S CA CB SINGLE NONE 2
32S CA C SINGLE NONE 3
32S CB CG SINGLE NONE 4
32S CG CD2 SINGLE NONE 5
32S CG CD1 DOUBLE NONE 6
32S CD2 CE2 DOUBLE NONE 7
32S CD2 SEL SINGLE NONE 8
32S CE2 NE1 SINGLE NONE 9
32S CE2 CZ2 SINGLE NONE 10
32S SEL CZ3 SINGLE NONE 11
32S CD1 NE1 SINGLE NONE 12
32S CZ2 CZ3 DOUBLE NONE 13
32S C O DOUBLE NONE 14
32S C OXT SINGLE NONE 15
#
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
32S MurckoScaffold S1 scaffold 'c1cc2[se]ccc2[nH]1' InChI=1S/C6H5NSe/c1-3-7-5-2-4-8-6(1)5/h1-4,7H GJCIQTNTPUDNRB-UHFFFAOYSA-N
32S peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
32S pyrrole F2 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
32S CG S1 1
32S CD2 S1 1
32S CE2 S1 1
32S SEL S1 1
32S CD1 S1 1
32S NE1 S1 1
32S CZ2 S1 1
32S CZ3 S1 1
32S O F1 1
32S C F1 1
32S CA F1 1
32S N F1 1
32S CE2 F2 1
32S CD2 F2 1
32S CG F2 1
32S CD1 F2 1
32S NE1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 32S
_pdbe_chem_comp_rdkit_properties.exactmw 257.991
_pdbe_chem_comp_rdkit_properties.amw 257.151
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 100.781
_pdbe_chem_comp_rdkit_properties.tpsa 79.110
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.304
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.082
_pdbe_chem_comp_rdkit_properties.chi0v 8.332
_pdbe_chem_comp_rdkit_properties.chi1v 5.200
_pdbe_chem_comp_rdkit_properties.chi2v 3.171
_pdbe_chem_comp_rdkit_properties.chi3v 3.171
_pdbe_chem_comp_rdkit_properties.chi4v 2.242
_pdbe_chem_comp_rdkit_properties.chi0n 16.619
_pdbe_chem_comp_rdkit_properties.chi1n 8.237
_pdbe_chem_comp_rdkit_properties.chi2n 1.481
_pdbe_chem_comp_rdkit_properties.chi3n 1.481
_pdbe_chem_comp_rdkit_properties.chi4n 0.895
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.031
_pdbe_chem_comp_rdkit_properties.kappa1 3.234
_pdbe_chem_comp_rdkit_properties.kappa2 3.612
_pdbe_chem_comp_rdkit_properties.kappa3 1.617
_pdbe_chem_comp_rdkit_properties.Phi 0.834
#
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
32S UniChem DrugBank DB03513
32S UniChem PDBe 32S
32S UniChem SureChEMBL SCHEMBL1031518
32S UniChem PubChem 15480320
32S UniChem Nikkaji J1.076.917E
32S UniChem 'Probes And Drugs' PD059724
#
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
32S N -1.728 -1.777 0.500 ETKDGv3 1
32S CA -2.132 -0.443 0.954 ETKDGv3 2
32S CB -0.954 0.297 1.617 ETKDGv3 3
32S CG 0.192 0.556 0.680 ETKDGv3 4
32S CD2 1.315 -0.355 0.433 ETKDGv3 5
32S CE2 2.057 0.250 -0.485 ETKDGv3 6
32S SEL 2.195 -1.839 0.709 ETKDGv3 7
32S CD1 0.331 1.625 -0.093 ETKDGv3 8
32S NE1 1.510 1.504 -0.870 ETKDGv3 9
32S CZ2 3.287 -0.306 -1.041 ETKDGv3 10
32S CZ3 3.719 -1.487 -0.627 ETKDGv3 11
32S C -2.743 0.365 -0.165 ETKDGv3 12
32S O -3.671 1.179 0.088 ETKDGv3 13
32S OXT -2.257 0.255 -1.465 ETKDGv3 14
32S H -1.080 -1.699 -0.317 ETKDGv3 15
32S H2 -2.579 -2.288 0.170 ETKDGv3 16
32S HA -2.910 -0.577 1.738 ETKDGv3 17
32S HB1 -0.585 -0.308 2.474 ETKDGv3 18
32S HB2 -1.314 1.263 2.036 ETKDGv3 19
32S HD1 -0.353 2.462 -0.143 ETKDGv3 20
32S HE1 1.880 2.178 -1.576 ETKDGv3 21
32S HZ2 3.841 0.245 -1.790 ETKDGv3 22
32S HZ3 4.629 -1.911 -1.031 ETKDGv3 23
32S HXT -2.649 0.811 -2.215 ETKDGv3 24
#