data_YDB
#
_chem_comp.id YDB
_chem_comp.name
"1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H12 B N7 O5 S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-01-25
_chem_comp.pdbx_modified_date 2023-06-30
_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 373.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YDB
_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 8FQW
_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
YDB N1 N1 N 0 1 N N N N N N -5.946 1.810 -63.373 8.722 -0.426 0.701 N1 YDB 1
YDB C1 C1 C 0 1 Y N N N N N -5.711 1.476 -64.761 7.346 -0.336 0.521 C1 YDB 2
YDB N2 N2 N 0 1 Y N N N N N -6.001 0.307 -65.307 6.507 0.152 1.379 N2 YDB 3
YDB N3 N3 N 0 1 Y N N N N N -5.690 0.187 -66.680 5.185 0.142 0.990 N3 YDB 4
YDB C2 C2 C 0 1 Y N N N N N -5.134 1.336 -67.182 4.950 -0.354 -0.184 C2 YDB 5
YDB S1 S1 S 0 1 N N N N N N -4.607 1.585 -68.896 3.361 -0.492 -0.934 S1 YDB 6
YDB C3 C3 C 0 1 N N N N N N -5.397 0.262 -69.844 2.254 0.206 0.322 C3 YDB 7
YDB C4 C4 C 0 1 N N N N N N -4.808 0.330 -71.240 0.834 0.159 -0.178 C4 YDB 8
YDB O1 O1 O 0 1 N N N N N N -4.031 1.187 -71.510 0.592 -0.301 -1.274 O1 YDB 9
YDB N4 N4 N 0 1 N N N N N N -5.211 -0.669 -72.206 -0.168 0.627 0.592 N4 YDB 10
YDB C5 C5 C 0 1 N N R N N N -4.694 -0.650 -73.560 -1.549 0.581 0.106 C5 YDB 11
YDB C6 C6 C 0 1 N N N N N N -3.278 -1.211 -73.665 -2.465 0.067 1.219 C6 YDB 12
YDB N5 N5 N 0 1 Y N N N N N -3.048 -2.283 -72.719 -3.846 0.021 0.733 N5 YDB 13
YDB C7 C7 C 0 1 Y N N N N N -3.031 -3.649 -73.008 -4.666 -1.049 0.743 C7 YDB 14
YDB C8 C8 C 0 1 Y N N N N N -2.767 -4.325 -71.825 -5.852 -0.643 0.198 C8 YDB 15
YDB C9 C9 C 0 1 N N N N N N -2.649 -5.840 -71.658 -7.046 -1.487 0.008 C9 YDB 16
YDB O2 O2 O 0 1 N N N N N N -2.432 -6.565 -72.674 -7.027 -2.652 0.350 O2 YDB 17
YDB O3 O3 O 0 1 N N N N N N -2.756 -6.351 -70.504 -8.159 -0.964 -0.544 O3 YDB 18
YDB N6 N6 N 0 1 Y N N N N N -2.615 -3.394 -70.817 -5.745 0.655 -0.136 N6 YDB 19
YDB N7 N7 N 0 1 Y N N N N N -2.789 -2.122 -71.377 -4.571 1.083 0.173 N7 YDB 20
YDB B1 B1 B 0 1 N N N N N N -5.695 -1.467 -74.459 -2.002 2.022 -0.321 B1 YDB 21
YDB O5 O4 O 0 1 N N N N N N -6.351 -2.369 -73.693 -2.959 2.188 -1.357 O5 YDB 22
YDB O6 O5 O 0 1 N N N N N N -5.027 -2.111 -75.443 -1.455 3.160 0.329 O6 YDB 23
YDB S2 S2 S 0 1 Y N N N N N -5.002 2.602 -65.916 6.470 -0.861 -0.913 S2 YDB 24
YDB H1 H1 H 0 1 N N N N N N -5.647 2.749 -63.200 9.125 -0.108 1.525 H1 YDB 25
YDB H2 H2 H 0 1 N N N N N N -6.922 1.729 -63.171 9.278 -0.810 0.006 H2 YDB 26
YDB H3 H3 H 0 1 N N N N N N -6.485 0.418 -69.882 2.336 -0.375 1.241 H3 YDB 27
YDB H4 H4 H 0 1 N N N N N N -5.182 -0.715 -69.387 2.536 1.240 0.520 H4 YDB 28
YDB H5 H5 H 0 1 N N N N N N -5.856 -1.384 -71.935 0.026 0.994 1.469 H5 YDB 29
YDB H6 H6 H 0 1 N N N N N N -4.682 0.386 -73.929 -1.610 -0.088 -0.752 H6 YDB 30
YDB H7 H7 H 0 1 N N N N N N -3.123 -1.597 -74.683 -2.150 -0.934 1.515 H7 YDB 31
YDB H8 H8 H 0 1 N N N N N N -2.560 -0.402 -73.466 -2.404 0.736 2.077 H8 YDB 32
YDB H9 H9 H 0 1 N N N N N N -3.194 -4.098 -73.977 -4.431 -2.036 1.111 H9 YDB 33
YDB H10 H10 H 0 1 N N N N N N -2.649 -7.293 -70.563 -8.916 -1.556 -0.648 H10 YDB 34
YDB H11 H11 H 0 1 N N N N N N -6.820 -1.917 -73.002 -3.273 1.357 -1.738 H11 YDB 35
YDB H12 H12 H 0 1 N N N N N N -4.566 -1.478 -75.981 -0.812 2.947 1.020 H12 YDB 36
#
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
YDB O6 B1 SING N N 1
YDB B1 O5 SING N N 2
YDB B1 C5 SING N N 3
YDB C6 C5 SING N N 4
YDB C6 N5 SING N N 5
YDB C5 N4 SING N N 6
YDB C7 N5 SING Y N 7
YDB C7 C8 DOUB Y N 8
YDB N5 N7 SING Y N 9
YDB O2 C9 DOUB N N 10
YDB N4 C4 SING N N 11
YDB C8 C9 SING N N 12
YDB C8 N6 SING Y N 13
YDB C9 O3 SING N N 14
YDB O1 C4 DOUB N N 15
YDB N7 N6 DOUB Y N 16
YDB C4 C3 SING N N 17
YDB C3 S1 SING N N 18
YDB S1 C2 SING N N 19
YDB C2 N3 DOUB Y N 20
YDB C2 S2 SING Y N 21
YDB N3 N2 SING Y N 22
YDB S2 C1 SING Y N 23
YDB N2 C1 DOUB Y N 24
YDB C1 N1 SING N N 25
YDB N1 H1 SING N N 26
YDB N1 H2 SING N N 27
YDB C3 H3 SING N N 28
YDB C3 H4 SING N N 29
YDB N4 H5 SING N N 30
YDB C5 H6 SING N N 31
YDB C6 H7 SING N N 32
YDB C6 H8 SING N N 33
YDB C7 H9 SING N N 34
YDB O3 H10 SING N N 35
YDB O5 H11 SING N N 36
YDB O6 H12 SING N N 37
#
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
YDB SMILES ACDLabs 12.01 O=C(CSc1nnc(N)s1)NC(Cn1cc(nn1)C(=O)O)B(O)O
YDB InChI InChI 1.06 InChI=1S/C9H12BN7O5S2/c11-8-14-15-9(24-8)23-3-6(18)12-5(10(21)22)2-17-1-4(7(19)20)13-16-17/h1,5,21-22H,2-3H2,(H2,11,14)(H,12,18)(H,19,20)/t5-/m0/s1
YDB InChIKey InChI 1.06 JADCONPWNUDUNV-YFKPBYRVSA-N
YDB SMILES_CANONICAL CACTVS 3.385 Nc1sc(SCC(=O)N[C@@H](Cn2cc(nn2)C(O)=O)B(O)O)nn1
YDB SMILES CACTVS 3.385 Nc1sc(SCC(=O)N[CH](Cn2cc(nn2)C(O)=O)B(O)O)nn1
YDB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 B([C@H](Cn1cc(nn1)C(=O)O)NC(=O)CSc2nnc(s2)N)(O)O
YDB SMILES "OpenEye OEToolkits" 2.0.7 B(C(Cn1cc(nn1)C(=O)O)NC(=O)CSc2nnc(s2)N)(O)O
#
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
YDB "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid"
YDB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{R})-2-[2-[(5-azanyl-1,3,4-thiadiazol-2-yl)sulfanyl]ethanoylamino]-2-(dihydroxyboranyl)ethyl]-1,2,3-triazole-4-carboxylic 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
YDB 'Create component' 2023-01-25 RCSB
YDB 'Initial release' 2023-07-05 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
YDB N1 N 11.652 -8.283 1
YDB C1 C 10.771 -7.070 2
YDB N2 N 9.271 -7.070 3
YDB N3 N 8.807 -5.643 4
YDB C2 C 10.021 -4.762 5
YDB S1 S 10.021 -3.262 6
YDB C3 C 8.722 -2.512 7
YDB C4 C 8.722 -1.012 8
YDB O1 O 10.021 -0.262 9
YDB N4 N 7.422 -0.262 10
YDB C5 C 7.422 1.238 11
YDB C6 C 6.123 1.988 12
YDB N5 N 6.123 3.488 13
YDB C7 C 4.910 4.370 14
YDB C8 C 5.373 5.797 15
YDB C9 C 4.492 7.010 16
YDB O2 O 5.102 8.380 17
YDB O3 O 3.000 6.854 18
YDB N6 N 6.873 5.797 19
YDB N7 N 7.337 4.370 20
YDB B1 B 8.722 1.988 21
YDB O5 O 8.722 3.488 22
YDB O6 O 10.021 1.238 23
YDB S2 S 11.234 -5.643 24
#
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
YDB O6 B1 SINGLE NONE 1
YDB B1 O5 SINGLE NONE 2
YDB B1 C5 SINGLE NONE 3
YDB C5 C6 SINGLE BEGINWEDGE 4
YDB C6 N5 SINGLE NONE 5
YDB C5 N4 SINGLE NONE 6
YDB C7 N5 SINGLE NONE 7
YDB C7 C8 DOUBLE NONE 8
YDB N5 N7 SINGLE NONE 9
YDB O2 C9 DOUBLE NONE 10
YDB N4 C4 SINGLE NONE 11
YDB C8 C9 SINGLE NONE 12
YDB C8 N6 SINGLE NONE 13
YDB C9 O3 SINGLE NONE 14
YDB O1 C4 DOUBLE NONE 15
YDB N7 N6 DOUBLE NONE 16
YDB C4 C3 SINGLE NONE 17
YDB C3 S1 SINGLE NONE 18
YDB S1 C2 SINGLE NONE 19
YDB C2 N3 DOUBLE NONE 20
YDB C2 S2 SINGLE NONE 21
YDB N3 N2 SINGLE NONE 22
YDB S2 C1 SINGLE NONE 23
YDB N2 C1 DOUBLE NONE 24
YDB C1 N1 SINGLE NONE 25
#
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
YDB MurckoScaffold S1 scaffold O=C(CSc1nncs1)NCCn1ccnn1 InChI=1S/C8H10N6OS2/c15-7(5-16-8-12-11-6-17-8)9-1-3-14-4-2-10-13-14/h2,4,6H,1,3,5H2,(H,9,15) RPNUKQPBZRRSLY-UHFFFAOYSA-N
YDB amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YDB thiadiazole F2 fragment c1nncs1 InChI=1S/C2H2N2S/c1-3-4-2-5-1/h1-2H MBIZXFATKUQOOA-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
YDB C1 S1 1
YDB N2 S1 1
YDB N3 S1 1
YDB C2 S1 1
YDB S1 S1 1
YDB C3 S1 1
YDB C4 S1 1
YDB O1 S1 1
YDB N4 S1 1
YDB C5 S1 1
YDB C6 S1 1
YDB N5 S1 1
YDB C7 S1 1
YDB C8 S1 1
YDB N6 S1 1
YDB N7 S1 1
YDB S2 S1 1
YDB N4 F1 1
YDB C4 F1 1
YDB O1 F1 1
YDB C3 F1 1
YDB C1 F2 1
YDB N2 F2 1
YDB N3 F2 1
YDB C2 F2 1
YDB S2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YDB
_pdbe_chem_comp_rdkit_properties.exactmw 373.043
_pdbe_chem_comp_rdkit_properties.amw 373.185
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 12
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 24
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 15
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 160.062
_pdbe_chem_comp_rdkit_properties.tpsa 189.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.844
_pdbe_chem_comp_rdkit_properties.CrippenMR 83.629
_pdbe_chem_comp_rdkit_properties.chi0v 12.699
_pdbe_chem_comp_rdkit_properties.chi1v 7.211
_pdbe_chem_comp_rdkit_properties.chi2v 3.480
_pdbe_chem_comp_rdkit_properties.chi3v 3.480
_pdbe_chem_comp_rdkit_properties.chi4v 2.210
_pdbe_chem_comp_rdkit_properties.chi0n 23.066
_pdbe_chem_comp_rdkit_properties.chi1n 11.144
_pdbe_chem_comp_rdkit_properties.chi2n 1.926
_pdbe_chem_comp_rdkit_properties.chi3n 1.926
_pdbe_chem_comp_rdkit_properties.chi4n 1.073
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.225
_pdbe_chem_comp_rdkit_properties.kappa1 7.771
_pdbe_chem_comp_rdkit_properties.kappa2 8.046
_pdbe_chem_comp_rdkit_properties.kappa3 5.154
_pdbe_chem_comp_rdkit_properties.Phi 2.606
#
_pdbe_chem_comp_external_mappings.comp_id YDB
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id YDB
#
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
YDB N1 6.379 3.477 -0.484 ETKDGv3 1
YDB C1 5.287 2.929 0.249 ETKDGv3 2
YDB N2 4.577 3.628 1.075 ETKDGv3 3
YDB N3 3.549 2.896 1.694 ETKDGv3 4
YDB C2 3.497 1.656 1.326 ETKDGv3 5
YDB S1 2.285 0.503 1.961 ETKDGv3 6
YDB C3 1.086 0.861 0.639 ETKDGv3 7
YDB C4 -0.125 0.006 0.824 ETKDGv3 8
YDB O1 -1.150 0.494 1.372 ETKDGv3 9
YDB N4 -0.102 -1.368 0.409 ETKDGv3 10
YDB C5 -1.289 -2.227 0.435 ETKDGv3 11
YDB C6 -1.812 -2.456 -0.992 ETKDGv3 12
YDB N5 -2.179 -1.189 -1.614 ETKDGv3 13
YDB C7 -3.287 -0.372 -1.271 ETKDGv3 14
YDB C8 -3.037 0.827 -1.773 ETKDGv3 15
YDB C9 -3.889 2.013 -1.647 ETKDGv3 16
YDB O2 -3.522 3.106 -2.153 ETKDGv3 17
YDB O3 -5.102 1.935 -0.969 ETKDGv3 18
YDB N6 -1.766 0.810 -2.425 ETKDGv3 19
YDB N7 -1.289 -0.363 -2.307 ETKDGv3 20
YDB B1 -0.924 -3.619 1.136 ETKDGv3 21
YDB O5 -1.615 -4.024 2.358 ETKDGv3 22
YDB O6 0.114 -4.478 0.571 ETKDGv3 23
YDB S2 4.756 1.230 0.135 ETKDGv3 24
YDB H1 6.640 4.481 -0.372 ETKDGv3 25
YDB H2 6.924 2.875 -1.139 ETKDGv3 26
YDB H3 1.541 0.647 -0.352 ETKDGv3 27
YDB H4 0.800 1.935 0.673 ETKDGv3 28
YDB H5 0.768 -1.733 -0.043 ETKDGv3 29
YDB H6 -2.097 -1.761 1.040 ETKDGv3 30
YDB H7 -2.707 -3.115 -0.964 ETKDGv3 31
YDB H8 -1.036 -2.954 -1.613 ETKDGv3 32
YDB H9 -4.141 -0.675 -0.679 ETKDGv3 33
YDB H10 -5.698 2.749 -0.875 ETKDGv3 34
YDB H11 -1.068 -3.645 3.092 ETKDGv3 35
YDB H12 -0.368 -5.080 -0.050 ETKDGv3 36
#