data_3VU
#
_chem_comp.id 3VU
_chem_comp.name
"{(3R)-6-[(3-amino-1,2,4-thiadiazol-5-yl)oxy]-1-hydroxy-4,5-dimethyl-1,3-dihydro-2,1-benzoxaborol-3-yl}acetic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H14 B N3 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-11-19
_chem_comp.pdbx_modified_date 2015-07-31
_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 335.143
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3VU
_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 4WZ4
_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
3VU C1 C1 C 0 1 Y N N N N N -6.637 -12.493 19.336 0.312 1.372 -0.824 C1 3VU 1
3VU C2 C2 C 0 1 Y N N N N N -6.463 -13.829 19.690 1.098 0.281 -1.160 C2 3VU 2
3VU C3 C3 C 0 1 Y N N N N N -5.215 -14.453 19.716 0.522 -0.977 -1.281 C3 3VU 3
3VU O4 O1 O 0 1 N N N N N N -5.729 -10.312 17.019 -2.084 3.583 0.003 O4 3VU 4
3VU C7 C4 C 0 1 N N N N N N -2.658 -11.716 17.158 -3.440 -0.826 0.783 C7 3VU 5
3VU C8 C5 C 0 1 N N N N N N -1.816 -10.593 16.574 -4.930 -0.803 1.007 C8 3VU 6
3VU C9 C6 C 0 1 N N N N N N -2.700 -14.321 19.400 -1.446 -2.519 -1.195 C9 3VU 7
3VU C10 C7 C 0 1 N N N N N N -5.091 -15.927 20.036 1.380 -2.162 -1.647 C10 3VU 8
3VU C11 C8 C 0 1 Y N N N N N -8.522 -14.833 19.084 3.271 0.219 -0.334 C11 3VU 9
3VU C12 C9 C 0 1 Y N N N N N -10.317 -15.670 18.164 5.198 -0.023 0.785 C12 3VU 10
3VU O1 O2 O 0 1 N N N N N N -0.990 -10.002 17.233 -5.469 -1.509 2.013 O1 3VU 11
3VU O2 O3 O 0 1 N N N N N N -2.069 -10.257 15.345 -5.640 -0.147 0.281 O2 3VU 12
3VU C6 C10 C 0 1 N N R N N N -3.200 -11.378 18.551 -3.091 0.055 -0.417 C6 3VU 13
3VU O O4 O 0 1 N N N N N N -3.881 -10.107 18.537 -3.400 1.419 -0.135 O 3VU 14
3VU B B1 B 0 1 N N N N N N -5.229 -10.357 18.295 -2.207 2.186 -0.219 B 3VU 15
3VU C5 C11 C 0 1 Y N N N N N -4.262 -12.345 19.040 -1.622 -0.070 -0.722 C5 3VU 16
3VU C C12 C 0 1 Y N N N N N -5.520 -11.737 18.954 -1.050 1.197 -0.605 C 3VU 17
3VU C4 C13 C 0 1 Y N N N N N -4.075 -13.692 19.400 -0.833 -1.149 -1.067 C4 3VU 18
3VU O3 O5 O 0 1 N N N N N N -7.606 -14.579 20.059 2.431 0.443 -1.372 O3 3VU 19
3VU S S1 S 0 1 Y N N N N N -8.467 -14.221 17.431 2.848 -0.146 1.296 S 3VU 20
3VU N1 N1 N 0 1 Y N N N N N -9.881 -14.992 17.052 4.456 -0.260 1.834 N1 3VU 21
3VU N N2 N 0 1 Y N N N N N -9.590 -15.596 19.326 4.585 0.229 -0.353 N 3VU 22
3VU N2 N3 N 0 1 N N N N N N -11.415 -16.424 18.098 6.590 -0.035 0.868 N2 3VU 23
3VU H1 H1 H 0 1 N N N N N N -7.620 -12.045 19.356 0.755 2.352 -0.729 H1 3VU 24
3VU H2 H2 H 0 1 N N N N N N -5.030 -10.097 16.412 -2.916 4.020 0.233 H2 3VU 25
3VU H3 H3 H 0 1 N N N N N N -3.507 -11.907 16.486 -2.933 -0.449 1.671 H3 3VU 26
3VU H4 H4 H 0 1 N N N N N N -2.037 -12.621 17.231 -3.118 -1.849 0.589 H4 3VU 27
3VU H5 H5 H 0 1 N N N N N N -2.245 -14.209 20.395 -1.689 -2.712 -2.240 H5 3VU 28
3VU H6 H6 H 0 1 N N N N N N -2.786 -15.390 19.154 -0.738 -3.269 -0.842 H6 3VU 29
3VU H7 H7 H 0 1 N N N N N N -2.069 -13.822 18.650 -2.356 -2.567 -0.596 H7 3VU 30
3VU H8 H8 H 0 1 N N N N N N -4.952 -16.057 21.119 1.765 -2.625 -0.739 H8 3VU 31
3VU H9 H9 H 0 1 N N N N N N -6.006 -16.449 19.719 0.781 -2.887 -2.198 H9 3VU 32
3VU H10 H10 H 0 1 N N N N N N -4.225 -16.346 19.502 2.212 -1.830 -2.268 H10 3VU 33
3VU H11 H11 H 0 1 N N N N N N -0.605 -9.308 16.711 -6.429 -1.462 2.118 H11 3VU 34
3VU H12 H12 H 0 1 N N N N N N -2.366 -11.359 19.268 -3.671 -0.263 -1.283 H12 3VU 35
3VU H13 H13 H 0 1 N N N N N N -11.793 -16.383 17.173 7.125 0.144 0.079 H13 3VU 36
3VU H14 H14 H 0 1 N N N N N N -11.183 -17.371 18.322 7.024 -0.222 1.715 H14 3VU 37
#
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
3VU O2 C8 DOUB N N 1
3VU C8 C7 SING N N 2
3VU C8 O1 SING N N 3
3VU O4 B SING N N 4
3VU N1 S SING Y N 5
3VU N1 C12 DOUB Y N 6
3VU C7 C6 SING N N 7
3VU S C11 SING Y N 8
3VU N2 C12 SING N N 9
3VU C12 N SING Y N 10
3VU B O SING N N 11
3VU B C SING N N 12
3VU O C6 SING N N 13
3VU C6 C5 SING N N 14
3VU C C5 DOUB Y N 15
3VU C C1 SING Y N 16
3VU C5 C4 SING Y N 17
3VU C11 N DOUB Y N 18
3VU C11 O3 SING N N 19
3VU C1 C2 DOUB Y N 20
3VU C9 C4 SING N N 21
3VU C4 C3 DOUB Y N 22
3VU C2 C3 SING Y N 23
3VU C2 O3 SING N N 24
3VU C3 C10 SING N N 25
3VU C1 H1 SING N N 26
3VU O4 H2 SING N N 27
3VU C7 H3 SING N N 28
3VU C7 H4 SING N N 29
3VU C9 H5 SING N N 30
3VU C9 H6 SING N N 31
3VU C9 H7 SING N N 32
3VU C10 H8 SING N N 33
3VU C10 H9 SING N N 34
3VU C10 H10 SING N N 35
3VU O1 H11 SING N N 36
3VU C6 H12 SING N N 37
3VU N2 H13 SING N N 38
3VU N2 H14 SING N N 39
#
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
3VU SMILES ACDLabs 12.01 O=C(O)CC3OB(O)c2cc(Oc1nc(ns1)N)c(c(c23)C)C
3VU InChI InChI 1.03 InChI=1S/C13H14BN3O5S/c1-5-6(2)11-7(14(20)22-9(11)4-10(18)19)3-8(5)21-13-16-12(15)17-23-13/h3,9,20H,4H2,1-2H3,(H2,15,17)(H,18,19)/t9-/m1/s1
3VU InChIKey InChI 1.03 CXFHZAGALDYYDH-SECBINFHSA-N
3VU SMILES_CANONICAL CACTVS 3.385 Cc1c(C)c2[C@@H](CC(O)=O)OB(O)c2cc1Oc3snc(N)n3
3VU SMILES CACTVS 3.385 Cc1c(C)c2[CH](CC(O)=O)OB(O)c2cc1Oc3snc(N)n3
3VU SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 B1(c2cc(c(c(c2[C@H](O1)CC(=O)O)C)C)Oc3nc(ns3)N)O
3VU SMILES "OpenEye OEToolkits" 1.9.2 B1(c2cc(c(c(c2C(O1)CC(=O)O)C)C)Oc3nc(ns3)N)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
3VU "SYSTEMATIC NAME" ACDLabs 12.01 "{(3R)-6-[(3-amino-1,2,4-thiadiazol-5-yl)oxy]-1-hydroxy-4,5-dimethyl-1,3-dihydro-2,1-benzoxaborol-3-yl}acetic acid"
3VU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "2-[(3R)-6-[(3-azanyl-1,2,4-thiadiazol-5-yl)oxy]-4,5-dimethyl-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]ethanoic 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
3VU 'Create component' 2014-11-19 RCSB
3VU 'Initial release' 2015-08-05 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
3VU C1 C 6.812 -0.094 1
3VU C2 C 5.513 0.656 2
3VU C3 C 5.513 2.156 3
3VU O4 O 9.996 -1.227 4
3VU C7 C 9.996 4.039 5
3VU C8 C 11.464 4.348 6
3VU C9 C 6.812 4.406 7
3VU C10 C 4.213 2.906 8
3VU C11 C 4.213 -1.594 9
3VU C12 C 4.963 -3.902 10
3VU O1 O 12.466 3.232 11
3VU O2 O 11.930 5.774 12
3VU C6 C 9.530 2.613 13
3VU O O 10.405 1.406 14
3VU B B 9.530 0.199 15
3VU C5 C 8.111 2.156 16
3VU C C 8.111 0.656 17
3VU C4 C 6.812 2.906 18
3VU O3 O 4.213 -0.094 19
3VU S S 3.000 -2.476 20
3VU N1 N 3.463 -3.902 21
3VU N N 5.427 -2.476 22
3VU N2 N 5.845 -5.116 23
#
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
3VU O2 C8 DOUBLE NONE 1
3VU C8 C7 SINGLE NONE 2
3VU C8 O1 SINGLE NONE 3
3VU O4 B SINGLE NONE 4
3VU N1 S SINGLE NONE 5
3VU N1 C12 DOUBLE NONE 6
3VU C6 C7 SINGLE BEGINWEDGE 7
3VU S C11 SINGLE NONE 8
3VU N2 C12 SINGLE NONE 9
3VU C12 N SINGLE NONE 10
3VU B O SINGLE NONE 11
3VU B C SINGLE NONE 12
3VU O C6 SINGLE NONE 13
3VU C6 C5 SINGLE NONE 14
3VU C C5 SINGLE NONE 15
3VU C C1 DOUBLE NONE 16
3VU C5 C4 DOUBLE NONE 17
3VU C11 N DOUBLE NONE 18
3VU C11 O3 SINGLE NONE 19
3VU C1 C2 SINGLE NONE 20
3VU C9 C4 SINGLE NONE 21
3VU C4 C3 SINGLE NONE 22
3VU C2 C3 DOUBLE NONE 23
3VU C2 O3 SINGLE NONE 24
3VU C3 C10 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
3VU MurckoScaffold S1 scaffold B1OCc2ccc(Oc3ncns3)cc21 InChI=1S/C9H7BN2O2S/c1-2-7(14-9-11-5-12-15-9)3-8-6(1)4-13-10-8/h1-3,5,10H,4H2 QGJOYCXJTJKJIM-UHFFFAOYSA-N
3VU phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
3VU C1 S1 1
3VU C2 S1 1
3VU C3 S1 1
3VU C11 S1 1
3VU C12 S1 1
3VU C6 S1 1
3VU O S1 1
3VU B S1 1
3VU C5 S1 1
3VU C S1 1
3VU C4 S1 1
3VU O3 S1 1
3VU S S1 1
3VU N1 S1 1
3VU N S1 1
3VU C1 F1 1
3VU C F1 1
3VU C5 F1 1
3VU C4 F1 1
3VU C3 F1 1
3VU C2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3VU
_pdbe_chem_comp_rdkit_properties.exactmw 335.075
_pdbe_chem_comp_rdkit_properties.amw 335.150
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.308
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 155.697
_pdbe_chem_comp_rdkit_properties.tpsa 127.790
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.707
_pdbe_chem_comp_rdkit_properties.CrippenMR 81.155
_pdbe_chem_comp_rdkit_properties.chi0v 11.685
_pdbe_chem_comp_rdkit_properties.chi1v 6.585
_pdbe_chem_comp_rdkit_properties.chi2v 3.319
_pdbe_chem_comp_rdkit_properties.chi3v 3.319
_pdbe_chem_comp_rdkit_properties.chi4v 2.294
_pdbe_chem_comp_rdkit_properties.chi0n 24.868
_pdbe_chem_comp_rdkit_properties.chi1n 12.523
_pdbe_chem_comp_rdkit_properties.chi2n 2.734
_pdbe_chem_comp_rdkit_properties.chi3n 2.734
_pdbe_chem_comp_rdkit_properties.chi4n 1.850
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.165
_pdbe_chem_comp_rdkit_properties.kappa1 6.041
_pdbe_chem_comp_rdkit_properties.kappa2 5.799
_pdbe_chem_comp_rdkit_properties.kappa3 2.876
_pdbe_chem_comp_rdkit_properties.Phi 1.523
#
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
3VU UniChem ChEMBL CHEMBL4470848
3VU UniChem PDBe 3VU
3VU UniChem ZINC ZINC000263620333
3VU UniChem PubChem 137348183
#
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
3VU C1 0.190 0.939 1.571 ETKDGv3 1
3VU C2 1.128 -0.034 0.965 ETKDGv3 2
3VU C3 0.760 -0.745 -0.139 ETKDGv3 3
3VU O4 -2.513 2.339 2.695 ETKDGv3 4
3VU C7 -3.796 -0.376 -0.265 ETKDGv3 5
3VU C8 -5.192 -0.005 -0.653 ETKDGv3 6
3VU C9 -0.983 -1.210 -2.038 ETKDGv3 7
3VU C10 1.682 -1.788 -0.721 ETKDGv3 8
3VU C11 3.559 0.254 0.984 ETKDGv3 9
3VU C12 5.790 0.615 0.698 ETKDGv3 10
3VU O1 -5.594 -0.118 -1.980 ETKDGv3 11
3VU O2 -5.992 0.443 0.212 ETKDGv3 12
3VU C6 -2.827 0.788 -0.532 ETKDGv3 13
3VU O -3.199 1.911 0.266 ETKDGv3 14
3VU B -2.164 2.029 1.311 ETKDGv3 15
3VU C5 -1.404 0.408 -0.184 ETKDGv3 16
3VU C -0.985 1.128 0.978 ETKDGv3 17
3VU C4 -0.575 -0.474 -0.786 ETKDGv3 18
3VU O3 2.377 -0.204 1.569 ETKDGv3 19
3VU S 3.708 1.214 -0.486 ETKDGv3 20
3VU N1 5.461 1.279 -0.375 ETKDGv3 21
3VU N 4.728 0.026 1.486 ETKDGv3 22
3VU N2 7.155 0.473 1.083 ETKDGv3 23
3VU H1 0.463 1.495 2.458 ETKDGv3 24
3VU H2 -2.930 1.510 3.044 ETKDGv3 25
3VU H3 -3.768 -0.651 0.813 ETKDGv3 26
3VU H4 -3.497 -1.271 -0.848 ETKDGv3 27
3VU H5 -1.332 -2.229 -1.771 ETKDGv3 28
3VU H6 -0.121 -1.291 -2.732 ETKDGv3 29
3VU H7 -1.787 -0.685 -2.591 ETKDGv3 30
3VU H8 2.232 -1.359 -1.584 ETKDGv3 31
3VU H9 1.102 -2.671 -1.062 ETKDGv3 32
3VU H10 2.413 -2.162 0.025 ETKDGv3 33
3VU H11 -6.531 0.144 -2.263 ETKDGv3 34
3VU H12 -2.877 1.087 -1.601 ETKDGv3 35
3VU H13 7.404 -0.061 1.945 ETKDGv3 36
3VU H14 7.916 0.901 0.509 ETKDGv3 37
#