data_K5G
#
_chem_comp.id K5G
_chem_comp.name 4-(3-bromophenoxy)-N-[(3S)-2-oxothiolan-3-yl]butanamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H16 Br N O3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-10-30
_chem_comp.pdbx_modified_date 2019-03-29
_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 358.251
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K5G
_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 6MWL
_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
K5G BR1 BR1 BR 0 0 N N N N N N 63.249 11.397 16.967 -6.800 0.849 0.149 BR1 K5G 1
K5G C02 C1 C 0 1 Y N N N N N 64.163 10.150 18.131 -5.249 -0.199 -0.116 C02 K5G 2
K5G C03 C2 C 0 1 Y N N N N N 63.634 8.890 18.279 -4.001 0.337 0.143 C03 K5G 3
K5G C04 C3 C 0 1 Y N N N N N 64.276 7.987 19.094 -2.864 -0.433 -0.052 C04 K5G 4
K5G C18 C4 C 0 1 Y N N N N N 65.439 8.321 19.778 -2.981 -1.739 -0.506 C18 K5G 5
K5G C19 C5 C 0 1 Y N N N N N 65.968 9.598 19.613 -4.231 -2.270 -0.763 C19 K5G 6
K5G C20 C6 C 0 1 Y N N N N N 65.328 10.512 18.784 -5.364 -1.503 -0.563 C20 K5G 7
K5G O05 O1 O 0 1 N N N N N N 63.699 6.760 19.215 -1.635 0.091 0.201 O05 K5G 8
K5G C06 C7 C 0 1 N N N N N N 64.278 5.745 19.929 -0.509 -0.759 -0.022 C06 K5G 9
K5G C07 C8 C 0 1 N N N N N N 63.521 4.477 19.790 0.777 -0.001 0.315 C07 K5G 10
K5G C08 C9 C 0 1 N N N N N N 62.108 4.458 20.294 1.983 -0.911 0.076 C08 K5G 11
K5G C09 C10 C 0 1 N N N N N N 61.390 3.153 20.187 3.249 -0.164 0.408 C09 K5G 12
K5G O10 O2 O 0 1 N N N N N N 61.290 2.664 19.064 3.192 0.983 0.797 O10 K5G 13
K5G N11 N1 N 0 1 N N N N N N 60.871 2.473 21.345 4.445 -0.771 0.273 N11 K5G 14
K5G C12 C11 C 0 1 N N S N N N 60.330 1.456 21.311 5.676 -0.045 0.595 C12 K5G 15
K5G C13 C12 C 0 1 N N N N N N 60.939 0.395 22.390 6.752 -1.043 1.028 C13 K5G 16
K5G C14 C13 C 0 1 N N N N N N 59.850 -0.653 22.585 8.114 -0.370 0.776 C14 K5G 17
K5G S15 S1 S 0 1 N N N N N N 58.428 0.088 22.497 7.841 0.669 -0.692 S15 K5G 18
K5G C16 C14 C 0 1 N N N N N N 58.903 1.489 21.697 6.126 0.730 -0.614 C16 K5G 19
K5G O17 O3 O 0 1 N N N N N N 58.207 2.450 21.425 5.400 1.300 -1.401 O17 K5G 20
K5G H1 H1 H 0 1 N N N N N N 62.727 8.613 17.763 -3.912 1.353 0.496 H1 K5G 21
K5G H2 H2 H 0 1 N N N N N N 65.923 7.604 20.425 -2.097 -2.339 -0.659 H2 K5G 22
K5G H3 H3 H 0 1 N N N N N N 66.875 9.878 20.129 -4.323 -3.286 -1.117 H3 K5G 23
K5G H4 H4 H 0 1 N N N N N N 65.739 11.502 18.650 -6.339 -1.922 -0.761 H4 K5G 24
K5G H5 H5 H 0 1 N N N N N N 65.303 5.590 19.562 -0.587 -1.641 0.614 H5 K5G 25
K5G H6 H6 H 0 1 N N N N N N 64.308 6.028 20.992 -0.486 -1.066 -1.067 H6 K5G 26
K5G H7 H7 H 0 1 N N N N N N 63.493 4.225 18.720 0.856 0.881 -0.321 H7 K5G 27
K5G H8 H8 H 0 1 N N N N N N 62.126 4.746 21.356 1.905 -1.793 0.712 H8 K5G 28
K5G H9 H9 H 0 1 N N N N N N 60.987 2.911 22.236 4.491 -1.689 -0.038 H9 K5G 29
K5G H10 H10 H 0 1 N N N N N N 60.400 0.965 20.329 5.480 0.648 1.413 H10 K5G 30
K5G H11 H11 H 0 1 N N N N N N 61.855 -0.070 21.997 6.641 -1.274 2.087 H11 K5G 31
K5G H12 H12 H 0 1 N N N N N N 61.163 0.899 23.342 6.672 -1.955 0.437 H12 K5G 32
K5G H13 H13 H 0 1 N N N N N N 59.922 -1.418 21.797 8.399 0.244 1.630 H13 K5G 33
K5G H14 H14 H 0 1 N N N N N N 59.962 -1.130 23.570 8.878 -1.121 0.576 H14 K5G 34
K5G H15 H15 H 0 1 N N N N N N 64.076 3.700 20.335 0.754 0.306 1.361 H15 K5G 35
K5G H16 H16 H 0 1 N N N N N N 61.537 5.204 19.722 2.006 -1.218 -0.969 H16 K5G 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
K5G BR1 C02 SING N N 1
K5G C02 C03 DOUB Y N 2
K5G C02 C20 SING Y N 3
K5G C03 C04 SING Y N 4
K5G C20 C19 DOUB Y N 5
K5G O10 C09 DOUB N N 6
K5G C04 O05 SING N N 7
K5G C04 C18 DOUB Y N 8
K5G O05 C06 SING N N 9
K5G C19 C18 SING Y N 10
K5G C07 C06 SING N N 11
K5G C07 C08 SING N N 12
K5G C09 C08 SING N N 13
K5G C09 N11 SING N N 14
K5G C12 N11 SING N N 15
K5G C12 C16 SING N N 16
K5G C12 C13 SING N N 17
K5G O17 C16 DOUB N N 18
K5G C16 S15 SING N N 19
K5G C13 C14 SING N N 20
K5G S15 C14 SING N N 21
K5G C03 H1 SING N N 22
K5G C18 H2 SING N N 23
K5G C19 H3 SING N N 24
K5G C20 H4 SING N N 25
K5G C06 H5 SING N N 26
K5G C06 H6 SING N N 27
K5G C07 H7 SING N N 28
K5G C08 H8 SING N N 29
K5G N11 H9 SING N N 30
K5G C12 H10 SING N N 31
K5G C13 H11 SING N N 32
K5G C13 H12 SING N N 33
K5G C14 H13 SING N N 34
K5G C14 H14 SING N N 35
K5G C07 H15 SING N N 36
K5G C08 H16 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
K5G SMILES ACDLabs 12.01 Brc2cc(OCCCC(NC1C(SCC1)=O)=O)ccc2
K5G InChI InChI 1.03 InChI=1S/C14H16BrNO3S/c15-10-3-1-4-11(9-10)19-7-2-5-13(17)16-12-6-8-20-14(12)18/h1,3-4,9,12H,2,5-8H2,(H,16,17)/t12-/m0/s1
K5G InChIKey InChI 1.03 WTRVPDIAMVDWRQ-LBPRGKRZSA-N
K5G SMILES_CANONICAL CACTVS 3.385 Brc1cccc(OCCCC(=O)N[C@H]2CCSC2=O)c1
K5G SMILES CACTVS 3.385 Brc1cccc(OCCCC(=O)N[CH]2CCSC2=O)c1
K5G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cc(cc(c1)Br)OCCCC(=O)N[C@H]2CCSC2=O
K5G SMILES "OpenEye OEToolkits" 2.0.6 c1cc(cc(c1)Br)OCCCC(=O)NC2CCSC2=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
K5G "SYSTEMATIC NAME" ACDLabs 12.01 4-(3-bromophenoxy)-N-[(3S)-2-oxothiolan-3-yl]butanamide
K5G "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-(3-bromanylphenoxy)-~{N}-[(3~{S})-2-oxidanylidenethiolan-3-yl]butanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
K5G 'Create component' 2018-10-30 RCSB
K5G 'Initial release' 2019-04-03 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
K5G BR1 Br 3.000 -6.779 1
K5G C02 C 4.299 -6.029 2
K5G C03 C 4.299 -4.529 3
K5G C04 C 5.598 -3.779 4
K5G C18 C 6.897 -4.529 5
K5G C19 C 6.897 -6.029 6
K5G C20 C 5.598 -6.779 7
K5G O05 O 5.598 -2.279 8
K5G C06 C 6.897 -1.529 9
K5G C07 C 6.897 -0.029 10
K5G C08 C 8.196 0.721 11
K5G C09 C 8.196 2.221 12
K5G O10 O 6.897 2.971 13
K5G N11 N 9.495 2.971 14
K5G C12 C 9.495 4.471 15
K5G C13 C 10.709 5.353 16
K5G C14 C 10.245 6.779 17
K5G S15 S 8.745 6.779 18
K5G C16 C 8.282 5.353 19
K5G O17 O 6.855 4.889 20
#
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
K5G BR1 C02 SINGLE NONE 1
K5G C02 C03 DOUBLE NONE 2
K5G C02 C20 SINGLE NONE 3
K5G C03 C04 SINGLE NONE 4
K5G C20 C19 DOUBLE NONE 5
K5G O10 C09 DOUBLE NONE 6
K5G C04 O05 SINGLE NONE 7
K5G C04 C18 DOUBLE NONE 8
K5G O05 C06 SINGLE NONE 9
K5G C19 C18 SINGLE NONE 10
K5G C07 C06 SINGLE NONE 11
K5G C07 C08 SINGLE NONE 12
K5G C09 C08 SINGLE NONE 13
K5G C09 N11 SINGLE NONE 14
K5G C12 N11 SINGLE BEGINDASH 15
K5G C12 C16 SINGLE NONE 16
K5G C12 C13 SINGLE NONE 17
K5G O17 C16 DOUBLE NONE 18
K5G C16 S15 SINGLE NONE 19
K5G C13 C14 SINGLE NONE 20
K5G S15 C14 SINGLE NONE 21
#
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
K5G MurckoScaffold S1 scaffold 'O=C(CCCOc1ccccc1)N[C@H]1CCSC1=O' InChI=1S/C14H17NO3S/c16-13(15-12-8-10-19-14(12)17)7-4-9-18-11-5-2-1-3-6-11/h1-3,5-6,12H,4,7-10H2,(H,15,16)/t12-/m0/s1 POEMXECLTTUQIS-LBPRGKRZSA-N
K5G amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
K5G peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
K5G phenyl F3 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
K5G C02 S1 1
K5G C03 S1 1
K5G C04 S1 1
K5G C18 S1 1
K5G C19 S1 1
K5G C20 S1 1
K5G O05 S1 1
K5G C06 S1 1
K5G C07 S1 1
K5G C08 S1 1
K5G C09 S1 1
K5G O10 S1 1
K5G N11 S1 1
K5G C12 S1 1
K5G C13 S1 1
K5G C14 S1 1
K5G S15 S1 1
K5G C16 S1 1
K5G O17 S1 1
K5G N11 F1 1
K5G C09 F1 1
K5G O10 F1 1
K5G C08 F1 1
K5G O17 F2 1
K5G C16 F2 1
K5G C12 F2 1
K5G N11 F2 1
K5G C02 F3 1
K5G C03 F3 1
K5G C04 F3 1
K5G C18 F3 1
K5G C19 F3 1
K5G C20 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K5G
_pdbe_chem_comp_rdkit_properties.exactmw 357.003
_pdbe_chem_comp_rdkit_properties.amw 358.257
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 152.860
_pdbe_chem_comp_rdkit_properties.tpsa 55.400
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.294
_pdbe_chem_comp_rdkit_properties.CrippenMR 82.274
_pdbe_chem_comp_rdkit_properties.chi0v 11.861
_pdbe_chem_comp_rdkit_properties.chi1v 6.470
_pdbe_chem_comp_rdkit_properties.chi2v 2.644
_pdbe_chem_comp_rdkit_properties.chi3v 2.644
_pdbe_chem_comp_rdkit_properties.chi4v 1.647
_pdbe_chem_comp_rdkit_properties.chi0n 25.458
_pdbe_chem_comp_rdkit_properties.chi1n 12.808
_pdbe_chem_comp_rdkit_properties.chi2n 1.665
_pdbe_chem_comp_rdkit_properties.chi3n 1.665
_pdbe_chem_comp_rdkit_properties.chi4n 0.934
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.010
_pdbe_chem_comp_rdkit_properties.kappa1 4.745
_pdbe_chem_comp_rdkit_properties.kappa2 7.688
_pdbe_chem_comp_rdkit_properties.kappa3 4.830
_pdbe_chem_comp_rdkit_properties.Phi 1.824
#
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
K5G UniChem PDBe K5G
K5G UniChem SureChEMBL SCHEMBL19308416
K5G UniChem PubChem 130387784
#
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
K5G BR1 -7.134 -1.335 1.190 ETKDGv3 1
K5G C02 -5.399 -0.558 1.369 ETKDGv3 2
K5G C03 -4.872 0.157 0.366 ETKDGv3 3
K5G C04 -3.526 0.761 0.497 ETKDGv3 4
K5G C18 -2.839 0.588 1.646 ETKDGv3 5
K5G C19 -3.422 -0.201 2.751 ETKDGv3 6
K5G C20 -4.637 -0.746 2.620 ETKDGv3 7
K5G O05 -3.030 1.499 -0.591 ETKDGv3 8
K5G C06 -1.719 2.059 -0.693 ETKDGv3 9
K5G C07 -0.688 0.966 -0.992 ETKDGv3 10
K5G C08 0.721 1.554 -1.103 ETKDGv3 11
K5G C09 1.719 0.472 -1.381 ETKDGv3 12
K5G O10 2.099 0.266 -2.566 ETKDGv3 13
K5G N11 2.204 -0.351 -0.311 ETKDGv3 14
K5G C12 3.186 -1.417 -0.532 ETKDGv3 15
K5G C13 4.601 -0.837 -0.597 ETKDGv3 16
K5G C14 5.201 -0.894 0.806 ETKDGv3 17
K5G S15 4.700 -2.470 1.560 ETKDGv3 18
K5G C16 3.190 -2.365 0.621 ETKDGv3 19
K5G O17 2.194 -2.993 0.943 ETKDGv3 20
K5G H1 -5.430 0.296 -0.552 ETKDGv3 21
K5G H2 -1.858 1.017 1.791 ETKDGv3 22
K5G H3 -2.862 -0.337 3.667 ETKDGv3 23
K5G H4 -5.061 -1.323 3.431 ETKDGv3 24
K5G H5 -1.461 2.621 0.229 ETKDGv3 25
K5G H6 -1.721 2.786 -1.533 ETKDGv3 26
K5G H7 -0.705 0.203 -0.185 ETKDGv3 27
K5G H8 0.993 2.065 -0.154 ETKDGv3 28
K5G H9 1.876 -0.146 0.661 ETKDGv3 29
K5G H10 2.945 -1.973 -1.464 ETKDGv3 30
K5G H11 4.607 0.205 -0.985 ETKDGv3 31
K5G H12 5.220 -1.464 -1.276 ETKDGv3 32
K5G H13 4.806 -0.056 1.420 ETKDGv3 33
K5G H14 6.308 -0.825 0.762 ETKDGv3 34
K5G H15 -0.959 0.466 -1.947 ETKDGv3 35
K5G H16 0.751 2.308 -1.920 ETKDGv3 36
#