data_7RD
#
_chem_comp.id 7RD
_chem_comp.name (R,E)-3-(4-AZIDOBUTYL)-4-HYDROXY-5-METHYL-5-(2-METHYLBUTA-1,3-DIEN-1-YL)THIOPHEN-2(5H)-ONE
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H19 N3 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-09-19
_chem_comp.pdbx_modified_date 2014-09-05
_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 293.385
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7RD
_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 4C71
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
7RD N2 N2 N -1 1 N N N N N N -13.157 -25.286 39.419 7.451 -1.324 -0.001 N2 7RD 1
7RD N1 N1 N 1 1 N N N N N N -12.083 -25.590 39.635 6.707 -0.536 0.297 N1 7RD 2
7RD N N N 0 1 N N N N N N -10.977 -25.931 40.021 5.963 0.252 0.595 N 7RD 3
7RD C12 C12 C 0 1 N N N N N N -10.764 -25.857 41.442 4.725 0.417 -0.170 C12 7RD 4
7RD C11 C11 C 0 1 N N N N N N -9.737 -26.936 41.701 3.523 0.189 0.748 C11 7RD 5
7RD C10 C10 C 0 1 N N N N N N -9.258 -26.942 43.125 2.230 0.362 -0.052 C10 7RD 6
7RD C9 C9 C 0 1 N N N N N N -8.866 -25.553 43.582 1.028 0.134 0.867 C9 7RD 7
7RD C8 C8 C 0 1 N N N N N N -7.528 -25.100 43.063 -0.246 0.304 0.079 C8 7RD 8
7RD C7 C7 C 0 1 N N N N N N -7.391 -23.997 42.064 -0.803 1.584 -0.104 C7 7RD 9
7RD O O O 0 1 N N N N N N -8.217 -23.307 41.543 -0.356 2.635 0.320 O 7RD 10
7RD S S S 0 1 N N N N N N -5.667 -23.703 41.839 -2.276 1.380 -1.069 S 7RD 11
7RD C13 C13 C 0 1 N N N N N N -6.353 -25.573 43.524 -0.846 -0.743 -0.449 C13 7RD 12
7RD O1 O1 O 0 1 N N N N N N -6.201 -26.575 44.360 -0.368 -1.998 -0.320 O1 7RD 13
7RD C5 C5 C 0 1 N N R N N N -5.055 -24.900 43.112 -2.113 -0.430 -1.207 C5 7RD 14
7RD C6 C6 C 0 1 N N N N N N -4.565 -23.996 44.298 -1.972 -0.845 -2.673 C6 7RD 15
7RD C4 C4 C 0 1 N N N N N N -4.096 -25.900 42.565 -3.296 -1.116 -0.574 C4 7RD 16
7RD C2 C2 C 0 1 N N N N N N -2.890 -25.692 42.036 -3.822 -0.634 0.547 C2 7RD 17
7RD C3 C3 C 0 1 N N N N N N -2.335 -24.306 41.830 -3.130 0.483 1.285 C3 7RD 18
7RD C1 C1 C 0 1 N N N N N N -2.069 -26.780 41.575 -5.081 -1.191 1.067 C1 7RD 19
7RD C C C 0 1 N N N N N N -0.897 -26.718 41.023 -5.607 -0.708 2.188 C 7RD 20
7RD H121 H121 H 0 0 N N N N N N -10.377 -24.869 41.731 4.683 1.426 -0.580 H121 7RD 21
7RD H122 H122 H 0 0 N N N N N N -11.695 -26.061 41.990 4.702 -0.306 -0.985 H122 7RD 22
7RD H111 H111 H 0 0 N N N N N N -10.188 -27.914 41.476 3.565 -0.820 1.158 H111 7RD 23
7RD H112 H112 H 0 0 N N N N N N -8.875 -26.769 41.039 3.545 0.913 1.563 H112 7RD 24
7RD H101 H101 H 0 0 N N N N N N -10.064 -27.317 43.772 2.188 1.371 -0.461 H101 7RD 25
7RD H102 H102 H 0 0 N N N N N N -8.384 -27.605 43.206 2.207 -0.362 -0.866 H102 7RD 26
7RD H91C H91C H 0 0 N N N N N N -9.632 -24.844 43.234 1.069 -0.876 1.276 H91C 7RD 27
7RD H92C H92C H 0 0 N N N N N N -8.832 -25.546 44.681 1.050 0.857 1.682 H92C 7RD 28
7RD H1 H1 H 0 1 N N N N N N -5.276 -26.711 44.528 0.449 -2.106 0.186 H1 7RD 29
7RD H61C H61C H 0 0 N N N N N N -4.180 -24.631 45.109 -1.100 -0.356 -3.107 H61C 7RD 30
7RD H62C H62C H 0 0 N N N N N N -3.765 -23.329 43.944 -1.850 -1.926 -2.734 H62C 7RD 31
7RD H63C H63C H 0 0 N N N N N N -5.406 -23.394 44.672 -2.865 -0.548 -3.222 H63C 7RD 32
7RD H4 H4 H 0 1 N N N N N N -4.420 -26.929 42.602 -3.716 -2.000 -1.031 H4 7RD 33
7RD H31C H31C H 0 0 N N N N N N -1.332 -24.375 41.383 -3.422 1.440 0.852 H31C 7RD 34
7RD H32C H32C H 0 0 N N N N N N -2.998 -23.742 41.158 -3.418 0.456 2.336 H32C 7RD 35
7RD H33C H33C H 0 0 N N N N N N -2.270 -23.789 42.799 -2.050 0.360 1.200 H33C 7RD 36
7RD HA HA H 0 1 N N N N N N -2.479 -27.771 41.705 -5.577 -1.991 0.538 HA 7RD 37
7RD HC1 HC1 H 0 1 N N N N N N -0.392 -27.625 40.724 -5.111 0.092 2.717 HC1 7RD 38
7RD HC2 HC2 H 0 1 N N N N N N -0.426 -25.760 40.862 -6.531 -1.117 2.569 HC2 7RD 39
#
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
7RD N2 N1 DOUB N N 1
7RD N1 N DOUB N N 2
7RD N C12 SING N N 3
7RD C12 C11 SING N N 4
7RD C11 C10 SING N N 5
7RD C10 C9 SING N N 6
7RD C9 C8 SING N N 7
7RD C8 C7 SING N N 8
7RD C8 C13 DOUB N N 9
7RD C7 O DOUB N N 10
7RD C7 S SING N N 11
7RD S C5 SING N N 12
7RD C13 O1 SING N N 13
7RD C13 C5 SING N N 14
7RD C5 C6 SING N N 15
7RD C5 C4 SING N N 16
7RD C4 C2 DOUB N E 17
7RD C2 C3 SING N N 18
7RD C2 C1 SING N N 19
7RD C1 C DOUB N N 20
7RD C12 H121 SING N N 21
7RD C12 H122 SING N N 22
7RD C11 H111 SING N N 23
7RD C11 H112 SING N N 24
7RD C10 H101 SING N N 25
7RD C10 H102 SING N N 26
7RD C9 H91C SING N N 27
7RD C9 H92C SING N N 28
7RD O1 H1 SING N N 29
7RD C6 H61C SING N N 30
7RD C6 H62C SING N N 31
7RD C6 H63C SING N N 32
7RD C4 H4 SING N N 33
7RD C3 H31C SING N N 34
7RD C3 H32C SING N N 35
7RD C3 H33C SING N N 36
7RD C1 HA SING N N 37
7RD C HC1 SING N N 38
7RD C HC2 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
7RD SMILES ACDLabs 12.01 O=C1SC(/C=C(/C=C)C)(C(O)=C1CCCC/N=[N+]=[N-])C
7RD InChI InChI 1.03 InChI=1S/C14H19N3O2S/c1-4-10(2)9-14(3)12(18)11(13(19)20-14)7-5-6-8-16-17-15/h4,9,18H,1,5-8H2,2-3H3/b10-9+/t14-/m1/s1
7RD InChIKey InChI 1.03 YWCFDTCBMVZYIG-ATWMFIQVSA-N
7RD SMILES_CANONICAL CACTVS 3.385 C\C(C=C)=C/[C@@]1(C)SC(=O)C(=C1O)CCCCN=[N+]=[N-]
7RD SMILES CACTVS 3.385 CC(C=C)=C[C]1(C)SC(=O)C(=C1O)CCCCN=[N+]=[N-]
7RD SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C/C(=C\[C@@]1(C(=C(C(=O)S1)CCCCN=[N+]=[N-])O)C)/C=C
7RD SMILES "OpenEye OEToolkits" 1.9.2 CC(=CC1(C(=C(C(=O)S1)CCCCN=[N+]=[N-])O)C)C=C
#
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
7RD "SYSTEMATIC NAME" ACDLabs 12.01 (5R)-3-(4-azidobutyl)-4-hydroxy-5-methyl-5-[(1E)-2-methylbuta-1,3-dien-1-yl]thiophen-2(5H)-one
7RD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (5R)-3-(4-azidobutyl)-5-methyl-5-[(1E)-2-methylbuta-1,3-dienyl]-4-oxidanyl-thiophen-2-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7RD 'Create component' 2013-09-19 EBI
7RD 'Initial release' 2013-10-09 RCSB
7RD 'Modify descriptor' 2014-09-05 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
7RD N2 N 5.377 -6.850 1
7RD N1 N 4.767 -5.480 2
7RD N N 4.156 -4.110 3
7RD C12 C 5.038 -2.896 4
7RD C11 C 4.428 -1.526 5
7RD C10 C 5.310 -0.312 6
7RD C9 C 4.699 1.058 7
7RD C8 C 5.581 2.272 8
7RD C7 C 7.081 2.272 9
7RD O O 7.963 1.058 10
7RD S S 7.545 3.698 11
7RD C13 C 5.118 3.698 12
7RD O1 O 3.691 4.162 13
7RD C5 C 6.331 4.580 14
7RD C6 C 5.449 5.793 15
7RD C4 C 7.213 5.793 16
7RD C2 C 8.705 5.637 17
7RD C3 C 9.315 4.266 18
7RD C1 C 9.586 6.850 19
7RD C C 11.078 6.694 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
7RD N2 N1 DOUBLE NONE 1
7RD N1 N DOUBLE NONE 2
7RD N C12 SINGLE NONE 3
7RD C12 C11 SINGLE NONE 4
7RD C11 C10 SINGLE NONE 5
7RD C10 C9 SINGLE NONE 6
7RD C9 C8 SINGLE NONE 7
7RD C8 C7 SINGLE NONE 8
7RD C8 C13 DOUBLE NONE 9
7RD C7 O DOUBLE NONE 10
7RD C7 S SINGLE NONE 11
7RD S C5 SINGLE NONE 12
7RD C13 O1 SINGLE NONE 13
7RD C13 C5 SINGLE NONE 14
7RD C5 C6 SINGLE BEGINDASH 15
7RD C5 C4 SINGLE ENDUPRIGHT 16
7RD C4 C2 DOUBLE NONE 17
7RD C2 C3 SINGLE ENDDOWNRIGHT 18
7RD C2 C1 SINGLE ENDUPRIGHT 19
7RD C1 C DOUBLE NONE 20
#
_pdbe_chem_comp_substructure.comp_id 7RD
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles O=C1C=CCS1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C4H4OS/c5-4-2-1-3-6-4/h1-2H,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys NMSLUAZZTFUUFZ-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
7RD C8 S1 1
7RD C7 S1 1
7RD O S1 1
7RD S S1 1
7RD C13 S1 1
7RD C5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7RD
_pdbe_chem_comp_rdkit_properties.exactmw 293.120
_pdbe_chem_comp_rdkit_properties.amw 293.392
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_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 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 149.403
_pdbe_chem_comp_rdkit_properties.tpsa 86.060
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.444
_pdbe_chem_comp_rdkit_properties.CrippenMR 82.476
_pdbe_chem_comp_rdkit_properties.chi0v 10.383
_pdbe_chem_comp_rdkit_properties.chi1v 5.507
_pdbe_chem_comp_rdkit_properties.chi2v 2.807
_pdbe_chem_comp_rdkit_properties.chi3v 2.807
_pdbe_chem_comp_rdkit_properties.chi4v 1.943
_pdbe_chem_comp_rdkit_properties.chi0n 28.566
_pdbe_chem_comp_rdkit_properties.chi1n 14.098
_pdbe_chem_comp_rdkit_properties.chi2n 1.823
_pdbe_chem_comp_rdkit_properties.chi3n 1.823
_pdbe_chem_comp_rdkit_properties.chi4n 1.072
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.650
_pdbe_chem_comp_rdkit_properties.kappa1 3.960
_pdbe_chem_comp_rdkit_properties.kappa2 7.217
_pdbe_chem_comp_rdkit_properties.kappa3 3.920
_pdbe_chem_comp_rdkit_properties.Phi 1.429
#
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
7RD UniChem ChEMBL CHEMBL4556828
7RD UniChem PDBe 7RD
7RD UniChem ZINC ZINC000098208579
7RD UniChem SureChEMBL SCHEMBL12968098
7RD UniChem SureChEMBL SCHEMBL16800140
7RD UniChem PubChem 136446118
7RD UniChem BindingDb 214777
#
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
7RD N2 7.321 1.510 2.996 ETKDGv3 1
7RD N1 6.721 1.220 1.962 ETKDGv3 2
7RD N 6.122 0.930 0.927 ETKDGv3 3
7RD C12 4.692 0.657 0.950 ETKDGv3 4
7RD C11 4.209 0.328 -0.465 ETKDGv3 5
7RD C10 2.684 0.166 -0.547 ETKDGv3 6
7RD C9 2.191 -1.133 0.107 ETKDGv3 7
7RD C8 0.703 -1.289 -0.077 ETKDGv3 8
7RD C7 0.125 -2.066 -1.153 ETKDGv3 9
7RD O 0.812 -2.651 -2.032 ETKDGv3 10
7RD S -1.648 -2.104 -1.154 ETKDGv3 11
7RD C13 -0.227 -0.683 0.663 ETKDGv3 12
7RD O1 0.074 0.155 1.741 ETKDGv3 13
7RD C5 -1.669 -0.931 0.269 ETKDGv3 14
7RD C6 -2.385 -1.568 1.473 ETKDGv3 15
7RD C4 -2.295 0.397 -0.146 ETKDGv3 16
7RD C2 -3.576 0.630 -0.518 ETKDGv3 17
7RD C3 -4.635 -0.447 -0.577 ETKDGv3 18
7RD C1 -3.952 2.036 -0.824 ETKDGv3 19
7RD C -5.205 2.492 -0.779 ETKDGv3 20
7RD H121 4.500 -0.201 1.630 ETKDGv3 21
7RD H122 4.155 1.551 1.334 ETKDGv3 22
7RD H111 4.506 1.160 -1.141 ETKDGv3 23
7RD H112 4.710 -0.596 -0.829 ETKDGv3 24
7RD H101 2.396 0.153 -1.621 ETKDGv3 25
7RD H102 2.187 1.044 -0.080 ETKDGv3 26
7RD H91C 2.441 -1.156 1.187 ETKDGv3 27
7RD H92C 2.713 -1.998 -0.356 ETKDGv3 28
7RD H1 1.019 0.374 2.028 ETKDGv3 29
7RD H61C -2.525 -0.821 2.284 ETKDGv3 30
7RD H62C -3.373 -1.983 1.199 ETKDGv3 31
7RD H63C -1.785 -2.413 1.875 ETKDGv3 32
7RD H4 -1.629 1.255 -0.128 ETKDGv3 33
7RD H31C -4.228 -1.432 -0.862 ETKDGv3 34
7RD H32C -5.145 -0.522 0.406 ETKDGv3 35
7RD H33C -5.390 -0.205 -1.353 ETKDGv3 36
7RD HA -3.170 2.749 -1.060 ETKDGv3 37
7RD HC1 -6.038 1.860 -0.502 ETKDGv3 38
7RD HC2 -5.406 3.532 -1.000 ETKDGv3 39
#