data_D3B
#
_chem_comp.id D3B
_chem_comp.name 1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H17 N3 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-12-15
_chem_comp.pdbx_modified_date 2018-10-05
_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 335.378
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D3B
_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 6FAF
_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
D3B C3 C1 C 0 1 Y N N N N N 13.396 33.461 18.731 3.490 2.311 0.335 C3 D3B 1
D3B C4 C2 C 0 1 Y N N N N N 13.762 34.410 19.673 3.917 0.998 0.273 C4 D3B 2
D3B C5 C3 C 0 1 Y N N N N N 14.366 35.590 19.258 3.019 -0.012 -0.022 C5 D3B 3
D3B C6 C4 C 0 1 Y N N N N N 14.593 35.842 17.910 1.690 0.287 -0.257 C6 D3B 4
D3B C7 C5 C 0 1 Y N N N N N 11.106 35.643 14.334 -3.323 0.298 -0.240 C7 D3B 5
D3B C8 C6 C 0 1 Y N N N N N 11.033 36.341 13.123 -3.047 -1.062 -0.290 C8 D3B 6
D3B N20 N1 N 0 1 N N N N N N 12.322 35.611 15.072 -2.323 1.228 -0.548 N20 D3B 7
D3B C22 C7 C 0 1 N N N N N N 13.580 35.322 14.591 -1.042 0.974 -0.218 C22 D3B 8
D3B O23 O1 O 0 1 N N N N N N 13.868 35.307 13.396 -0.741 -0.099 0.270 O23 D3B 9
D3B N24 N2 N 0 1 N N N N N N 14.494 35.053 15.582 -0.094 1.908 -0.428 N24 D3B 10
D3B C1 C8 C 0 1 Y N N N N N 14.237 34.876 16.963 1.255 1.603 -0.197 C1 D3B 11
D3B C2 C9 C 0 1 Y N N N N N 13.635 33.681 17.377 2.158 2.619 0.106 C2 D3B 12
D3B C9 C10 C 0 1 Y N N N N N 9.853 36.404 12.394 -4.037 -1.977 0.009 C9 D3B 13
D3B C10 C11 C 0 1 Y N N N N N 8.731 35.770 12.913 -5.302 -1.541 0.358 C10 D3B 14
D3B C11 C12 C 0 1 Y N N N N N 8.787 35.075 14.109 -5.580 -0.187 0.408 C11 D3B 15
D3B C12 C13 C 0 1 Y N N N N N 9.969 34.978 14.843 -4.594 0.733 0.111 C12 D3B 16
D3B O1 O2 O 0 1 N N N N N N 12.997 32.933 16.435 1.735 3.909 0.179 O1 D3B 17
D3B S2 S1 S 0 1 N N N N N N 14.929 36.752 20.467 3.570 -1.683 -0.100 S2 D3B 18
D3B O3 O3 O 0 1 N N N N N N 15.262 36.010 21.643 2.642 -2.375 -0.924 O3 D3B 19
D3B O4 O4 O 0 1 N N N N N N 13.945 37.789 20.562 4.964 -1.634 -0.371 O4 D3B 20
D3B N5 N3 N 0 1 N N N N N N 16.285 37.434 19.936 3.413 -2.322 1.420 N5 D3B 21
D3B C13 C14 C 0 1 N N N N N N 10.022 34.151 16.102 -4.899 2.208 0.161 C13 D3B 22
D3B C14 C15 C 0 1 N N N N N N 9.802 37.112 11.062 -3.739 -3.454 -0.046 C14 D3B 23
D3B H1 H1 H 0 1 N N N N N N 12.922 32.544 19.050 4.194 3.097 0.566 H1 D3B 24
D3B H2 H2 H 0 1 N N N N N N 13.579 34.233 20.723 4.954 0.759 0.455 H2 D3B 25
D3B H3 H3 H 0 1 N N N N N N 15.040 36.774 17.597 0.991 -0.503 -0.488 H3 D3B 26
D3B H4 H4 H 0 1 N N N N N N 11.913 36.841 12.748 -2.060 -1.404 -0.563 H4 D3B 27
D3B H5 H5 H 0 1 N N N N N N 12.256 35.822 16.047 -2.553 2.055 -0.999 H5 D3B 28
D3B H6 H6 H 0 1 N N N N N N 15.449 34.973 15.295 -0.344 2.792 -0.740 H6 D3B 29
D3B H7 H7 H 0 1 N N N N N N 7.797 35.820 12.373 -6.075 -2.258 0.591 H7 D3B 30
D3B H8 H8 H 0 1 N N N N N N 7.894 34.596 14.483 -6.569 0.151 0.681 H8 D3B 31
D3B H9 H9 H 0 1 N N N N N N 12.634 32.154 16.841 1.441 4.178 1.060 H9 D3B 32
D3B H10 H10 H 0 1 N N N N N N 16.614 38.094 20.612 3.236 -3.270 1.532 H10 D3B 33
D3B H11 H11 H 0 1 N N N N N N 16.979 36.729 19.794 3.497 -1.749 2.198 H11 D3B 34
D3B H12 H12 H 0 1 N N N N N N 10.294 33.115 15.850 -5.254 2.539 -0.815 H12 D3B 35
D3B H13 H13 H 0 1 N N N N N N 10.774 34.572 16.785 -5.669 2.395 0.909 H13 D3B 36
D3B H14 H14 H 0 1 N N N N N N 9.036 34.163 16.590 -3.995 2.758 0.424 H14 D3B 37
D3B H15 H15 H 0 1 N N N N N N 9.527 38.166 11.217 -3.947 -3.829 -1.048 H15 D3B 38
D3B H16 H16 H 0 1 N N N N N N 10.789 37.057 10.580 -2.690 -3.621 0.195 H16 D3B 39
D3B H17 H17 H 0 1 N N N N N N 9.052 36.628 10.418 -4.366 -3.978 0.676 H17 D3B 40
#
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
D3B C14 C9 SING N N 1
D3B C9 C10 DOUB Y N 2
D3B C9 C8 SING Y N 3
D3B C10 C11 SING Y N 4
D3B C8 C7 DOUB Y N 5
D3B O23 C22 DOUB N N 6
D3B C11 C12 DOUB Y N 7
D3B C7 C12 SING Y N 8
D3B C7 N20 SING N N 9
D3B C22 N20 SING N N 10
D3B C22 N24 SING N N 11
D3B C12 C13 SING N N 12
D3B N24 C1 SING N N 13
D3B O1 C2 SING N N 14
D3B C1 C2 DOUB Y N 15
D3B C1 C6 SING Y N 16
D3B C2 C3 SING Y N 17
D3B C6 C5 DOUB Y N 18
D3B C3 C4 DOUB Y N 19
D3B C5 C4 SING Y N 20
D3B C5 S2 SING N N 21
D3B N5 S2 SING N N 22
D3B S2 O4 DOUB N N 23
D3B S2 O3 DOUB N N 24
D3B C3 H1 SING N N 25
D3B C4 H2 SING N N 26
D3B C6 H3 SING N N 27
D3B C8 H4 SING N N 28
D3B N20 H5 SING N N 29
D3B N24 H6 SING N N 30
D3B C10 H7 SING N N 31
D3B C11 H8 SING N N 32
D3B O1 H9 SING N N 33
D3B N5 H10 SING N N 34
D3B N5 H11 SING N N 35
D3B C13 H12 SING N N 36
D3B C13 H13 SING N N 37
D3B C13 H14 SING N N 38
D3B C14 H15 SING N N 39
D3B C14 H16 SING N N 40
D3B C14 H17 SING N N 41
#
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
D3B InChI InChI 1.03 InChI=1S/C15H17N3O4S/c1-9-3-4-10(2)12(7-9)17-15(20)18-13-8-11(23(16,21)22)5-6-14(13)19/h3-8,19H,1-2H3,(H2,16,21,22)(H2,17,18,20)
D3B InChIKey InChI 1.03 ITJAYNQSUKWUOO-UHFFFAOYSA-N
D3B SMILES_CANONICAL CACTVS 3.385 Cc1ccc(C)c(NC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)c1
D3B SMILES CACTVS 3.385 Cc1ccc(C)c(NC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)c1
D3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 Cc1ccc(c(c1)NC(=O)Nc2cc(ccc2O)S(=O)(=O)N)C
D3B SMILES "OpenEye OEToolkits" 2.0.6 Cc1ccc(c(c1)NC(=O)Nc2cc(ccc2O)S(=O)(=O)N)C
#
_pdbx_chem_comp_identifier.comp_id D3B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier 1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D3B 'Create component' 2017-12-15 RCSB
D3B 'Initial release' 2018-10-10 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
D3B C3 C 5.104 -4.035 1
D3B C4 C 6.404 -4.785 2
D3B C5 C 7.702 -4.035 3
D3B C6 C 7.702 -2.535 4
D3B C7 C 9.002 2.715 5
D3B C8 C 9.002 4.215 6
D3B N20 N 7.702 1.965 7
D3B C22 C 7.702 0.465 8
D3B O23 O 9.002 -0.285 9
D3B N24 N 6.404 -0.285 10
D3B C1 C 6.404 -1.785 11
D3B C2 C 5.104 -2.535 12
D3B C9 C 10.301 4.965 13
D3B C10 C 11.600 4.215 14
D3B C11 C 11.600 2.715 15
D3B C12 C 10.301 1.965 16
D3B O1 O 3.805 -1.785 17
D3B S2 S 9.002 -4.785 18
D3B O3 O 10.301 -5.535 19
D3B O4 O 9.752 -3.486 20
D3B N5 N 8.252 -6.084 21
D3B C13 C 10.301 0.465 22
D3B C14 C 10.301 6.465 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
D3B C14 C9 SINGLE NONE 1
D3B C9 C10 SINGLE NONE 2
D3B C9 C8 DOUBLE NONE 3
D3B C10 C11 DOUBLE NONE 4
D3B C8 C7 SINGLE NONE 5
D3B O23 C22 DOUBLE NONE 6
D3B C11 C12 SINGLE NONE 7
D3B C7 C12 DOUBLE NONE 8
D3B C7 N20 SINGLE NONE 9
D3B C22 N20 SINGLE NONE 10
D3B C22 N24 SINGLE NONE 11
D3B C12 C13 SINGLE NONE 12
D3B N24 C1 SINGLE NONE 13
D3B O1 C2 SINGLE NONE 14
D3B C1 C2 SINGLE NONE 15
D3B C1 C6 DOUBLE NONE 16
D3B C2 C3 DOUBLE NONE 17
D3B C6 C5 SINGLE NONE 18
D3B C3 C4 SINGLE NONE 19
D3B C5 C4 DOUBLE NONE 20
D3B C5 S2 SINGLE NONE 21
D3B N5 S2 SINGLE NONE 22
D3B S2 O4 DOUBLE NONE 23
D3B S2 O3 DOUBLE NONE 24
#
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
D3B MurckoScaffold S1 scaffold O=C(Nc1ccccc1)Nc1ccccc1 InChI=1S/C13H12N2O/c16-13(14-11-7-3-1-4-8-11)15-12-9-5-2-6-10-12/h1-10H,(H2,14,15,16) GWEHVDNNLFDJLR-UHFFFAOYSA-N
D3B 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
D3B C3 S1 1
D3B C4 S1 1
D3B C5 S1 1
D3B C6 S1 1
D3B C7 S1 1
D3B C8 S1 1
D3B N20 S1 1
D3B C22 S1 1
D3B O23 S1 1
D3B N24 S1 1
D3B C1 S1 1
D3B C2 S1 1
D3B C9 S1 1
D3B C10 S1 1
D3B C11 S1 1
D3B C12 S1 1
D3B C3 F1 1
D3B C2 F1 1
D3B C1 F1 1
D3B C6 F1 1
D3B C5 F1 1
D3B C4 F1 1
D3B C7 F1 2
D3B C8 F1 2
D3B C9 F1 2
D3B C10 F1 2
D3B C11 F1 2
D3B C12 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id D3B
_pdbe_chem_comp_rdkit_properties.exactmw 335.094
_pdbe_chem_comp_rdkit_properties.amw 335.385
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 40
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.133
_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 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 157.943
_pdbe_chem_comp_rdkit_properties.tpsa 121.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.859
_pdbe_chem_comp_rdkit_properties.CrippenMR 85.817
_pdbe_chem_comp_rdkit_properties.chi0v 11.699
_pdbe_chem_comp_rdkit_properties.chi1v 6.963
_pdbe_chem_comp_rdkit_properties.chi2v 2.922
_pdbe_chem_comp_rdkit_properties.chi3v 2.922
_pdbe_chem_comp_rdkit_properties.chi4v 1.678
_pdbe_chem_comp_rdkit_properties.chi0n 27.883
_pdbe_chem_comp_rdkit_properties.chi1n 13.720
_pdbe_chem_comp_rdkit_properties.chi2n 2.202
_pdbe_chem_comp_rdkit_properties.chi3n 2.202
_pdbe_chem_comp_rdkit_properties.chi4n 1.272
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.580
_pdbe_chem_comp_rdkit_properties.kappa1 5.217
_pdbe_chem_comp_rdkit_properties.kappa2 6.269
_pdbe_chem_comp_rdkit_properties.kappa3 4.209
_pdbe_chem_comp_rdkit_properties.Phi 1.422
#
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
D3B UniChem ChEMBL CHEMBL4286620
D3B UniChem PDBe D3B
D3B UniChem PubChem 134817797
D3B UniChem BindingDb 50465673
#
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
D3B C3 4.467 -1.855 1.121 ETKDGv3 1
D3B C4 4.914 -1.024 -0.012 ETKDGv3 2
D3B C5 4.056 -0.192 -0.619 ETKDGv3 3
D3B C6 2.663 -0.092 -0.127 ETKDGv3 4
D3B C7 -2.696 0.056 0.410 ETKDGv3 5
D3B C8 -2.571 0.928 -0.788 ETKDGv3 6
D3B N20 -1.524 -0.274 1.179 ETKDGv3 7
D3B C22 -0.255 -0.585 0.585 ETKDGv3 8
D3B O23 -0.172 -0.806 -0.655 ETKDGv3 9
D3B N24 0.908 -0.705 1.418 ETKDGv3 10
D3B C1 2.241 -0.852 0.902 ETKDGv3 11
D3B C2 3.201 -1.788 1.556 ETKDGv3 12
D3B C9 -3.651 1.260 -1.513 ETKDGv3 13
D3B C10 -4.986 0.789 -1.086 ETKDGv3 14
D3B C11 -5.114 0.021 -0.000 ETKDGv3 15
D3B C12 -3.922 -0.376 0.790 ETKDGv3 16
D3B O1 2.808 -2.617 2.607 ETKDGv3 17
D3B S2 4.590 0.814 -1.961 ETKDGv3 18
D3B O3 3.411 1.184 -2.818 ETKDGv3 19
D3B O4 5.578 0.056 -2.803 ETKDGv3 20
D3B N5 5.330 2.251 -1.352 ETKDGv3 21
D3B C13 -4.113 -1.245 2.003 ETKDGv3 22
D3B C14 -3.521 2.175 -2.695 ETKDGv3 23
D3B H1 5.168 -2.533 1.591 ETKDGv3 24
D3B H2 5.942 -1.096 -0.346 ETKDGv3 25
D3B H3 1.998 0.631 -0.580 ETKDGv3 26
D3B H4 -1.599 1.319 -1.064 ETKDGv3 27
D3B H5 -1.597 -0.320 2.220 ETKDGv3 28
D3B H6 0.771 -0.715 2.453 ETKDGv3 29
D3B H7 -5.867 1.070 -1.649 ETKDGv3 30
D3B H8 -6.100 -0.311 0.300 ETKDGv3 31
D3B H9 1.853 -2.656 2.939 ETKDGv3 32
D3B H10 6.119 1.951 -0.736 ETKDGv3 33
D3B H11 4.628 2.718 -0.735 ETKDGv3 34
D3B H12 -3.402 -2.099 1.981 ETKDGv3 35
D3B H13 -3.947 -0.647 2.923 ETKDGv3 36
D3B H14 -5.142 -1.662 2.038 ETKDGv3 37
D3B H15 -3.479 3.227 -2.345 ETKDGv3 38
D3B H16 -4.389 2.057 -3.378 ETKDGv3 39
D3B H17 -2.598 1.943 -3.268 ETKDGv3 40
#