data_58K
#
_chem_comp.id 58K
_chem_comp.name cyclopeptin
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H16 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-08-20
_chem_comp.pdbx_modified_date 2015-11-20
_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 280.321
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 58K
_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 5DAW
_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
58K C4 C1 C 0 1 N N N N N N -25.057 -19.973 -3.489 -0.733 0.038 -1.514 C4 58K 1
58K C7 C2 C 0 1 N N S N N N -25.077 -22.411 -3.959 0.215 -1.525 0.101 C7 58K 2
58K C8 C3 C 0 1 N N N N N N -25.098 -23.835 -3.317 0.551 -0.420 1.104 C8 58K 3
58K C10 C4 C 0 1 Y N N N N N -24.782 -25.144 -1.365 3.037 -0.427 1.396 C10 58K 4
58K C13 C5 C 0 1 Y N N N N N -23.015 -23.333 -0.241 3.315 1.712 -0.333 C13 58K 5
58K C15 C6 C 0 1 N N N N N N -25.800 -22.303 -5.177 -1.104 -2.151 0.464 C15 58K 6
58K C20 C7 C 0 1 Y N N N N N -22.691 -19.128 -6.835 -3.250 2.000 1.295 C20 58K 7
58K C12 C8 C 0 1 Y N N N N N -23.334 -24.502 0.448 4.432 1.150 0.255 C12 58K 8
58K C11 C9 C 0 1 Y N N N N N -24.222 -25.410 -0.118 4.293 0.080 1.120 C11 58K 9
58K C14 C10 C 0 1 Y N N N N N -23.576 -23.069 -1.498 2.060 1.198 -0.066 C14 58K 10
58K C9 C11 C 0 1 Y N N N N N -24.482 -23.974 -2.073 1.920 0.132 0.803 C9 58K 11
58K O16 O1 O 0 1 N N N N N N -26.702 -23.089 -5.459 -1.155 -3.349 0.651 O16 58K 12
58K N17 N1 N 0 1 N N N N N N -25.523 -21.281 -6.097 -2.215 -1.431 0.585 N17 58K 13
58K C18 C12 C 0 1 Y N N N N N -24.524 -20.328 -5.859 -2.295 -0.049 0.457 C18 58K 14
58K C19 C13 C 0 1 Y N N N N N -23.727 -20.047 -6.962 -3.115 0.632 1.361 C19 58K 15
58K C1 C14 C 0 1 Y N N N N N -22.450 -18.503 -5.613 -2.583 2.718 0.305 C1 58K 16
58K C2 C15 C 0 1 Y N N N N N -23.246 -18.797 -4.505 -1.775 2.063 -0.594 C2 58K 17
58K C3 C16 C 0 1 Y N N N N N -24.285 -19.721 -4.633 -1.619 0.669 -0.529 C3 58K 18
58K O5 O2 O 0 1 N N N N N N -25.442 -19.016 -2.821 -0.771 0.452 -2.657 O5 58K 19
58K N6 N2 N 0 1 N N N N N N -25.482 -21.219 -3.151 0.114 -0.954 -1.242 N6 58K 20
58K C23 C17 C 0 1 N N N N N N -26.387 -21.404 -1.979 0.962 -1.485 -2.312 C23 58K 21
58K H1 H1 H 0 1 N N N N N N -24.021 -22.240 -4.216 0.998 -2.283 0.117 H1 58K 22
58K H2 H2 H 0 1 N N N N N N -26.151 -24.133 -3.202 -0.188 0.378 1.027 H2 58K 23
58K H3 H3 H 0 1 N N N N N N -24.597 -24.522 -4.015 0.538 -0.830 2.114 H3 58K 24
58K H4 H4 H 0 1 N N N N N N -25.466 -25.859 -1.797 2.928 -1.263 2.071 H4 58K 25
58K H5 H5 H 0 1 N N N N N N -22.329 -22.624 0.198 3.422 2.554 -1.002 H5 58K 26
58K H6 H6 H 0 1 N N N N N N -22.070 -18.897 -7.688 -3.883 2.517 2.002 H6 58K 27
58K H7 H7 H 0 1 N N N N N N -22.895 -24.701 1.414 5.412 1.551 0.047 H7 58K 28
58K H8 H8 H 0 1 N N N N N N -24.477 -26.318 0.408 5.165 -0.359 1.580 H8 58K 29
58K H9 H9 H 0 1 N N N N N N -23.310 -22.165 -2.026 1.187 1.638 -0.526 H9 58K 30
58K H10 H10 H 0 1 N N N N N N -26.052 -21.231 -6.944 -3.036 -1.906 0.790 H10 58K 31
58K H11 H11 H 0 1 N N N N N N -23.910 -20.537 -7.907 -3.648 0.078 2.120 H11 58K 32
58K H12 H12 H 0 1 N N N N N N -21.645 -17.789 -5.523 -2.701 3.790 0.243 H12 58K 33
58K H13 H13 H 0 1 N N N N N N -23.060 -18.314 -3.557 -1.260 2.625 -1.360 H13 58K 34
58K H14 H14 H 0 1 N N N N N N -26.579 -20.430 -1.506 0.758 -0.948 -3.238 H14 58K 35
58K H15 H15 H 0 1 N N N N N N -27.338 -21.841 -2.316 2.010 -1.356 -2.041 H15 58K 36
58K H16 H16 H 0 1 N N N N N N -25.911 -22.078 -1.251 0.751 -2.545 -2.451 H16 58K 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
58K C19 C20 DOUB Y N 1
58K C19 C18 SING Y N 2
58K C20 C1 SING Y N 3
58K N17 C18 SING N N 4
58K N17 C15 SING N N 5
58K C18 C3 DOUB Y N 6
58K C1 C2 DOUB Y N 7
58K O16 C15 DOUB N N 8
58K C15 C7 SING N N 9
58K C3 C2 SING Y N 10
58K C3 C4 SING N N 11
58K C7 C8 SING N N 12
58K C7 N6 SING N N 13
58K C4 N6 SING N N 14
58K C4 O5 DOUB N N 15
58K C8 C9 SING N N 16
58K N6 C23 SING N N 17
58K C9 C14 DOUB Y N 18
58K C9 C10 SING Y N 19
58K C14 C13 SING Y N 20
58K C10 C11 DOUB Y N 21
58K C13 C12 DOUB Y N 22
58K C11 C12 SING Y N 23
58K C7 H1 SING N N 24
58K C8 H2 SING N N 25
58K C8 H3 SING N N 26
58K C10 H4 SING N N 27
58K C13 H5 SING N N 28
58K C20 H6 SING N N 29
58K C12 H7 SING N N 30
58K C11 H8 SING N N 31
58K C14 H9 SING N N 32
58K N17 H10 SING N N 33
58K C19 H11 SING N N 34
58K C1 H12 SING N N 35
58K C2 H13 SING N N 36
58K C23 H14 SING N N 37
58K C23 H15 SING N N 38
58K C23 H16 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
58K SMILES ACDLabs 12.01 C2(N(C(Cc1ccccc1)C(=O)Nc3c2cccc3)C)=O
58K InChI InChI 1.03 InChI=1S/C17H16N2O2/c1-19-15(11-12-7-3-2-4-8-12)16(20)18-14-10-6-5-9-13(14)17(19)21/h2-10,15H,11H2,1H3,(H,18,20)/t15-/m0/s1
58K InChIKey InChI 1.03 KSQNKZMAMGACTL-HNNXBMFYSA-N
58K SMILES_CANONICAL CACTVS 3.385 CN1[C@@H](Cc2ccccc2)C(=O)Nc3ccccc3C1=O
58K SMILES CACTVS 3.385 CN1[CH](Cc2ccccc2)C(=O)Nc3ccccc3C1=O
58K SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CN1[C@H](C(=O)Nc2ccccc2C1=O)Cc3ccccc3
58K SMILES "OpenEye OEToolkits" 1.9.2 CN1C(C(=O)Nc2ccccc2C1=O)Cc3ccccc3
#
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
58K "SYSTEMATIC NAME" ACDLabs 12.01 (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
58K "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (3S)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
58K 'Create component' 2015-08-20 EBI
58K 'Initial release' 2015-11-25 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
58K C4 C 9.613 -1.033 1
58K C7 C 7.500 0.653 2
58K C8 C 6.000 0.653 3
58K C10 C 6.000 -1.946 4
58K C13 C 3.000 -1.946 5
58K C15 C 8.151 2.004 6
58K C20 C 13.486 1.434 7
58K C12 C 3.750 -3.244 8
58K C11 C 5.250 -3.244 9
58K C14 C 3.750 -0.646 10
58K C9 C 5.250 -0.646 11
58K O16 O 7.216 3.177 12
58K N17 N 9.613 2.338 13
58K C18 C 10.786 1.403 14
58K C19 C 12.127 2.205 15
58K C1 C 13.486 -0.129 16
58K C2 C 12.127 -0.899 17
58K C3 C 10.786 -0.097 18
58K O5 O 9.947 -2.495 19
58K N6 N 8.151 -0.699 20
58K C23 C 7.216 -1.872 21
#
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
58K C19 C20 DOUBLE NONE 1
58K C19 C18 SINGLE NONE 2
58K C20 C1 SINGLE NONE 3
58K N17 C18 SINGLE NONE 4
58K N17 C15 SINGLE NONE 5
58K C18 C3 DOUBLE NONE 6
58K C1 C2 DOUBLE NONE 7
58K O16 C15 DOUBLE NONE 8
58K C15 C7 SINGLE NONE 9
58K C3 C2 SINGLE NONE 10
58K C3 C4 SINGLE NONE 11
58K C7 C8 SINGLE BEGINWEDGE 12
58K C7 N6 SINGLE NONE 13
58K C4 N6 SINGLE NONE 14
58K C4 O5 DOUBLE NONE 15
58K C8 C9 SINGLE NONE 16
58K N6 C23 SINGLE NONE 17
58K C9 C14 SINGLE NONE 18
58K C9 C10 DOUBLE NONE 19
58K C14 C13 DOUBLE NONE 20
58K C10 C11 SINGLE NONE 21
58K C13 C12 SINGLE NONE 22
58K C11 C12 DOUBLE NONE 23
#
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
58K MurckoScaffold S1 scaffold 'O=C1N[C@@H](Cc2ccccc2)C(=O)Nc2ccccc21' InChI=1S/C16H14N2O2/c19-15-12-8-4-5-9-13(12)17-16(20)14(18-15)10-11-6-2-1-3-7-11/h1-9,14H,10H2,(H,17,20)(H,18,19)/t14-/m0/s1 IOYQGXYNQRRATP-AWEZNQCLSA-N
58K amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
58K peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
58K phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
58K Z56040660 F4 fragment CCC(C)NC(=O)c1ccccc1N InChI=1S/C11H16N2O/c1-3-8(2)13-11(14)9-6-4-5-7-10(9)12/h4-8H,3,12H2,1-2H3,(H,13,14) UOKULICTTSTSHO-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
58K C4 S1 1
58K C7 S1 1
58K C8 S1 1
58K C10 S1 1
58K C13 S1 1
58K C15 S1 1
58K C20 S1 1
58K C12 S1 1
58K C11 S1 1
58K C14 S1 1
58K C9 S1 1
58K O16 S1 1
58K N17 S1 1
58K C18 S1 1
58K C19 S1 1
58K C1 S1 1
58K C2 S1 1
58K C3 S1 1
58K O5 S1 1
58K N6 S1 1
58K N17 F1 1
58K C15 F1 1
58K O16 F1 1
58K C7 F1 1
58K N6 F1 2
58K C4 F1 2
58K O5 F1 2
58K C3 F1 2
58K O16 F2 1
58K C15 F2 1
58K C7 F2 1
58K N6 F2 1
58K C10 F3 1
58K C9 F3 1
58K C14 F3 1
58K C13 F3 1
58K C12 F3 1
58K C11 F3 1
58K C20 F3 2
58K C19 F3 2
58K C18 F3 2
58K C3 F3 2
58K C2 F3 2
58K C1 F3 2
58K C9 F4 1
58K C8 F4 1
58K C7 F4 1
58K C15 F4 1
58K N6 F4 1
58K C4 F4 1
58K O5 F4 1
58K C3 F4 1
58K C2 F4 1
58K C1 F4 1
58K C20 F4 1
58K C19 F4 1
58K C18 F4 1
58K N17 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 58K
_pdbe_chem_comp_rdkit_properties.exactmw 280.121
_pdbe_chem_comp_rdkit_properties.amw 280.327
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.176
_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 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 145.478
_pdbe_chem_comp_rdkit_properties.tpsa 49.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.832
_pdbe_chem_comp_rdkit_properties.CrippenMR 79.743
_pdbe_chem_comp_rdkit_properties.chi0v 10.211
_pdbe_chem_comp_rdkit_properties.chi1v 5.526
_pdbe_chem_comp_rdkit_properties.chi2v 2.468
_pdbe_chem_comp_rdkit_properties.chi3v 2.468
_pdbe_chem_comp_rdkit_properties.chi4v 1.548
_pdbe_chem_comp_rdkit_properties.chi0n 26.211
_pdbe_chem_comp_rdkit_properties.chi1n 13.473
_pdbe_chem_comp_rdkit_properties.chi2n 2.468
_pdbe_chem_comp_rdkit_properties.chi3n 2.468
_pdbe_chem_comp_rdkit_properties.chi4n 1.548
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.620
_pdbe_chem_comp_rdkit_properties.kappa1 4.195
_pdbe_chem_comp_rdkit_properties.kappa2 5.402
_pdbe_chem_comp_rdkit_properties.kappa3 2.521
_pdbe_chem_comp_rdkit_properties.Phi 1.079
#
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
58K UniChem PDBe 58K
58K UniChem ChEBI 71333
58K UniChem ZINC ZINC000005967239
58K UniChem PubChem 179574
58K UniChem 'Probes And Drugs' PD064215
58K UniChem ACTor 50886-63-0
58K UniChem 'PubChem TPHARMA' 15974832
#
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
58K C4 -1.368 -0.769 0.699 ETKDGv3 1
58K C7 0.148 -0.046 -1.150 ETKDGv3 2
58K C8 1.619 -0.212 -1.607 ETKDGv3 3
58K C10 3.197 -1.420 -0.114 ETKDGv3 4
58K C13 3.619 0.886 1.449 ETKDGv3 5
58K C15 -0.834 0.017 -2.275 ETKDGv3 6
58K C20 -4.231 2.445 0.265 ETKDGv3 7
58K C12 4.304 -0.376 1.795 ETKDGv3 8
58K C11 4.104 -1.471 1.052 ETKDGv3 9
58K C14 2.797 0.936 0.394 ETKDGv3 10
58K C9 2.564 -0.276 -0.433 ETKDGv3 11
58K O16 -0.471 -0.191 -3.464 ETKDGv3 12
58K N17 -2.216 0.265 -1.990 ETKDGv3 13
58K C18 -2.694 0.820 -0.748 ETKDGv3 14
58K C19 -3.713 1.897 -0.837 ETKDGv3 15
58K C1 -3.800 1.980 1.591 ETKDGv3 16
58K C2 -2.896 1.002 1.696 ETKDGv3 17
58K C3 -2.303 0.372 0.483 ETKDGv3 18
58K O5 -1.505 -1.476 1.736 ETKDGv3 19
58K N6 -0.315 -1.091 -0.226 ETKDGv3 20
58K C23 0.002 -2.512 -0.422 ETKDGv3 21
58K H1 0.105 0.938 -0.630 ETKDGv3 22
58K H2 1.743 -1.092 -2.272 ETKDGv3 23
58K H3 1.899 0.671 -2.222 ETKDGv3 24
58K H4 3.049 -2.319 -0.700 ETKDGv3 25
58K H5 3.786 1.771 2.050 ETKDGv3 26
58K H6 -4.970 3.233 0.184 ETKDGv3 27
58K H7 4.967 -0.412 2.649 ETKDGv3 28
58K H8 4.606 -2.396 1.303 ETKDGv3 29
58K H9 2.303 1.867 0.145 ETKDGv3 30
58K H10 -2.869 0.282 -2.807 ETKDGv3 31
58K H11 -4.038 2.249 -1.808 ETKDGv3 32
58K H12 -4.220 2.429 2.481 ETKDGv3 33
58K H13 -2.592 0.675 2.683 ETKDGv3 34
58K H14 -0.934 -3.109 -0.455 ETKDGv3 35
58K H15 0.630 -2.873 0.419 ETKDGv3 36
58K H16 0.530 -2.694 -1.377 ETKDGv3 37
#