data_KM2
#
_chem_comp.id KM2
_chem_comp.name 7-[[(2~{S})-1-azanylpropan-2-yl]amino]-1-benzothiophene-2-carboximidamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H16 N4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-06-07
_chem_comp.pdbx_modified_date 2020-06-12
_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 248.347
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code KM2
_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 6RX2
_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
KM2 C10 C1 C 0 1 Y N N N N N -19.388 -22.336 -6.559 0.914 2.952 -0.332 C10 KM2 1
KM2 C15 C2 C 0 1 N N N N N N -18.574 -21.633 -0.856 4.237 -1.594 -0.180 C15 KM2 2
KM2 C17 C3 C 0 1 N N N N N N -16.751 -22.739 -2.101 3.991 0.120 1.621 C17 KM2 3
KM2 S01 S1 S 0 1 Y N N N N N -19.219 -17.954 -5.026 -1.110 -1.058 0.198 S01 KM2 4
KM2 C02 C4 C 0 1 Y N N N N N -19.126 -19.744 -5.371 -0.155 0.408 0.009 C02 KM2 5
KM2 C03 C5 C 0 1 Y N N N N N -19.766 -19.911 -6.628 -1.007 1.501 -0.181 C03 KM2 6
KM2 C04 C6 C 0 1 Y N N N N N -20.270 -18.701 -7.254 -2.364 1.135 -0.170 C04 KM2 7
KM2 C05 C7 C 0 1 Y N N N N N -20.058 -17.516 -6.518 -2.609 -0.164 0.016 C05 KM2 8
KM2 C06 C8 C 0 1 N N N N N N -20.445 -16.014 -6.826 -3.955 -0.765 0.062 C06 KM2 9
KM2 N07 N1 N 0 1 N N N N N N -21.062 -15.643 -7.902 -5.011 -0.013 -0.085 N07 KM2 10
KM2 N08 N2 N 0 1 N N N N N N -20.023 -15.040 -5.777 -4.097 -2.123 0.260 N08 KM2 11
KM2 C09 C9 C 0 1 Y N N N N N -19.881 -21.210 -7.210 -0.436 2.786 -0.348 C09 KM2 12
KM2 C11 C10 C 0 1 Y N N N N N -18.735 -22.207 -5.323 1.760 1.866 -0.152 C11 KM2 13
KM2 C12 C11 C 0 1 Y N N N N N -18.591 -20.926 -4.681 1.236 0.600 0.018 C12 KM2 14
KM2 N13 N3 N 0 1 N N N N N N -17.909 -20.913 -3.335 2.090 -0.490 0.208 N13 KM2 15
KM2 C14 C12 C 0 1 N N S N N N -18.069 -22.024 -2.295 3.541 -0.291 0.217 C14 KM2 16
KM2 N16 N4 N 0 1 N N N N N N -19.460 -22.655 -0.188 3.717 -2.052 -1.475 N16 KM2 17
KM2 H1 H1 H 0 1 N N N N N N -19.508 -23.312 -7.006 1.332 3.939 -0.465 H1 KM2 18
KM2 H2 H2 H 0 1 N N N N N N -17.693 -21.476 -0.217 5.311 -1.423 -0.260 H2 KM2 19
KM2 H3 H3 H 0 1 N N N N N N -19.140 -20.693 -0.937 4.046 -2.354 0.577 H3 KM2 20
KM2 H4 H4 H 0 1 N N N N N N -16.872 -23.536 -1.353 5.071 0.269 1.627 H4 KM2 21
KM2 H5 H5 H 0 1 N N N N N N -16.429 -23.179 -3.056 3.495 1.048 1.904 H5 KM2 22
KM2 H6 H6 H 0 1 N N N N N N -15.993 -22.022 -1.753 3.728 -0.664 2.331 H6 KM2 23
KM2 H7 H7 H 0 1 N N N N N N -20.770 -18.708 -8.211 -3.156 1.857 -0.304 H7 KM2 24
KM2 H8 H8 H 0 1 N N N N N N -21.208 -14.654 -7.928 -5.896 -0.409 -0.055 H8 KM2 25
KM2 H9 H9 H 0 1 N N N N N N -19.537 -15.360 -4.964 -3.312 -2.682 0.369 H9 KM2 26
KM2 H10 H10 H 0 1 N N N N N N -20.226 -14.067 -5.888 -4.982 -2.519 0.290 H10 KM2 27
KM2 H11 H11 H 0 1 N N N N N N -20.359 -21.320 -8.172 -1.078 3.642 -0.489 H11 KM2 28
KM2 H12 H12 H 0 1 N N N N N N -18.332 -23.087 -4.844 2.830 2.012 -0.146 H12 KM2 29
KM2 H13 H13 H 0 1 N N N N N N -16.929 -20.857 -3.526 1.722 -1.379 0.335 H13 KM2 30
KM2 H14 H14 H 0 1 N N N N N N -18.787 -22.753 -2.699 3.805 0.493 -0.493 H14 KM2 31
KM2 H15 H15 H 0 1 N N N N N N -19.730 -22.323 0.716 4.161 -2.912 -1.760 H15 KM2 32
KM2 H16 H16 H 0 1 N N N N N N -20.276 -22.804 -0.746 2.714 -2.156 -1.446 H16 KM2 33
#
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
KM2 N07 C06 DOUB N N 1
KM2 C04 C03 SING Y N 2
KM2 C04 C05 DOUB Y N 3
KM2 C09 C03 DOUB Y N 4
KM2 C09 C10 SING Y N 5
KM2 C06 C05 SING N N 6
KM2 C06 N08 SING N N 7
KM2 C03 C02 SING Y N 8
KM2 C10 C11 DOUB Y N 9
KM2 C05 S01 SING Y N 10
KM2 C02 S01 SING Y N 11
KM2 C02 C12 DOUB Y N 12
KM2 C11 C12 SING Y N 13
KM2 C12 N13 SING N N 14
KM2 N13 C14 SING N N 15
KM2 C14 C17 SING N N 16
KM2 C14 C15 SING N N 17
KM2 C15 N16 SING N N 18
KM2 C10 H1 SING N N 19
KM2 C15 H2 SING N N 20
KM2 C15 H3 SING N N 21
KM2 C17 H4 SING N N 22
KM2 C17 H5 SING N N 23
KM2 C17 H6 SING N N 24
KM2 C04 H7 SING N N 25
KM2 N07 H8 SING N N 26
KM2 N08 H9 SING N N 27
KM2 N08 H10 SING N N 28
KM2 C09 H11 SING N N 29
KM2 C11 H12 SING N N 30
KM2 N13 H13 SING N N 31
KM2 C14 H14 SING N N 32
KM2 N16 H15 SING N N 33
KM2 N16 H16 SING N N 34
#
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
KM2 InChI InChI 1.03 InChI=1S/C12H16N4S/c1-7(6-13)16-9-4-2-3-8-5-10(12(14)15)17-11(8)9/h2-5,7,16H,6,13H2,1H3,(H3,14,15)/t7-/m0/s1
KM2 InChIKey InChI 1.03 ZAZAVGHCOORPKF-ZETCQYMHSA-N
KM2 SMILES_CANONICAL CACTVS 3.385 C[C@@H](CN)Nc1cccc2cc(sc12)C(N)=N
KM2 SMILES CACTVS 3.385 C[CH](CN)Nc1cccc2cc(sc12)C(N)=N
KM2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\c1cc2cccc(c2s1)N[C@@H](C)CN)/N"
KM2 SMILES "OpenEye OEToolkits" 2.0.7 CC(CN)Nc1cccc2c1sc(c2)C(=N)N
#
_pdbx_chem_comp_identifier.comp_id KM2
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 7-[[(2~{S})-1-azanylpropan-2-yl]amino]-1-benzothiophene-2-carboximidamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
KM2 'Create component' 2019-06-07 EBI
KM2 'Initial release' 2020-06-17 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
KM2 C10 C 5.104 3.163 1
KM2 C15 C 5.104 -2.837 2
KM2 C17 C 3.805 -0.587 3
KM2 S01 S 9.122 1.206 4
KM2 C02 C 7.702 1.663 5
KM2 C03 C 7.702 3.163 6
KM2 C04 C 9.122 3.620 7
KM2 C05 C 9.997 2.413 8
KM2 C06 C 11.497 2.413 9
KM2 N07 N 12.247 3.712 10
KM2 N08 N 12.247 1.114 11
KM2 C09 C 6.404 3.913 12
KM2 C11 C 5.104 1.663 13
KM2 C12 C 6.404 0.913 14
KM2 N13 N 6.404 -0.587 15
KM2 C14 C 5.104 -1.337 16
KM2 N16 N 3.805 -3.587 17
KM2 H8 H 11.497 5.011 18
#
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
KM2 N07 C06 DOUBLE NONE 1
KM2 C04 C03 SINGLE NONE 2
KM2 C04 C05 DOUBLE NONE 3
KM2 C09 C03 SINGLE NONE 4
KM2 C09 C10 DOUBLE NONE 5
KM2 C06 C05 SINGLE ENDUPRIGHT 6
KM2 C06 N08 SINGLE ENDDOWNRIGHT 7
KM2 C03 C02 DOUBLE NONE 8
KM2 C10 C11 SINGLE NONE 9
KM2 C05 S01 SINGLE NONE 10
KM2 C02 S01 SINGLE NONE 11
KM2 C02 C12 SINGLE NONE 12
KM2 C11 C12 DOUBLE NONE 13
KM2 C12 N13 SINGLE NONE 14
KM2 N13 C14 SINGLE NONE 15
KM2 C14 C17 SINGLE BEGINDASH 16
KM2 C14 C15 SINGLE NONE 17
KM2 C15 N16 SINGLE NONE 18
#
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
KM2 MurckoScaffold S1 scaffold c1ccc2sccc2c1 InChI=1S/C8H6S/c1-2-4-8-7(3-1)5-6-9-8/h1-6H FCEHBMOGCRZNNI-UHFFFAOYSA-N
KM2 benzothiophen F1 fragment c1ccc2sccc2c1 InChI=1S/C8H6S/c1-2-4-8-7(3-1)5-6-9-8/h1-6H FCEHBMOGCRZNNI-UHFFFAOYSA-N
KM2 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
KM2 thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
KM2 C10 S1 1
KM2 S01 S1 1
KM2 C02 S1 1
KM2 C03 S1 1
KM2 C04 S1 1
KM2 C05 S1 1
KM2 C09 S1 1
KM2 C11 S1 1
KM2 C12 S1 1
KM2 C02 F1 1
KM2 C03 F1 1
KM2 C04 F1 1
KM2 C05 F1 1
KM2 S01 F1 1
KM2 C09 F1 1
KM2 C10 F1 1
KM2 C11 F1 1
KM2 C12 F1 1
KM2 C10 F2 1
KM2 C09 F2 1
KM2 C03 F2 1
KM2 C02 F2 1
KM2 C12 F2 1
KM2 C11 F2 1
KM2 C02 F3 1
KM2 C03 F3 1
KM2 C04 F3 1
KM2 C05 F3 1
KM2 S01 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id KM2
_pdbe_chem_comp_rdkit_properties.exactmw 248.110
_pdbe_chem_comp_rdkit_properties.amw 248.355
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 126.956
_pdbe_chem_comp_rdkit_properties.tpsa 87.920
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.081
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.684
_pdbe_chem_comp_rdkit_properties.chi0v 9.014
_pdbe_chem_comp_rdkit_properties.chi1v 5.093
_pdbe_chem_comp_rdkit_properties.chi2v 2.876
_pdbe_chem_comp_rdkit_properties.chi3v 2.876
_pdbe_chem_comp_rdkit_properties.chi4v 1.976
_pdbe_chem_comp_rdkit_properties.chi0n 24.197
_pdbe_chem_comp_rdkit_properties.chi1n 11.960
_pdbe_chem_comp_rdkit_properties.chi2n 1.786
_pdbe_chem_comp_rdkit_properties.chi3n 1.786
_pdbe_chem_comp_rdkit_properties.chi4n 1.130
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.590
_pdbe_chem_comp_rdkit_properties.kappa1 3.046
_pdbe_chem_comp_rdkit_properties.kappa2 4.728
_pdbe_chem_comp_rdkit_properties.kappa3 2.400
_pdbe_chem_comp_rdkit_properties.Phi 0.847
#
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
KM2 UniChem PDBe KM2
KM2 UniChem PubChem 146170567
#
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
KM2 C10 1.222 -2.652 -1.686 ETKDGv3 1
KM2 C15 -1.438 1.248 -1.699 ETKDGv3 2
KM2 C17 -3.320 0.980 -0.011 ETKDGv3 3
KM2 S01 0.011 0.205 1.652 ETKDGv3 4
KM2 C02 0.318 -0.858 0.263 ETKDGv3 5
KM2 C03 1.599 -1.221 0.242 ETKDGv3 6
KM2 C04 2.419 -0.646 1.330 ETKDGv3 7
KM2 C05 1.725 0.138 2.166 ETKDGv3 8
KM2 C06 2.256 0.846 3.350 ETKDGv3 9
KM2 N07 1.437 1.523 4.091 ETKDGv3 10
KM2 N08 3.648 0.803 3.690 ETKDGv3 11
KM2 C09 2.088 -2.159 -0.787 ETKDGv3 12
KM2 C11 -0.210 -2.250 -1.652 ETKDGv3 13
KM2 C12 -0.647 -1.372 -0.731 ETKDGv3 14
KM2 N13 -2.027 -0.986 -0.698 ETKDGv3 15
KM2 C14 -2.543 0.316 -1.152 ETKDGv3 16
KM2 N16 -2.020 2.450 -2.290 ETKDGv3 17
KM2 H1 1.564 -3.346 -2.442 ETKDGv3 18
KM2 H2 -0.844 0.713 -2.473 ETKDGv3 19
KM2 H3 -0.751 1.546 -0.878 ETKDGv3 20
KM2 H4 -3.813 1.909 -0.365 ETKDGv3 21
KM2 H5 -2.642 1.232 0.831 ETKDGv3 22
KM2 H6 -4.108 0.292 0.361 ETKDGv3 23
KM2 H7 3.473 -0.862 1.430 ETKDGv3 24
KM2 H8 1.761 2.043 4.937 ETKDGv3 25
KM2 H9 4.347 0.297 3.105 ETKDGv3 26
KM2 H10 4.000 1.300 4.538 ETKDGv3 27
KM2 H11 3.130 -2.454 -0.810 ETKDGv3 28
KM2 H12 -0.894 -2.658 -2.385 ETKDGv3 29
KM2 H13 -2.729 -1.744 -0.539 ETKDGv3 30
KM2 H14 -3.258 0.120 -1.981 ETKDGv3 31
KM2 H15 -2.518 2.175 -3.168 ETKDGv3 32
KM2 H16 -1.234 3.076 -2.579 ETKDGv3 33
#