data_K5Z
#
_chem_comp.id K5Z
_chem_comp.name 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H17 N3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-04-29
_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 259.370
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K5Z
_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 6RJL
_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
K5Z C10 C1 C 0 1 Y N N N N N 20.701 -22.575 -7.352 1.316 -2.013 -1.064 C10 K5Z 1
K5Z C13 C2 C 0 1 Y N N N N N 20.986 -22.627 -10.109 2.934 -2.245 1.176 C13 K5Z 2
K5Z C15 C3 C 0 1 N N N N N N 22.916 -21.242 -5.606 1.011 1.556 0.895 C15 K5Z 3
K5Z C17 C4 C 0 1 N N N N N N 25.185 -20.524 -4.697 2.926 2.897 0.012 C17 K5Z 4
K5Z C02 C5 C 0 1 Y N N N N N 22.124 -20.116 -6.286 -0.230 0.789 0.519 C02 K5Z 5
K5Z C03 C6 C 0 1 Y N N N N N 21.262 -20.212 -7.375 -0.249 -0.514 0.170 C03 K5Z 6
K5Z C04 C7 C 0 1 Y N N N N N 20.684 -19.004 -7.775 -1.509 -1.010 -0.131 C04 K5Z 7
K5Z C05 C8 C 0 1 Y N N N N N 21.037 -17.891 -7.017 -2.491 -0.091 -0.018 C05 K5Z 8
K5Z C06 C9 C 0 1 N N N N N N 20.599 -16.429 -7.156 -3.919 -0.339 -0.275 C06 K5Z 9
K5Z C09 C10 C 0 1 Y N N N N N 21.036 -21.414 -8.034 0.977 -1.347 0.112 C09 K5Z 10
K5Z C11 C11 C 0 1 Y N N N N N 20.503 -23.757 -8.048 2.454 -2.792 -1.110 C11 K5Z 11
K5Z C12 C12 C 0 1 Y N N N N N 20.644 -23.783 -9.427 3.262 -2.908 0.007 C12 K5Z 12
K5Z C14 C13 C 0 1 Y N N N N N 21.186 -21.447 -9.412 1.794 -1.468 1.235 C14 K5Z 13
K5Z C16 C14 C 0 1 N N N N N N 23.720 -20.802 -4.378 1.695 2.074 -0.373 C16 K5Z 14
K5Z N08 N1 N 0 1 N N N N N N 19.922 -15.952 -8.346 -4.834 0.683 -0.127 N08 K5Z 15
K5Z N07 N2 N 0 1 N N N N N N 20.829 -15.618 -6.226 -4.320 -1.527 -0.645 N07 K5Z 16
K5Z N18 N3 N 0 1 N N N N N N 25.974 -20.541 -3.476 3.582 3.394 -1.205 N18 K5Z 17
K5Z S01 S1 S 0 1 Y N N N N N 22.135 -18.459 -5.826 -1.803 1.446 0.482 S01 K5Z 18
K5Z H101 H1 H 0 0 N N N N N N 20.594 -22.558 -6.277 0.686 -1.923 -1.936 H101 K5Z 19
K5Z H131 H2 H 0 0 N N N N N N 21.097 -22.646 -11.183 3.567 -2.339 2.045 H131 K5Z 20
K5Z H151 H3 H 0 0 N N N N N N 22.205 -22.020 -5.290 0.739 2.399 1.530 H151 K5Z 21
K5Z H152 H4 H 0 0 N N N N N N 23.616 -21.662 -6.343 1.695 0.900 1.434 H152 K5Z 22
K5Z H172 H5 H 0 0 N N N N N N 25.561 -21.297 -5.384 2.620 3.741 0.630 H172 K5Z 23
K5Z H171 H6 H 0 0 N N N N N N 25.273 -19.536 -5.173 3.622 2.271 0.570 H171 K5Z 24
K5Z H041 H7 H 0 0 N N N N N N 20.009 -18.938 -8.616 -1.686 -2.034 -0.426 H041 K5Z 25
K5Z H111 H8 H 0 0 N N N N N N 20.239 -24.659 -7.516 2.715 -3.312 -2.020 H111 K5Z 26
K5Z H121 H9 H 0 0 N N N N N N 20.487 -24.704 -9.969 4.154 -3.514 -0.035 H121 K5Z 27
K5Z H141 H10 H 0 0 N N N N N N 21.460 -20.548 -9.944 1.539 -0.951 2.148 H141 K5Z 28
K5Z H161 H11 H 0 0 N N N N N N 23.269 -19.884 -3.973 2.001 1.230 -0.991 H161 K5Z 29
K5Z H162 H12 H 0 0 N N N N N N 23.671 -21.599 -3.622 0.999 2.700 -0.931 H162 K5Z 30
K5Z H082 H13 H 0 0 N N N N N N 19.648 -14.993 -8.415 -4.537 1.564 0.147 H082 K5Z 31
K5Z H071 H15 H 0 0 N N N N N N 21.300 -16.052 -5.458 -3.676 -2.245 -0.749 H071 K5Z 32
K5Z H4 H16 H 0 1 N N N N N N 26.932 -20.358 -3.695 2.938 3.924 -1.772 H4 K5Z 33
K5Z H3 H18 H 0 1 N N N N N N 25.635 -19.838 -2.850 4.399 3.941 -0.978 H3 K5Z 34
K5Z H081 H19 H 0 0 N N N N N N 19.729 -16.582 -9.098 -5.775 0.519 -0.296 H081 K5Z 35
#
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
K5Z C13 C12 DOUB Y N 1
K5Z C13 C14 SING Y N 2
K5Z C12 C11 SING Y N 3
K5Z C14 C09 DOUB Y N 4
K5Z N08 C06 SING N N 5
K5Z C11 C10 DOUB Y N 6
K5Z C09 C03 SING N N 7
K5Z C09 C10 SING Y N 8
K5Z C04 C03 SING Y N 9
K5Z C04 C05 DOUB Y N 10
K5Z C03 C02 DOUB Y N 11
K5Z C06 C05 SING N N 12
K5Z C06 N07 DOUB N N 13
K5Z C05 S01 SING Y N 14
K5Z C02 S01 SING Y N 15
K5Z C02 C15 SING N N 16
K5Z C15 C16 SING N N 17
K5Z C17 C16 SING N N 18
K5Z C17 N18 SING N N 19
K5Z C10 H101 SING N N 20
K5Z C13 H131 SING N N 21
K5Z C15 H151 SING N N 22
K5Z C15 H152 SING N N 23
K5Z C17 H172 SING N N 24
K5Z C17 H171 SING N N 25
K5Z C04 H041 SING N N 26
K5Z C11 H111 SING N N 27
K5Z C12 H121 SING N N 28
K5Z C14 H141 SING N N 29
K5Z C16 H161 SING N N 30
K5Z C16 H162 SING N N 31
K5Z N08 H082 SING N N 32
K5Z N07 H071 SING N N 33
K5Z N18 H4 SING N N 34
K5Z N18 H3 SING N N 35
K5Z N08 H081 SING N N 36
#
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
K5Z InChI InChI 1.03 InChI=1S/C14H17N3S/c15-8-4-7-12-11(9-13(18-12)14(16)17)10-5-2-1-3-6-10/h1-3,5-6,9H,4,7-8,15H2,(H3,16,17)
K5Z InChIKey InChI 1.03 MCPMDVYDZQBIHS-UHFFFAOYSA-N
K5Z SMILES_CANONICAL CACTVS 3.385 NCCCc1sc(cc1c2ccccc2)C(N)=N
K5Z SMILES CACTVS 3.385 NCCCc1sc(cc1c2ccccc2)C(N)=N
K5Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\c1cc(c(s1)CCCN)c2ccccc2)/N"
K5Z SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)c2cc(sc2CCCN)C(=N)N
#
_pdbx_chem_comp_identifier.comp_id K5Z
_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 5-(3-azanylpropyl)-4-phenyl-thiophene-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
K5Z 'Create component' 2019-04-29 PDBE
K5Z 'Other modification' 2019-06-27 PDBE
K5Z 'Other modification' 2019-06-28 PDBE
K5Z '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
K5Z C10 C 11.480 -2.822 1
K5Z C13 C 8.882 -4.322 2
K5Z C15 C 7.540 -0.154 3
K5Z C17 C 4.999 0.386 4
K5Z C02 C 8.967 0.309 5
K5Z C03 C 10.181 -0.572 6
K5Z C04 C 11.394 0.309 7
K5Z C05 C 10.931 1.736 8
K5Z C06 C 11.812 2.950 9
K5Z C09 C 10.181 -2.072 10
K5Z C11 C 11.480 -4.322 11
K5Z C12 C 10.181 -5.072 12
K5Z C14 C 8.882 -2.822 13
K5Z C16 C 6.426 0.850 14
K5Z N08 N 11.202 4.320 15
K5Z N07 N 13.304 2.793 16
K5Z N18 N 3.884 1.390 17
K5Z S01 S 9.431 1.736 18
K5Z H071 H 14.186 4.006 19
#
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
K5Z C13 C12 DOUBLE NONE 1
K5Z C13 C14 SINGLE NONE 2
K5Z C12 C11 SINGLE NONE 3
K5Z C14 C09 DOUBLE NONE 4
K5Z N08 C06 SINGLE ENDUPRIGHT 5
K5Z C11 C10 DOUBLE NONE 6
K5Z C09 C03 SINGLE NONE 7
K5Z C09 C10 SINGLE NONE 8
K5Z C04 C03 SINGLE NONE 9
K5Z C04 C05 DOUBLE NONE 10
K5Z C03 C02 DOUBLE NONE 11
K5Z C06 C05 SINGLE ENDUPRIGHT 12
K5Z C06 N07 DOUBLE NONE 13
K5Z C05 S01 SINGLE NONE 14
K5Z C02 S01 SINGLE NONE 15
K5Z C02 C15 SINGLE NONE 16
K5Z C15 C16 SINGLE NONE 17
K5Z C17 C16 SINGLE NONE 18
K5Z C17 N18 SINGLE NONE 19
#
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
K5Z MurckoScaffold S1 scaffold c1ccc(-c2ccsc2)cc1 InChI=1S/C10H8S/c1-2-4-9(5-3-1)10-6-7-11-8-10/h1-8H ZDQZVKVIYAPRON-UHFFFAOYSA-N
K5Z phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
K5Z thiophen F2 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
K5Z C10 S1 1
K5Z C13 S1 1
K5Z C02 S1 1
K5Z C03 S1 1
K5Z C04 S1 1
K5Z C05 S1 1
K5Z C09 S1 1
K5Z C11 S1 1
K5Z C12 S1 1
K5Z C14 S1 1
K5Z S01 S1 1
K5Z C10 F1 1
K5Z C11 F1 1
K5Z C12 F1 1
K5Z C13 F1 1
K5Z C14 F1 1
K5Z C09 F1 1
K5Z C02 F2 1
K5Z C03 F2 1
K5Z C04 F2 1
K5Z C05 F2 1
K5Z S01 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K5Z
_pdbe_chem_comp_rdkit_properties.exactmw 259.114
_pdbe_chem_comp_rdkit_properties.amw 259.378
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.214
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 135.129
_pdbe_chem_comp_rdkit_properties.tpsa 75.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.101
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.293
_pdbe_chem_comp_rdkit_properties.chi0v 9.566
_pdbe_chem_comp_rdkit_properties.chi1v 5.396
_pdbe_chem_comp_rdkit_properties.chi2v 2.854
_pdbe_chem_comp_rdkit_properties.chi3v 2.854
_pdbe_chem_comp_rdkit_properties.chi4v 1.980
_pdbe_chem_comp_rdkit_properties.chi0n 25.750
_pdbe_chem_comp_rdkit_properties.chi1n 12.815
_pdbe_chem_comp_rdkit_properties.chi2n 1.855
_pdbe_chem_comp_rdkit_properties.chi3n 1.855
_pdbe_chem_comp_rdkit_properties.chi4n 1.174
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.650
_pdbe_chem_comp_rdkit_properties.kappa1 3.265
_pdbe_chem_comp_rdkit_properties.kappa2 5.797
_pdbe_chem_comp_rdkit_properties.kappa3 2.776
_pdbe_chem_comp_rdkit_properties.Phi 1.052
#
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
K5Z UniChem PDBe K5Z
K5Z UniChem PubChem 146170551
#
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
K5Z C10 -1.643 -2.193 0.659 ETKDGv3 1
K5Z C13 -1.550 -2.715 -2.108 ETKDGv3 2
K5Z C15 1.104 -0.582 1.723 ETKDGv3 3
K5Z C17 3.061 -0.003 0.192 ETKDGv3 4
K5Z C02 0.155 0.427 1.134 ETKDGv3 5
K5Z C03 -0.815 0.203 0.233 ETKDGv3 6
K5Z C04 -1.470 1.439 -0.268 ETKDGv3 7
K5Z C05 -0.992 2.574 0.254 ETKDGv3 8
K5Z C06 -1.453 3.952 -0.049 ETKDGv3 9
K5Z C09 -1.193 -1.131 -0.275 ETKDGv3 10
K5Z C11 -1.988 -3.400 0.192 ETKDGv3 11
K5Z C12 -1.933 -3.676 -1.258 ETKDGv3 12
K5Z C14 -1.171 -1.381 -1.597 ETKDGv3 13
K5Z C16 2.119 -1.103 0.694 ETKDGv3 14
K5Z N08 -1.002 5.045 0.755 ETKDGv3 15
K5Z N07 -2.251 4.200 -1.042 ETKDGv3 16
K5Z N18 4.047 -0.566 -0.724 ETKDGv3 17
K5Z S01 0.306 2.177 1.406 ETKDGv3 18
K5Z H101 -1.716 -1.991 1.720 ETKDGv3 19
K5Z H131 -1.514 -2.914 -3.171 ETKDGv3 20
K5Z H151 1.648 -0.119 2.574 ETKDGv3 21
K5Z H152 0.537 -1.438 2.140 ETKDGv3 22
K5Z H172 2.474 0.773 -0.346 ETKDGv3 23
K5Z H171 3.579 0.478 1.052 ETKDGv3 24
K5Z H041 -2.278 1.400 -0.984 ETKDGv3 25
K5Z H111 -2.319 -4.172 0.874 ETKDGv3 26
K5Z H121 -2.210 -4.653 -1.631 ETKDGv3 27
K5Z H141 -0.858 -0.619 -2.299 ETKDGv3 28
K5Z H161 1.588 -1.561 -0.169 ETKDGv3 29
K5Z H162 2.723 -1.902 1.177 ETKDGv3 30
K5Z H082 -0.377 4.897 1.577 ETKDGv3 31
K5Z H071 -2.617 3.470 -1.691 ETKDGv3 32
K5Z H4 4.614 0.225 -1.107 ETKDGv3 33
K5Z H3 4.706 -1.161 -0.171 ETKDGv3 34
K5Z H081 -1.309 6.020 0.537 ETKDGv3 35
#