data_VE0
#
_chem_comp.id VE0
_chem_comp.name N-hydroxy-2-(piperidin-1-yl)pyridine-3-carboximidamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-08-29
_chem_comp.pdbx_modified_date 2022-10-28
_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 220.271
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VE0
_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 7FLJ
_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
VE0 N1 N1 N 0 1 N N N N N N 4.727 19.294 -19.418 1.070 0.035 0.028 N1 VE0 1
VE0 C7 C1 C 0 1 N N N N N N 5.277 22.114 -19.918 3.837 -0.783 -0.078 C7 VE0 2
VE0 C8 C2 C 0 1 N N N N N N 4.386 21.287 -20.837 2.870 -1.043 -1.236 C8 VE0 3
VE0 N2 N2 N 0 1 N N N N N N 3.232 16.584 -22.030 -2.859 -1.502 -0.038 N2 VE0 4
VE0 C9 C3 C 0 1 N N N N N N 3.717 20.170 -20.047 1.794 0.045 -1.250 C9 VE0 5
VE0 C1 C4 C 0 1 Y N N N N N 3.349 15.863 -19.204 -2.371 1.337 0.003 C1 VE0 6
VE0 C5 C5 C 0 1 N N N N N N 5.611 20.075 -18.518 1.969 0.330 1.150 C5 VE0 7
VE0 C6 C6 C 0 1 N N N N N N 6.307 21.244 -19.212 3.051 -0.749 1.236 C6 VE0 8
VE0 N3 N3 N 0 1 N N N N N N 5.164 17.781 -21.633 -0.578 -1.861 0.215 N3 VE0 9
VE0 C4 C7 C 0 1 Y N N N N N 3.665 16.793 -17.054 -0.755 3.098 -0.056 C4 VE0 10
VE0 C3 C8 C 0 1 Y N N N N N 4.232 18.079 -18.859 0.004 0.919 0.001 C3 VE0 11
VE0 C2 C9 C 0 1 Y N N N N N 3.867 17.039 -19.747 -1.311 0.427 0.024 C2 VE0 12
VE0 O O1 O 0 1 N N N N N N 3.412 16.788 -23.333 -3.106 -2.895 0.006 O VE0 13
VE0 C10 C10 C 0 1 N N N N N N 4.109 17.160 -21.193 -1.569 -1.027 0.071 C10 VE0 14
VE0 N N4 N 0 1 Y N N N N N 4.126 17.929 -17.542 0.231 2.222 -0.030 N VE0 15
VE0 C C11 C 0 1 Y N N N N N 3.254 15.736 -17.841 -2.076 2.690 -0.040 C VE0 16
VE0 H1 H1 H 0 1 N N N N N N 5.801 22.874 -20.516 4.581 -1.579 -0.037 H1 VE0 17
VE0 H2 H2 H 0 1 N N N N N N 4.650 22.610 -19.163 4.337 0.175 -0.227 H2 VE0 18
VE0 H3 H3 H 0 1 N N N N N N 4.997 20.850 -21.640 3.418 -1.025 -2.178 H3 VE0 19
VE0 H4 H4 H 0 1 N N N N N N 3.614 21.936 -21.276 2.401 -2.018 -1.106 H4 VE0 20
VE0 H5 H5 H 0 1 N N N N N N 2.476 16.025 -21.689 -3.597 -0.882 -0.146 H5 VE0 21
VE0 H6 H6 H 0 1 N N N N N N 3.084 20.612 -19.263 1.096 -0.146 -2.065 H6 VE0 22
VE0 H7 H7 H 0 1 N N N N N N 3.093 19.571 -20.727 2.263 1.018 -1.394 H7 VE0 23
VE0 H8 H8 H 0 1 N N N N N N 3.026 15.060 -19.850 -3.395 0.994 0.015 H8 VE0 24
VE0 H9 H9 H 0 1 N N N N N N 5.003 20.472 -17.692 2.438 1.302 0.995 H9 VE0 25
VE0 H10 H10 H 0 1 N N N N N N 6.381 19.401 -18.115 1.398 0.346 2.079 H10 VE0 26
VE0 H11 H11 H 0 1 N N N N N N 7.024 20.856 -19.950 2.584 -1.720 1.405 H11 VE0 27
VE0 H12 H12 H 0 1 N N N N N N 6.842 21.847 -18.463 3.728 -0.522 2.059 H12 VE0 28
VE0 H13 H13 H 0 1 N N N N N N 5.731 18.131 -20.887 0.316 -1.527 0.390 H13 VE0 29
VE0 H14 H14 H 0 1 N N N N N N 3.606 16.684 -15.981 -0.527 4.153 -0.089 H14 VE0 30
VE0 H15 H15 H 0 1 N N N N N N 2.735 16.334 -23.821 -4.040 -3.132 -0.078 H15 VE0 31
VE0 H16 H16 H 0 1 N N N N N N 2.867 14.832 -17.395 -2.872 3.420 -0.062 H16 VE0 32
#
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
VE0 O N2 SING N N 1
VE0 N2 C10 SING N N 2
VE0 N3 C10 DOUB N N 3
VE0 C10 C2 SING N N 4
VE0 C8 C9 SING N N 5
VE0 C8 C7 SING N N 6
VE0 C9 N1 SING N N 7
VE0 C7 C6 SING N N 8
VE0 C2 C1 DOUB Y N 9
VE0 C2 C3 SING Y N 10
VE0 N1 C3 SING N N 11
VE0 N1 C5 SING N N 12
VE0 C6 C5 SING N N 13
VE0 C1 C SING Y N 14
VE0 C3 N DOUB Y N 15
VE0 C C4 DOUB Y N 16
VE0 N C4 SING Y N 17
VE0 C7 H1 SING N N 18
VE0 C7 H2 SING N N 19
VE0 C8 H3 SING N N 20
VE0 C8 H4 SING N N 21
VE0 N2 H5 SING N N 22
VE0 C9 H6 SING N N 23
VE0 C9 H7 SING N N 24
VE0 C1 H8 SING N N 25
VE0 C5 H9 SING N N 26
VE0 C5 H10 SING N N 27
VE0 C6 H11 SING N N 28
VE0 C6 H12 SING N N 29
VE0 N3 H13 SING N N 30
VE0 C4 H14 SING N N 31
VE0 O H15 SING N N 32
VE0 C H16 SING N N 33
#
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
VE0 SMILES ACDLabs 12.01 N=C(NO)c1cccnc1N1CCCCC1
VE0 InChI InChI 1.06 InChI=1S/C11H16N4O/c12-10(14-16)9-5-4-6-13-11(9)15-7-2-1-3-8-15/h4-6,16H,1-3,7-8H2,(H2,12,14)
VE0 InChIKey InChI 1.06 JZHHKLUPBPYXRR-UHFFFAOYSA-N
VE0 SMILES_CANONICAL CACTVS 3.385 ONC(=N)c1cccnc1N2CCCCC2
VE0 SMILES CACTVS 3.385 ONC(=N)c1cccnc1N2CCCCC2
VE0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/c1cccnc1N2CCCCC2)\NO"
VE0 SMILES "OpenEye OEToolkits" 2.0.7 c1cc(c(nc1)N2CCCCC2)C(=N)NO
#
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
VE0 "SYSTEMATIC NAME" ACDLabs 12.01 N-hydroxy-2-(piperidin-1-yl)pyridine-3-carboximidamide
VE0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-oxidanyl-2-piperidin-1-yl-pyridine-3-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
VE0 'Create component' 2022-08-29 RCSB
VE0 'Initial release' 2022-11-02 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
VE0 N1 N 7.702 -0.608 1
VE0 C7 C 10.301 0.892 2
VE0 C8 C 10.301 -0.608 3
VE0 N2 N 6.404 1.643 4
VE0 C9 C 9.002 -1.357 5
VE0 C1 C 3.805 -1.357 6
VE0 C5 C 7.702 0.892 7
VE0 C6 C 9.002 1.643 8
VE0 N3 N 3.805 1.643 9
VE0 C4 C 5.104 -3.607 10
VE0 C3 C 6.404 -1.357 11
VE0 C2 C 5.104 -0.608 12
VE0 O O 6.404 3.143 13
VE0 C10 C 5.104 0.892 14
VE0 N N 6.404 -2.857 15
VE0 C C 3.805 -2.857 16
VE0 H13 H 2.506 0.892 17
#
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
VE0 O N2 SINGLE NONE 1
VE0 N2 C10 SINGLE ENDDOWNRIGHT 2
VE0 N3 C10 DOUBLE NONE 3
VE0 C10 C2 SINGLE ENDDOWNRIGHT 4
VE0 C8 C9 SINGLE NONE 5
VE0 C8 C7 SINGLE NONE 6
VE0 C9 N1 SINGLE NONE 7
VE0 C7 C6 SINGLE NONE 8
VE0 C2 C1 DOUBLE NONE 9
VE0 C2 C3 SINGLE NONE 10
VE0 N1 C3 SINGLE NONE 11
VE0 N1 C5 SINGLE NONE 12
VE0 C6 C5 SINGLE NONE 13
VE0 C1 C SINGLE NONE 14
VE0 C3 N DOUBLE NONE 15
VE0 C C4 DOUBLE NONE 16
VE0 N C4 SINGLE NONE 17
#
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
VE0 MurckoScaffold S1 scaffold c1ccc(N2CCCCC2)nc1 InChI=1S/C10H14N2/c1-4-8-12(9-5-1)10-6-2-3-7-11-10/h2-3,6-7H,1,4-5,8-9H2 AJEUJXWLOADTKA-UHFFFAOYSA-N
VE0 pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
VE0 Z1992316287 F2 fragment CCNc1ncccc1C InChI=1S/C8H12N2/c1-3-9-8-7(2)5-4-6-10-8/h4-6H,3H2,1-2H3,(H,9,10) DDVXXITYAVIOHO-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
VE0 N1 S1 1
VE0 C7 S1 1
VE0 C8 S1 1
VE0 C9 S1 1
VE0 C1 S1 1
VE0 C5 S1 1
VE0 C6 S1 1
VE0 C4 S1 1
VE0 C3 S1 1
VE0 C2 S1 1
VE0 N S1 1
VE0 C S1 1
VE0 C4 F1 1
VE0 C F1 1
VE0 C1 F1 1
VE0 C2 F1 1
VE0 C3 F1 1
VE0 N F1 1
VE0 C8 F2 1
VE0 C9 F2 1
VE0 N1 F2 1
VE0 C3 F2 1
VE0 N F2 1
VE0 C4 F2 1
VE0 C F2 1
VE0 C1 F2 1
VE0 C2 F2 1
VE0 C10 F2 1
VE0 C6 F2 2
VE0 C5 F2 2
VE0 N1 F2 2
VE0 C3 F2 2
VE0 N F2 2
VE0 C4 F2 2
VE0 C F2 2
VE0 C1 F2 2
VE0 C2 F2 2
VE0 C10 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id VE0
_pdbe_chem_comp_rdkit_properties.exactmw 220.132
_pdbe_chem_comp_rdkit_properties.amw 220.276
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 117.261
_pdbe_chem_comp_rdkit_properties.tpsa 72.240
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.941
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.962
_pdbe_chem_comp_rdkit_properties.chi0v 7.697
_pdbe_chem_comp_rdkit_properties.chi1v 3.998
_pdbe_chem_comp_rdkit_properties.chi2v 1.611
_pdbe_chem_comp_rdkit_properties.chi3v 1.611
_pdbe_chem_comp_rdkit_properties.chi4v 0.979
_pdbe_chem_comp_rdkit_properties.chi0n 23.697
_pdbe_chem_comp_rdkit_properties.chi1n 11.800
_pdbe_chem_comp_rdkit_properties.chi2n 1.611
_pdbe_chem_comp_rdkit_properties.chi3n 1.611
_pdbe_chem_comp_rdkit_properties.chi4n 0.979
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.620
_pdbe_chem_comp_rdkit_properties.kappa1 2.614
_pdbe_chem_comp_rdkit_properties.kappa2 4.937
_pdbe_chem_comp_rdkit_properties.kappa3 2.139
_pdbe_chem_comp_rdkit_properties.Phi 0.807
#
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
VE0 UniChem ZINC ZINC000019515571
VE0 UniChem eMolecules 31412285
VE0 UniChem PubChem 12254379
VE0 UniChem PubChem 57368839
VE0 UniChem PubChem 28212529
#
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
VE0 N1 0.542 0.315 -0.241 ETKDGv3 1
VE0 C7 3.322 0.611 0.620 ETKDGv3 2
VE0 C8 2.701 -0.751 0.239 ETKDGv3 3
VE0 N2 -1.606 0.064 1.954 ETKDGv3 4
VE0 C9 1.189 -0.795 0.474 ETKDGv3 5
VE0 C1 -2.858 -0.905 -1.278 ETKDGv3 6
VE0 C5 1.177 1.640 -0.278 ETKDGv3 7
VE0 C6 2.295 1.747 0.764 ETKDGv3 8
VE0 N3 -2.327 -2.108 1.383 ETKDGv3 9
VE0 C4 -1.769 0.200 -3.143 ETKDGv3 10
VE0 C3 -0.641 0.085 -1.026 ETKDGv3 11
VE0 C2 -1.828 -0.628 -0.460 ETKDGv3 12
VE0 O -1.629 -0.220 3.279 ETKDGv3 13
VE0 C10 -1.928 -0.940 0.985 ETKDGv3 14
VE0 N -0.657 0.464 -2.274 ETKDGv3 15
VE0 C -2.827 -0.475 -2.687 ETKDGv3 16
VE0 H1 3.871 0.510 1.582 ETKDGv3 17
VE0 H2 4.069 0.893 -0.154 ETKDGv3 18
VE0 H3 3.189 -1.563 0.819 ETKDGv3 19
VE0 H4 2.892 -0.949 -0.839 ETKDGv3 20
VE0 H5 -1.343 1.027 1.648 ETKDGv3 21
VE0 H6 0.798 -1.773 0.116 ETKDGv3 22
VE0 H7 0.980 -0.712 1.562 ETKDGv3 23
VE0 H8 -3.749 -1.396 -0.905 ETKDGv3 24
VE0 H9 0.415 2.422 -0.066 ETKDGv3 25
VE0 H10 1.596 1.822 -1.292 ETKDGv3 26
VE0 H11 2.806 2.729 0.665 ETKDGv3 27
VE0 H12 1.842 1.705 1.779 ETKDGv3 28
VE0 H13 -2.572 -2.872 0.714 ETKDGv3 29
VE0 H14 -1.738 0.534 -4.171 ETKDGv3 30
VE0 H15 -2.549 0.005 3.571 ETKDGv3 31
VE0 H16 -3.664 -0.686 -3.340 ETKDGv3 32
#