data_CJ9
#
_chem_comp.id CJ9
_chem_comp.name N4-cyclopropyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H19 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-04-24
_chem_comp.pdbx_modified_date 2020-10-23
_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 233.313
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CJ9
_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 6JVP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
CJ9 N01 N1 N 0 1 N N N N N N 26.863 10.649 -13.603 0.253 3.825 -0.308 N01 CJ9 1
CJ9 C02 C1 C 0 1 Y N N N N N 27.502 9.679 -14.484 0.386 2.458 -0.136 C02 CJ9 2
CJ9 N03 N2 N 0 1 Y N N N N N 28.830 9.532 -14.378 -0.702 1.721 0.027 N03 CJ9 3
CJ9 C04 C2 C 0 1 Y N N N N N 29.481 8.670 -15.145 -0.613 0.403 0.194 C04 CJ9 4
CJ9 C05 C3 C 0 1 Y N N N N N 28.745 7.913 -16.076 0.643 -0.196 0.196 C05 CJ9 5
CJ9 C06 C4 C 0 1 Y N N N N N 27.356 8.109 -16.160 1.762 0.611 0.022 C06 CJ9 6
CJ9 N07 N3 N 0 1 N N N N N N 26.548 7.354 -17.122 3.033 0.058 0.016 N07 CJ9 7
CJ9 C08 C5 C 0 1 N N N N N N 27.126 6.407 -18.088 3.204 -1.386 0.194 C08 CJ9 8
CJ9 C09 C6 C 0 1 N N N N N N 27.833 6.985 -19.317 4.542 -1.875 0.754 C09 CJ9 9
CJ9 C10 C7 C 0 1 N N N N N N 26.422 6.414 -19.452 4.202 -2.098 -0.722 C10 CJ9 10
CJ9 N11 N4 N 0 1 Y N N N N N 26.757 8.987 -15.348 1.596 1.922 -0.146 N11 CJ9 11
CJ9 N12 N5 N 0 1 N N N N N N 30.936 8.530 -14.990 -1.757 -0.362 0.365 N12 CJ9 12
CJ9 C13 C8 C 0 1 N N N N N N 31.820 7.627 -15.856 -1.827 -1.434 -0.635 C13 CJ9 13
CJ9 C14 C9 C 0 1 N N N N N N 33.034 8.423 -16.343 -3.020 -2.343 -0.329 C14 CJ9 14
CJ9 C15 C10 C 0 1 N N N N N N 33.744 9.107 -15.259 -4.306 -1.513 -0.352 C15 CJ9 15
CJ9 C16 C11 C 0 1 N N N N N N 32.904 9.983 -14.438 -4.188 -0.374 0.665 C16 CJ9 16
CJ9 C17 C12 C 0 1 N N N N N N 31.747 9.173 -13.854 -2.961 0.477 0.329 C17 CJ9 17
CJ9 H1 H1 H 0 1 N N N N N N 25.879 10.664 -13.781 -0.628 4.231 -0.307 H1 CJ9 18
CJ9 H2 H2 H 0 1 N N N N N N 27.026 10.392 -12.650 1.042 4.378 -0.424 H2 CJ9 19
CJ9 H3 H3 H 0 1 N N N N N N 29.239 7.195 -16.714 0.746 -1.263 0.330 H3 CJ9 20
CJ9 H4 H4 H 0 1 N N N N N N 26.058 8.036 -17.665 3.809 0.627 -0.106 H4 CJ9 21
CJ9 H5 H5 H 0 1 N N N N N N 27.483 5.436 -17.715 2.308 -1.933 0.484 H5 CJ9 22
CJ9 H6 H6 H 0 1 N N N N N N 28.686 6.452 -19.761 5.294 -1.122 0.989 H6 CJ9 23
CJ9 H7 H7 H 0 1 N N N N N N 27.997 8.070 -19.397 4.525 -2.744 1.411 H7 CJ9 24
CJ9 H8 H8 H 0 1 N N N N N N 25.570 7.088 -19.628 3.961 -3.114 -1.035 H8 CJ9 25
CJ9 H9 H9 H 0 1 N N N N N N 26.260 5.470 -19.992 4.731 -1.492 -1.458 H9 CJ9 26
CJ9 H10 H10 H 0 1 N N N N N N 31.243 7.270 -16.722 -1.948 -0.998 -1.627 H10 CJ9 27
CJ9 H11 H11 H 0 1 N N N N N N 32.160 6.766 -15.261 -0.908 -2.019 -0.605 H11 CJ9 28
CJ9 H12 H12 H 0 1 N N N N N N 33.732 7.731 -16.837 -3.081 -3.129 -1.080 H12 CJ9 29
CJ9 H13 H13 H 0 1 N N N N N N 32.691 9.176 -17.067 -2.892 -2.790 0.658 H13 CJ9 30
CJ9 H14 H14 H 0 1 N N N N N N 34.187 8.343 -14.603 -4.454 -1.097 -1.348 H14 CJ9 31
CJ9 H15 H15 H 0 1 N N N N N N 34.544 9.717 -15.704 -5.154 -2.147 -0.091 H15 CJ9 32
CJ9 H16 H16 H 0 1 N N N N N N 33.505 10.407 -13.620 -5.084 0.246 0.623 H16 CJ9 33
CJ9 H17 H17 H 0 1 N N N N N N 32.505 10.798 -15.060 -4.079 -0.790 1.667 H17 CJ9 34
CJ9 H18 H18 H 0 1 N N N N N N 31.094 9.838 -13.270 -2.866 1.281 1.060 H18 CJ9 35
CJ9 H19 H19 H 0 1 N N N N N N 32.147 8.385 -13.199 -3.077 0.904 -0.667 H19 CJ9 36
#
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
CJ9 C10 C09 SING N N 1
CJ9 C10 C08 SING N N 2
CJ9 C09 C08 SING N N 3
CJ9 C08 N07 SING N N 4
CJ9 N07 C06 SING N N 5
CJ9 C14 C13 SING N N 6
CJ9 C14 C15 SING N N 7
CJ9 C06 C05 DOUB Y N 8
CJ9 C06 N11 SING Y N 9
CJ9 C05 C04 SING Y N 10
CJ9 C13 N12 SING N N 11
CJ9 N11 C02 DOUB Y N 12
CJ9 C15 C16 SING N N 13
CJ9 C04 N12 SING N N 14
CJ9 C04 N03 DOUB Y N 15
CJ9 N12 C17 SING N N 16
CJ9 C02 N03 SING Y N 17
CJ9 C02 N01 SING N N 18
CJ9 C16 C17 SING N N 19
CJ9 N01 H1 SING N N 20
CJ9 N01 H2 SING N N 21
CJ9 C05 H3 SING N N 22
CJ9 N07 H4 SING N N 23
CJ9 C08 H5 SING N N 24
CJ9 C09 H6 SING N N 25
CJ9 C09 H7 SING N N 26
CJ9 C10 H8 SING N N 27
CJ9 C10 H9 SING N N 28
CJ9 C13 H10 SING N N 29
CJ9 C13 H11 SING N N 30
CJ9 C14 H12 SING N N 31
CJ9 C14 H13 SING N N 32
CJ9 C15 H14 SING N N 33
CJ9 C15 H15 SING N N 34
CJ9 C16 H16 SING N N 35
CJ9 C16 H17 SING N N 36
CJ9 C17 H18 SING N N 37
CJ9 C17 H19 SING N N 38
#
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
CJ9 InChI InChI 1.03 InChI=1S/C12H19N5/c13-12-15-10(14-9-4-5-9)8-11(16-12)17-6-2-1-3-7-17/h8-9H,1-7H2,(H3,13,14,15,16)
CJ9 InChIKey InChI 1.03 KEJKDPAZBYTTRQ-UHFFFAOYSA-N
CJ9 SMILES_CANONICAL CACTVS 3.385 Nc1nc(NC2CC2)cc(n1)N3CCCCC3
CJ9 SMILES CACTVS 3.385 Nc1nc(NC2CC2)cc(n1)N3CCCCC3
CJ9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1c(nc(nc1N2CCCCC2)N)NC3CC3
CJ9 SMILES "OpenEye OEToolkits" 2.0.6 c1c(nc(nc1N2CCCCC2)N)NC3CC3
#
_pdbx_chem_comp_identifier.comp_id CJ9
_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 ~{N}4-cyclopropyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CJ9 'Create component' 2019-04-24 PDBJ
CJ9 'Initial release' 2020-10-28 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
CJ9 N01 N 9.002 -2.350 1
CJ9 C02 C 7.702 -1.601 2
CJ9 N03 N 7.702 -0.101 3
CJ9 C04 C 6.404 0.649 4
CJ9 C05 C 5.104 -0.101 5
CJ9 C06 C 5.104 -1.601 6
CJ9 N07 N 3.805 -2.350 7
CJ9 C08 C 3.805 -3.850 8
CJ9 C09 C 4.555 -5.149 9
CJ9 C10 C 3.055 -5.149 10
CJ9 N11 N 6.404 -2.350 11
CJ9 N12 N 6.404 2.150 12
CJ9 C13 C 7.702 2.900 13
CJ9 C14 C 7.702 4.399 14
CJ9 C15 C 6.404 5.149 15
CJ9 C16 C 5.104 4.399 16
CJ9 C17 C 5.104 2.900 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
CJ9 C10 C09 SINGLE NONE 1
CJ9 C10 C08 SINGLE NONE 2
CJ9 C09 C08 SINGLE NONE 3
CJ9 C08 N07 SINGLE NONE 4
CJ9 N07 C06 SINGLE NONE 5
CJ9 C14 C13 SINGLE NONE 6
CJ9 C14 C15 SINGLE NONE 7
CJ9 C06 C05 DOUBLE NONE 8
CJ9 C06 N11 SINGLE NONE 9
CJ9 C05 C04 SINGLE NONE 10
CJ9 C13 N12 SINGLE NONE 11
CJ9 N11 C02 DOUBLE NONE 12
CJ9 C15 C16 SINGLE NONE 13
CJ9 C04 N12 SINGLE NONE 14
CJ9 C04 N03 DOUBLE NONE 15
CJ9 N12 C17 SINGLE NONE 16
CJ9 C02 N03 SINGLE NONE 17
CJ9 C02 N01 SINGLE NONE 18
CJ9 C16 C17 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
CJ9 MurckoScaffold S1 scaffold c1nc(NC2CC2)cc(N2CCCCC2)n1 InChI=1S/C12H18N4/c1-2-6-16(7-3-1)12-8-11(13-9-14-12)15-10-4-5-10/h8-10H,1-7H2,(H,13,14,15) KQUOGAYYNMYDDK-UHFFFAOYSA-N
CJ9 cyclopropane F1 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
CJ9 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
CJ9 C02 S1 1
CJ9 N03 S1 1
CJ9 C04 S1 1
CJ9 C05 S1 1
CJ9 C06 S1 1
CJ9 N07 S1 1
CJ9 C08 S1 1
CJ9 C09 S1 1
CJ9 C10 S1 1
CJ9 N11 S1 1
CJ9 N12 S1 1
CJ9 C13 S1 1
CJ9 C14 S1 1
CJ9 C15 S1 1
CJ9 C16 S1 1
CJ9 C17 S1 1
CJ9 C08 F1 1
CJ9 C10 F1 1
CJ9 C09 F1 1
CJ9 C05 F2 1
CJ9 C06 F2 1
CJ9 N11 F2 1
CJ9 C02 F2 1
CJ9 N03 F2 1
CJ9 C04 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CJ9
_pdbe_chem_comp_rdkit_properties.exactmw 233.164
_pdbe_chem_comp_rdkit_properties.amw 233.319
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_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 128.297
_pdbe_chem_comp_rdkit_properties.tpsa 67.070
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.482
_pdbe_chem_comp_rdkit_properties.CrippenMR 66.681
_pdbe_chem_comp_rdkit_properties.chi0v 8.236
_pdbe_chem_comp_rdkit_properties.chi1v 4.486
_pdbe_chem_comp_rdkit_properties.chi2v 1.762
_pdbe_chem_comp_rdkit_properties.chi3v 1.762
_pdbe_chem_comp_rdkit_properties.chi4v 1.052
_pdbe_chem_comp_rdkit_properties.chi0n 27.236
_pdbe_chem_comp_rdkit_properties.chi1n 13.828
_pdbe_chem_comp_rdkit_properties.chi2n 1.762
_pdbe_chem_comp_rdkit_properties.chi3n 1.762
_pdbe_chem_comp_rdkit_properties.chi4n 1.052
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.520
_pdbe_chem_comp_rdkit_properties.kappa1 2.439
_pdbe_chem_comp_rdkit_properties.kappa2 4.391
_pdbe_chem_comp_rdkit_properties.kappa3 2.595
_pdbe_chem_comp_rdkit_properties.Phi 0.630
#
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
CJ9 UniChem PDBe CJ9
CJ9 UniChem PubChem 154815497
#
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
CJ9 N01 1.610 -2.484 -2.529 ETKDGv3 1
CJ9 C02 1.228 -1.558 -1.515 ETKDGv3 2
CJ9 N03 -0.148 -1.167 -1.381 ETKDGv3 3
CJ9 C04 -0.526 -0.310 -0.475 ETKDGv3 4
CJ9 C05 0.485 0.244 0.458 ETKDGv3 5
CJ9 C06 1.764 -0.131 0.324 ETKDGv3 6
CJ9 N07 2.768 0.382 1.211 ETKDGv3 7
CJ9 C08 4.158 -0.052 1.114 ETKDGv3 8
CJ9 C09 5.168 1.048 1.393 ETKDGv3 9
CJ9 C10 4.910 0.597 -0.036 ETKDGv3 10
CJ9 N11 2.124 -1.064 -0.711 ETKDGv3 11
CJ9 N12 -1.917 0.046 -0.364 ETKDGv3 12
CJ9 C13 -2.942 -0.965 -0.666 ETKDGv3 13
CJ9 C14 -4.352 -0.465 -0.317 ETKDGv3 14
CJ9 C15 -4.345 0.239 1.045 ETKDGv3 15
CJ9 C16 -3.350 1.420 1.105 ETKDGv3 16
CJ9 C17 -2.332 1.420 -0.046 ETKDGv3 17
CJ9 H1 0.892 -2.880 -3.175 ETKDGv3 18
CJ9 H2 2.607 -2.773 -2.635 ETKDGv3 19
CJ9 H3 0.194 0.917 1.254 ETKDGv3 20
CJ9 H4 2.491 1.006 2.003 ETKDGv3 21
CJ9 H5 4.421 -1.101 1.364 ETKDGv3 22
CJ9 H6 4.743 2.046 1.635 ETKDGv3 23
CJ9 H7 6.131 0.689 1.813 ETKDGv3 24
CJ9 H8 4.327 1.324 -0.642 ETKDGv3 25
CJ9 H9 5.719 -0.029 -0.466 ETKDGv3 26
CJ9 H10 -2.734 -1.881 -0.071 ETKDGv3 27
CJ9 H11 -2.902 -1.231 -1.744 ETKDGv3 28
CJ9 H12 -5.055 -1.325 -0.291 ETKDGv3 29
CJ9 H13 -4.705 0.242 -1.099 ETKDGv3 30
CJ9 H14 -4.078 -0.505 1.828 ETKDGv3 31
CJ9 H15 -5.370 0.605 1.273 ETKDGv3 32
CJ9 H16 -2.801 1.380 2.071 ETKDGv3 33
CJ9 H17 -3.909 2.381 1.083 ETKDGv3 34
CJ9 H18 -2.801 1.866 -0.949 ETKDGv3 35
CJ9 H19 -1.471 2.069 0.215 ETKDGv3 36
#