data_487
#
_chem_comp.id 487
_chem_comp.name 6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H24 N6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-02-11
_chem_comp.pdbx_modified_date 2016-02-26
_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 264.370
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 487
_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 4Y5N
_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
487 C4 C1 C 0 1 Y N N N N N -10.488 2.463 0.253 -2.662 0.159 0.186 C4 487 1
487 C5 C2 C 0 1 N N N N N N -8.175 1.691 0.088 -3.772 2.123 1.179 C5 487 2
487 C6 C3 C 0 1 N N N N N N -8.788 3.508 1.672 -4.977 -0.102 0.989 C6 487 3
487 N1 N1 N 0 1 N N N N N N -12.444 0.735 -2.072 -1.589 -2.976 -1.122 N1 487 4
487 C7 C4 C 0 1 N N N N N N -12.382 6.058 1.540 3.077 1.219 -0.587 C7 487 5
487 C8 C5 C 0 1 N N N N N N -11.228 6.573 2.382 4.354 0.375 -0.380 C8 487 6
487 N2 N2 N 0 1 Y N N N N N -10.772 1.588 -0.735 -2.668 -1.118 -0.178 N2 487 7
487 C9 C6 C 0 1 N N N N N N -11.582 7.645 3.397 4.591 0.198 1.098 C9 487 8
487 C10 C7 C 0 1 N N N N N N -12.947 7.532 4.038 3.964 -1.098 1.649 C10 487 9
487 C11 C8 C 0 1 N N N N N N -13.467 6.143 4.350 2.565 -1.354 1.063 C11 487 10
487 C12 C9 C 0 1 N N N N N N -14.040 5.363 3.178 1.759 -0.082 0.973 C12 487 11
487 N3 N3 N 0 1 N N N N N N -9.202 2.545 0.657 -3.781 0.715 0.773 N3 487 12
487 N4 N4 N 0 1 Y N N N N N -11.377 3.248 0.877 -1.575 0.901 -0.011 N4 487 13
487 C3 C10 C 0 1 Y N N N N N -12.080 1.570 -1.091 -1.589 -1.649 -0.743 C3 487 14
487 N N5 N 0 1 Y N N N N N -13.050 2.332 -0.544 -0.507 -0.900 -0.941 N 487 15
487 C2 C11 C 0 1 Y N N N N N -12.636 3.140 0.437 -0.503 0.370 -0.573 C2 487 16
487 C1 C12 C 0 1 N N S N N N -13.684 3.993 1.131 0.724 1.214 -0.799 C1 487 17
487 C C13 C 0 1 N N N N N N -14.505 4.710 0.063 0.830 1.572 -2.283 C 487 18
487 N5 N6 N 0 1 N N N N N N -13.114 4.929 2.126 1.918 0.463 -0.390 N5 487 19
487 H1 H1 H 0 1 N N N N N N -7.206 1.921 0.555 -2.804 2.564 0.940 H1 487 20
487 H2 H2 H 0 1 N N N N N N -8.431 0.637 0.273 -4.557 2.660 0.648 H2 487 21
487 H3 H3 H 0 1 N N N N N N -8.110 1.868 -0.996 -3.947 2.192 2.253 H3 487 22
487 H4 H4 H 0 1 N N N N N N -9.662 4.083 2.011 -4.922 -0.575 1.970 H4 487 23
487 H5 H5 H 0 1 N N N N N N -8.347 2.973 2.526 -5.863 0.531 0.941 H5 487 24
487 H6 H6 H 0 1 N N N N N N -8.042 4.194 1.244 -5.037 -0.870 0.218 H6 487 25
487 H7 H7 H 0 1 N N N N N N -11.643 0.234 -2.398 -2.378 -3.522 -0.977 H7 487 26
487 H8 H8 H 0 1 N N N N N N -13.123 0.088 -1.724 -0.801 -3.363 -1.534 H8 487 27
487 H9 H9 H 0 1 N N N N N N -11.980 5.738 0.567 3.083 2.051 0.117 H9 487 28
487 H10 H10 H 0 1 N N N N N N -13.092 6.885 1.389 3.075 1.615 -1.603 H10 487 29
487 H11 H11 H 0 1 N N N N N N -10.800 5.719 2.927 4.225 -0.601 -0.848 H11 487 30
487 H12 H12 H 0 1 N N N N N N -10.472 6.989 1.700 5.206 0.886 -0.828 H12 487 31
487 H13 H13 H 0 1 N N N N N N -10.830 7.609 4.199 5.666 0.175 1.282 H13 487 32
487 H14 H14 H 0 1 N N N N N N -11.529 8.619 2.889 4.164 1.049 1.628 H14 487 33
487 H15 H15 H 0 1 N N N N N N -12.912 8.090 4.985 4.611 -1.939 1.400 H15 487 34
487 H16 H16 H 0 1 N N N N N N -13.669 8.008 3.358 3.886 -1.022 2.733 H16 487 35
487 H17 H17 H 0 1 N N N N N N -14.259 6.243 5.106 2.669 -1.781 0.066 H17 487 36
487 H18 H18 H 0 1 N N N N N N -12.634 5.558 4.767 2.036 -2.063 1.701 H18 487 37
487 H19 H19 H 0 1 N N N N N N -14.802 5.998 2.703 0.708 -0.297 1.163 H19 487 38
487 H20 H20 H 0 1 N N N N N N -14.518 4.461 3.587 2.126 0.639 1.703 H20 487 39
487 H21 H21 H 0 1 N N N N N N -14.364 3.310 1.662 0.650 2.128 -0.209 H21 487 40
487 H22 H22 H 0 1 N N N N N N -15.271 5.334 0.546 -0.056 2.130 -2.586 H22 487 41
487 H23 H23 H 0 1 N N N N N N -13.843 5.346 -0.543 1.717 2.184 -2.447 H23 487 42
487 H24 H24 H 0 1 N N N N N N -14.993 3.967 -0.585 0.904 0.659 -2.873 H24 487 43
#
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
487 N1 C3 SING N N 1
487 C3 N2 DOUB Y N 2
487 C3 N SING Y N 3
487 N2 C4 SING Y N 4
487 N C2 DOUB Y N 5
487 C C1 SING N N 6
487 C5 N3 SING N N 7
487 C4 N3 SING N N 8
487 C4 N4 DOUB Y N 9
487 C2 N4 SING Y N 10
487 C2 C1 SING N N 11
487 N3 C6 SING N N 12
487 C1 N5 SING N N 13
487 C7 N5 SING N N 14
487 C7 C8 SING N N 15
487 N5 C12 SING N N 16
487 C8 C9 SING N N 17
487 C12 C11 SING N N 18
487 C9 C10 SING N N 19
487 C10 C11 SING N N 20
487 C5 H1 SING N N 21
487 C5 H2 SING N N 22
487 C5 H3 SING N N 23
487 C6 H4 SING N N 24
487 C6 H5 SING N N 25
487 C6 H6 SING N N 26
487 N1 H7 SING N N 27
487 N1 H8 SING N N 28
487 C7 H9 SING N N 29
487 C7 H10 SING N N 30
487 C8 H11 SING N N 31
487 C8 H12 SING N N 32
487 C9 H13 SING N N 33
487 C9 H14 SING N N 34
487 C10 H15 SING N N 35
487 C10 H16 SING N N 36
487 C11 H17 SING N N 37
487 C11 H18 SING N N 38
487 C12 H19 SING N N 39
487 C12 H20 SING N N 40
487 C1 H21 SING N N 41
487 C H22 SING N N 42
487 C H23 SING N N 43
487 C H24 SING N N 44
#
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
487 SMILES ACDLabs 12.01 n1c(nc(nc1C(N2CCCCCC2)C)N(C)C)N
487 InChI InChI 1.03 InChI=1S/C13H24N6/c1-10(19-8-6-4-5-7-9-19)11-15-12(14)17-13(16-11)18(2)3/h10H,4-9H2,1-3H3,(H2,14,15,16,17)/t10-/m0/s1
487 InChIKey InChI 1.03 VXAHGJQOHMSESG-JTQLQIEISA-N
487 SMILES_CANONICAL CACTVS 3.385 C[C@H](N1CCCCCC1)c2nc(N)nc(n2)N(C)C
487 SMILES CACTVS 3.385 C[CH](N1CCCCCC1)c2nc(N)nc(n2)N(C)C
487 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C[C@@H](c1nc(nc(n1)N(C)C)N)N2CCCCCC2
487 SMILES "OpenEye OEToolkits" 1.9.2 CC(c1nc(nc(n1)N(C)C)N)N2CCCCCC2
#
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
487 "SYSTEMATIC NAME" ACDLabs 12.01 6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine
487 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 6-[(1S)-1-(azepan-1-yl)ethyl]-N2,N2-dimethyl-1,3,5-triazine-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
487 'Create component' 2015-02-11 EBI
487 'Initial release' 2016-03-02 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
487 C4 C 6.404 -2.768 1
487 C5 C 5.104 -5.018 2
487 C6 C 7.702 -5.018 3
487 N1 N 3.805 0.232 4
487 C7 C 7.650 2.383 5
487 C8 C 7.316 3.845 6
487 N2 N 5.104 -2.018 7
487 C9 C 8.252 5.018 8
487 C10 C 9.752 5.018 9
487 C11 C 10.687 3.845 10
487 C12 C 10.353 2.383 11
487 N3 N 6.404 -4.268 12
487 N4 N 7.702 -2.018 13
487 C3 C 5.104 -0.518 14
487 N N 6.404 0.232 15
487 C2 C 7.702 -0.518 16
487 C1 C 9.002 0.232 17
487 C C 10.301 -0.518 18
487 N5 N 9.002 1.732 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
487 N1 C3 SINGLE NONE 1
487 C3 N2 SINGLE NONE 2
487 C3 N DOUBLE NONE 3
487 N2 C4 DOUBLE NONE 4
487 N C2 SINGLE NONE 5
487 C1 C SINGLE BEGINWEDGE 6
487 C5 N3 SINGLE NONE 7
487 C4 N3 SINGLE NONE 8
487 C4 N4 SINGLE NONE 9
487 C2 N4 DOUBLE NONE 10
487 C2 C1 SINGLE NONE 11
487 N3 C6 SINGLE NONE 12
487 C1 N5 SINGLE NONE 13
487 C7 N5 SINGLE NONE 14
487 C7 C8 SINGLE NONE 15
487 N5 C12 SINGLE NONE 16
487 C8 C9 SINGLE NONE 17
487 C12 C11 SINGLE NONE 18
487 C9 C10 SINGLE NONE 19
487 C10 C11 SINGLE NONE 20
#
_pdbe_chem_comp_substructure.comp_id 487
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles c1ncnc(CN2CCCCCC2)n1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C10H16N4/c1-2-4-6-14(5-3-1)7-10-12-8-11-9-13-10/h8-9H,1-7H2
_pdbe_chem_comp_substructure.substructure_inchikeys NXDSMHXOHGFTHJ-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
487 C4 S1 1
487 C7 S1 1
487 C8 S1 1
487 N2 S1 1
487 C9 S1 1
487 C10 S1 1
487 C11 S1 1
487 C12 S1 1
487 N4 S1 1
487 C3 S1 1
487 N S1 1
487 C2 S1 1
487 C1 S1 1
487 N5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 487
_pdbe_chem_comp_rdkit_properties.exactmw 264.206
_pdbe_chem_comp_rdkit_properties.amw 264.377
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 43
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.769
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 148.429
_pdbe_chem_comp_rdkit_properties.tpsa 71.170
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.641
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.108
_pdbe_chem_comp_rdkit_properties.chi0v 9.183
_pdbe_chem_comp_rdkit_properties.chi1v 4.657
_pdbe_chem_comp_rdkit_properties.chi2v 1.770
_pdbe_chem_comp_rdkit_properties.chi3v 1.770
_pdbe_chem_comp_rdkit_properties.chi4v 1.030
_pdbe_chem_comp_rdkit_properties.chi0n 33.183
_pdbe_chem_comp_rdkit_properties.chi1n 16.551
_pdbe_chem_comp_rdkit_properties.chi2n 1.770
_pdbe_chem_comp_rdkit_properties.chi3n 1.770
_pdbe_chem_comp_rdkit_properties.chi4n 1.030
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.430
_pdbe_chem_comp_rdkit_properties.kappa1 2.662
_pdbe_chem_comp_rdkit_properties.kappa2 6.144
_pdbe_chem_comp_rdkit_properties.kappa3 3.529
_pdbe_chem_comp_rdkit_properties.Phi 0.861
#
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
487 UniChem PDBe 487
487 UniChem ZINC ZINC000009722332
487 UniChem PubChem 41187351
#
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
487 C4 -2.709 -0.603 -0.533 ETKDGv3 1
487 C5 -3.612 1.730 -0.722 ETKDGv3 2
487 C6 -4.767 -0.195 -1.925 ETKDGv3 3
487 N1 -1.815 -4.155 -0.648 ETKDGv3 4
487 C7 1.228 1.142 -0.070 ETKDGv3 5
487 C8 2.233 2.284 0.106 ETKDGv3 6
487 N2 -2.751 -1.869 -0.833 ETKDGv3 7
487 C9 3.631 1.950 -0.428 ETKDGv3 8
487 C10 4.236 0.672 0.178 ETKDGv3 9
487 C11 3.592 -0.601 -0.396 ETKDGv3 10
487 C12 2.305 -1.045 0.329 ETKDGv3 11
487 N3 -3.695 0.306 -1.059 ETKDGv3 12
487 N4 -1.663 -0.116 0.323 ETKDGv3 13
487 C3 -1.763 -2.771 -0.313 ETKDGv3 14
487 N -0.821 -2.322 0.462 ETKDGv3 15
487 C2 -0.764 -0.928 0.801 ETKDGv3 16
487 C1 0.356 -0.419 1.683 ETKDGv3 17
487 C -0.125 0.636 2.691 ETKDGv3 18
487 N5 1.529 0.074 0.911 ETKDGv3 19
487 H1 -2.642 2.141 -1.073 ETKDGv3 20
487 H2 -4.429 2.313 -1.197 ETKDGv3 21
487 H3 -3.687 1.859 0.378 ETKDGv3 22
487 H4 -5.448 0.620 -2.249 ETKDGv3 23
487 H5 -4.328 -0.661 -2.832 ETKDGv3 24
487 H6 -5.367 -0.952 -1.378 ETKDGv3 25
487 H7 -2.570 -4.517 -1.271 ETKDGv3 26
487 H8 -1.099 -4.819 -0.276 ETKDGv3 27
487 H9 1.238 0.764 -1.117 ETKDGv3 28
487 H10 0.222 1.580 0.087 ETKDGv3 29
487 H11 1.858 3.178 -0.438 ETKDGv3 30
487 H12 2.299 2.556 1.183 ETKDGv3 31
487 H13 4.302 2.803 -0.185 ETKDGv3 32
487 H14 3.600 1.872 -1.537 ETKDGv3 33
487 H15 4.166 0.689 1.288 ETKDGv3 34
487 H16 5.317 0.657 -0.080 ETKDGv3 35
487 H17 3.383 -0.469 -1.480 ETKDGv3 36
487 H18 4.329 -1.432 -0.328 ETKDGv3 37
487 H19 1.678 -1.626 -0.383 ETKDGv3 38
487 H20 2.608 -1.737 1.147 ETKDGv3 39
487 H21 0.682 -1.276 2.315 ETKDGv3 40
487 H22 -0.559 1.526 2.191 ETKDGv3 41
487 H23 -0.902 0.198 3.354 ETKDGv3 42
487 H24 0.726 0.967 3.323 ETKDGv3 43
#