data_AM9
#
_chem_comp.id AM9
_chem_comp.name
"6-(2,6-dimethylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C31 H30 N8 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-01-21
_chem_comp.pdbx_modified_date 2011-06-04
_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 530.623
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AM9
_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 3BYO
_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
AM9 C1 C1 C 0 1 Y N N N N N 25.759 35.800 82.930 0.717 -0.966 0.256 C1 AM9 1
AM9 N1 N1 N 0 1 Y N N N N N 25.574 36.546 84.069 -0.498 -1.482 0.116 N1 AM9 2
AM9 C2 C2 C 0 1 Y N N N N N 24.371 36.768 84.633 -1.560 -0.693 0.092 C2 AM9 3
AM9 C3 C3 C 0 1 Y N N N N N 23.214 36.141 83.938 -1.375 0.699 0.217 C3 AM9 4
AM9 C4 C4 C 0 1 Y N N N N N 23.389 35.328 82.727 -0.081 1.197 0.363 C4 AM9 5
AM9 N2 N2 N 0 1 Y N N N N N 24.682 35.202 82.277 0.926 0.339 0.377 N2 AM9 6
AM9 N3 N3 N 0 1 N N N N N N 27.045 35.726 82.415 1.802 -1.819 0.284 N3 AM9 7
AM9 C5 C5 C 0 1 Y N N N N N 28.233 36.421 82.761 3.102 -1.297 0.314 C5 AM9 8
AM9 C6 C6 C 0 1 Y N N N N N 28.153 37.686 83.517 4.103 -1.965 1.007 C6 AM9 9
AM9 C7 C7 C 0 1 Y N N N N N 29.312 38.347 83.982 5.384 -1.450 1.037 C7 AM9 10
AM9 C8 C8 C 0 1 Y N N N N N 30.536 37.684 83.649 5.671 -0.265 0.373 C8 AM9 11
AM9 C9 C9 C 0 1 Y N N N N N 30.672 36.421 82.868 4.671 0.403 -0.321 C9 AM9 12
AM9 C10 C10 C 0 1 Y N N N N N 29.478 35.777 82.410 3.391 -0.115 -0.355 C10 AM9 13
AM9 N4 N4 N 0 1 Y N N N N N 24.250 37.621 85.821 -2.840 -1.194 -0.053 N4 AM9 14
AM9 C11 C11 C 0 1 Y N N N N N 23.045 37.913 86.429 -3.922 -0.357 -0.076 C11 AM9 15
AM9 N5 N5 N 0 1 N N N N N N 21.892 37.337 85.833 -3.772 1.013 0.045 N5 AM9 16
AM9 C12 C12 C 0 1 N N N N N N 22.007 36.496 84.618 -2.553 1.574 0.190 C12 AM9 17
AM9 C13 C13 C 0 1 Y N N N N N 25.187 38.354 86.628 -3.312 -2.491 -0.195 C13 AM9 18
AM9 C14 C14 C 0 1 Y N N N N N 24.508 39.096 87.704 -4.708 -2.388 -0.302 C14 AM9 19
AM9 N6 N6 N 0 1 Y N N N N N 23.176 38.793 87.550 -5.019 -1.069 -0.223 N6 AM9 20
AM9 C15 C15 C 0 1 Y N N N N N 26.657 38.522 86.577 -2.703 -3.735 -0.244 C15 AM9 21
AM9 C16 C16 C 0 1 Y N N N N N 27.424 39.358 87.515 -3.472 -4.870 -0.398 C16 AM9 22
AM9 C17 C17 C 0 1 Y N N N N N 26.681 40.060 88.542 -4.852 -4.775 -0.504 C17 AM9 23
AM9 C18 C18 C 0 1 Y N N N N N 25.244 39.951 88.659 -5.473 -3.547 -0.457 C18 AM9 24
AM9 O1 O1 O 0 1 N N N N N N 21.024 36.087 84.012 -2.434 2.780 0.295 O1 AM9 25
AM9 C19 C19 C 0 1 Y N N N N N 20.676 37.486 86.446 -4.906 1.834 0.017 C19 AM9 26
AM9 C20 C20 C 0 1 Y N N N N N 20.154 36.434 87.317 -5.568 2.147 1.197 C20 AM9 27
AM9 C21 C21 C 0 1 Y N N N N N 18.855 36.605 87.953 -6.687 2.956 1.166 C21 AM9 28
AM9 C22 C22 C 0 1 Y N N N N N 18.055 37.775 87.767 -7.148 3.455 -0.039 C22 AM9 29
AM9 C23 C23 C 0 1 Y N N N N N 18.608 38.762 86.916 -6.491 3.144 -1.216 C23 AM9 30
AM9 C24 C24 C 0 1 Y N N N N N 19.884 38.671 86.241 -5.368 2.341 -1.191 C24 AM9 31
AM9 C25 C25 C 0 1 N N N N N N 20.318 39.788 85.316 -4.649 2.009 -2.473 C25 AM9 32
AM9 C26 C26 C 0 1 N N N N N N 20.981 35.179 87.517 -5.067 1.604 2.510 C26 AM9 33
AM9 N7 N7 N 0 1 N N N N N N 31.578 38.364 84.228 6.969 0.257 0.404 N7 AM9 34
AM9 C27 C27 C 0 1 N N N N N N 32.642 38.740 83.331 7.943 -0.724 -0.094 C27 AM9 35
AM9 C28 C28 C 0 1 N N N N N N 33.995 38.460 83.971 9.355 -0.146 0.030 C28 AM9 36
AM9 N8 N8 N 0 1 N N N N N N 33.945 39.015 85.334 9.437 1.107 -0.733 N8 AM9 37
AM9 C29 C29 C 0 1 N N N N N N 33.020 38.275 86.206 8.463 2.088 -0.235 C29 AM9 38
AM9 C30 C30 C 0 1 N N N N N N 31.662 38.748 85.695 7.051 1.510 -0.359 C30 AM9 39
AM9 C31 C31 C 0 1 N N N N N N 35.238 38.638 85.884 10.800 1.655 -0.701 C31 AM9 40
AM9 H4 H4 H 0 1 N N N N N N 22.556 34.860 82.223 0.095 2.258 0.461 H4 AM9 41
AM9 HN3 HN3 H 0 1 N N N N N N 27.154 35.068 81.670 1.665 -2.779 0.282 HN3 AM9 42
AM9 H6 H6 H 0 1 N N N N N N 27.184 38.117 83.720 3.879 -2.886 1.524 H6 AM9 43
AM9 H7 H7 H 0 1 N N N N N N 29.277 39.271 84.540 6.161 -1.969 1.577 H7 AM9 44
AM9 H9 H9 H 0 1 N N N N N N 31.645 36.003 82.654 4.894 1.325 -0.837 H9 AM9 45
AM9 H10 H10 H 0 1 N N N N N N 29.506 34.863 81.836 2.614 0.402 -0.898 H10 AM9 46
AM9 H15 H15 H 0 1 N N N N N N 27.200 37.999 85.804 -1.629 -3.816 -0.162 H15 AM9 47
AM9 H16 H16 H 0 1 N N N N N N 28.498 39.445 87.441 -2.997 -5.839 -0.437 H16 AM9 48
AM9 H17 H17 H 0 1 N N N N N N 27.217 40.684 89.242 -5.443 -5.670 -0.624 H17 AM9 49
AM9 H18 H18 H 0 1 N N N N N N 24.716 40.487 89.434 -6.548 -3.480 -0.541 H18 AM9 50
AM9 H21 H21 H 0 1 N N N N N N 18.481 35.817 88.590 -7.202 3.200 2.083 H21 AM9 51
AM9 H22 H22 H 0 1 N N N N N N 17.094 37.898 88.244 -8.023 4.088 -0.061 H22 AM9 52
AM9 H23 H23 H 0 1 N N N N N N 18.028 39.659 86.757 -6.854 3.535 -2.155 H23 AM9 53
AM9 H25 H25 H 0 1 N N N N N N 20.423 40.720 85.890 -5.072 1.100 -2.901 H25 AM9 54
AM9 H25A H25A H 0 0 N N N N N N 21.284 39.529 84.857 -4.766 2.832 -3.178 H25A AM9 55
AM9 H25B H25B H 0 0 N N N N N N 19.562 39.926 84.529 -3.590 1.855 -2.266 H25B AM9 56
AM9 H26 H26 H 0 1 N N N N N N 21.181 34.712 86.541 -4.349 2.301 2.941 H26 AM9 57
AM9 H26A H26A H 0 0 N N N N N N 21.934 35.441 88.000 -5.905 1.476 3.194 H26A AM9 58
AM9 H26B H26B H 0 0 N N N N N N 20.428 34.473 88.154 -4.583 0.641 2.344 H26B AM9 59
AM9 H27 H27 H 0 1 N N N N N N 32.554 38.159 82.401 7.872 -1.639 0.495 H27 AM9 60
AM9 H27A H27A H 0 0 N N N N N N 32.564 39.815 83.113 7.732 -0.947 -1.140 H27A AM9 61
AM9 H28 H28 H 0 1 N N N N N N 34.185 37.377 84.005 9.576 0.052 1.079 H28 AM9 62
AM9 H28A H28A H 0 0 N N N N N N 34.808 38.919 83.389 10.077 -0.861 -0.366 H28A AM9 63
AM9 H29 H29 H 0 1 N N N N N N 33.142 37.186 86.110 8.674 2.312 0.811 H29 AM9 64
AM9 H29A H29A H 0 0 N N N N N N 33.178 38.462 87.278 8.535 3.003 -0.824 H29A AM9 65
AM9 H30 H30 H 0 1 N N N N N N 31.571 39.838 85.809 6.830 1.312 -1.408 H30 AM9 66
AM9 H30A H30A H 0 0 N N N N N N 30.846 38.283 86.268 6.330 2.225 0.036 H30A AM9 67
AM9 H31 H31 H 0 1 N N N N N N 35.970 38.543 85.069 11.491 0.934 -1.137 H31 AM9 68
AM9 H31A H31A H 0 0 N N N N N N 35.575 39.411 86.591 10.832 2.582 -1.273 H31A AM9 69
AM9 H31B H31B H 0 0 N N N N N N 35.146 37.675 86.408 11.087 1.855 0.331 H31B AM9 70
#
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
AM9 N2 C1 DOUB Y N 1
AM9 N3 C1 SING N N 2
AM9 C1 N1 SING Y N 3
AM9 N1 C2 DOUB Y N 4
AM9 C3 C2 SING Y N 5
AM9 C2 N4 SING Y N 6
AM9 C4 C3 DOUB Y N 7
AM9 C3 C12 SING N N 8
AM9 N2 C4 SING Y N 9
AM9 C4 H4 SING N N 10
AM9 N3 C5 SING N N 11
AM9 N3 HN3 SING N N 12
AM9 C10 C5 DOUB Y N 13
AM9 C5 C6 SING Y N 14
AM9 C6 C7 DOUB Y N 15
AM9 C6 H6 SING N N 16
AM9 C8 C7 SING Y N 17
AM9 C7 H7 SING N N 18
AM9 C9 C8 DOUB Y N 19
AM9 C8 N7 SING N N 20
AM9 C10 C9 SING Y N 21
AM9 C9 H9 SING N N 22
AM9 C10 H10 SING N N 23
AM9 N4 C11 SING Y N 24
AM9 N4 C13 SING Y N 25
AM9 N5 C11 SING N N 26
AM9 C11 N6 DOUB Y N 27
AM9 C12 N5 SING N N 28
AM9 N5 C19 SING N N 29
AM9 O1 C12 DOUB N N 30
AM9 C15 C13 SING Y N 31
AM9 C13 C14 DOUB Y N 32
AM9 N6 C14 SING Y N 33
AM9 C14 C18 SING Y N 34
AM9 C15 C16 DOUB Y N 35
AM9 C15 H15 SING N N 36
AM9 C16 C17 SING Y N 37
AM9 C16 H16 SING N N 38
AM9 C17 C18 DOUB Y N 39
AM9 C17 H17 SING N N 40
AM9 C18 H18 SING N N 41
AM9 C24 C19 DOUB Y N 42
AM9 C19 C20 SING Y N 43
AM9 C20 C26 SING N N 44
AM9 C20 C21 DOUB Y N 45
AM9 C22 C21 SING Y N 46
AM9 C21 H21 SING N N 47
AM9 C23 C22 DOUB Y N 48
AM9 C22 H22 SING N N 49
AM9 C24 C23 SING Y N 50
AM9 C23 H23 SING N N 51
AM9 C25 C24 SING N N 52
AM9 C25 H25 SING N N 53
AM9 C25 H25A SING N N 54
AM9 C25 H25B SING N N 55
AM9 C26 H26 SING N N 56
AM9 C26 H26A SING N N 57
AM9 C26 H26B SING N N 58
AM9 C27 N7 SING N N 59
AM9 N7 C30 SING N N 60
AM9 C27 C28 SING N N 61
AM9 C27 H27 SING N N 62
AM9 C27 H27A SING N N 63
AM9 C28 N8 SING N N 64
AM9 C28 H28 SING N N 65
AM9 C28 H28A SING N N 66
AM9 N8 C31 SING N N 67
AM9 N8 C29 SING N N 68
AM9 C30 C29 SING N N 69
AM9 C29 H29 SING N N 70
AM9 C29 H29A SING N N 71
AM9 C30 H30 SING N N 72
AM9 C30 H30A SING N N 73
AM9 C31 H31 SING N N 74
AM9 C31 H31A SING N N 75
AM9 C31 H31B SING N N 76
#
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
AM9 SMILES ACDLabs 10.04 O=C3N(c1c(cccc1C)C)c6nc7ccccc7n6c2nc(ncc23)Nc4ccc(cc4)N5CCN(C)CC5
AM9 SMILES_CANONICAL CACTVS 3.341 CN1CCN(CC1)c2ccc(Nc3ncc4C(=O)N(c5nc6ccccc6n5c4n3)c7c(C)cccc7C)cc2
AM9 SMILES CACTVS 3.341 CN1CCN(CC1)c2ccc(Nc3ncc4C(=O)N(c5nc6ccccc6n5c4n3)c7c(C)cccc7C)cc2
AM9 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 Cc1cccc(c1N2c3nc4ccccc4n3-c5c(cnc(n5)Nc6ccc(cc6)N7CCN(CC7)C)C2=O)C
AM9 SMILES "OpenEye OEToolkits" 1.5.0 Cc1cccc(c1N2c3nc4ccccc4n3-c5c(cnc(n5)Nc6ccc(cc6)N7CCN(CC7)C)C2=O)C
AM9 InChI InChI 1.03 InChI=1S/C31H30N8O/c1-20-7-6-8-21(2)27(20)39-29(40)24-19-32-30(35-28(24)38-26-10-5-4-9-25(26)34-31(38)39)33-22-11-13-23(14-12-22)37-17-15-36(3)16-18-37/h4-14,19H,15-18H2,1-3H3,(H,32,33,35)
AM9 InChIKey InChI 1.03 BHJJWVDKNXABFS-UHFFFAOYSA-N
#
_pdbx_chem_comp_identifier.comp_id AM9
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 10.04
_pdbx_chem_comp_identifier.identifier
"6-(2,6-dimethylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
AM9 'Create component' 2008-01-21 RCSB
AM9 'Modify aromatic_flag' 2011-06-04 RCSB
AM9 'Modify descriptor' 2011-06-04 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
AM9 C1 C 13.409 0.236 1
AM9 N1 N 14.769 -0.534 2
AM9 C2 C 16.110 0.268 3
AM9 C3 C 16.110 1.768 4
AM9 C4 C 14.769 2.570 5
AM9 N2 N 13.409 1.799 6
AM9 N3 N 12.113 -0.519 7
AM9 C5 C 10.812 0.226 8
AM9 C6 C 10.806 1.726 9
AM9 C7 C 9.504 2.471 10
AM9 C8 C 8.208 1.716 11
AM9 C9 C 8.213 0.216 12
AM9 C10 C 9.515 -0.529 13
AM9 N4 N 17.409 -0.482 14
AM9 C11 C 18.708 0.268 15
AM9 N5 N 18.708 1.768 16
AM9 C12 C 17.409 2.518 17
AM9 C13 C 17.723 -1.940 18
AM9 C14 C 19.206 -2.095 19
AM9 N6 N 19.813 -0.733 20
AM9 C15 C 16.791 -3.183 21
AM9 C16 C 17.413 -4.606 22
AM9 C17 C 18.958 -4.768 23
AM9 C18 C 19.860 -3.503 24
AM9 O1 O 17.409 4.018 25
AM9 C19 C 20.007 2.518 26
AM9 C20 C 20.007 4.018 27
AM9 C21 C 21.306 4.768 28
AM9 C22 C 22.605 4.018 29
AM9 C23 C 22.605 2.518 30
AM9 C24 C 21.306 1.768 31
AM9 C25 C 21.306 0.268 32
AM9 C26 C 18.708 4.768 33
AM9 N7 N 6.906 2.461 34
AM9 C27 C 6.900 3.961 35
AM9 C28 C 5.598 4.706 36
AM9 N8 N 4.302 3.951 37
AM9 C29 C 4.308 2.451 38
AM9 C30 C 5.610 1.706 39
AM9 C31 C 3.000 4.696 40
#
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
AM9 N2 C1 SINGLE NONE 1
AM9 N3 C1 SINGLE NONE 2
AM9 C1 N1 DOUBLE NONE 3
AM9 N1 C2 SINGLE NONE 4
AM9 C3 C2 DOUBLE NONE 5
AM9 C2 N4 SINGLE NONE 6
AM9 C4 C3 SINGLE NONE 7
AM9 C3 C12 SINGLE NONE 8
AM9 N2 C4 DOUBLE NONE 9
AM9 N3 C5 SINGLE NONE 10
AM9 C10 C5 SINGLE NONE 11
AM9 C5 C6 DOUBLE NONE 12
AM9 C6 C7 SINGLE NONE 13
AM9 C8 C7 DOUBLE NONE 14
AM9 C9 C8 SINGLE NONE 15
AM9 C8 N7 SINGLE NONE 16
AM9 C10 C9 DOUBLE NONE 17
AM9 N4 C11 SINGLE NONE 18
AM9 N4 C13 SINGLE NONE 19
AM9 N5 C11 SINGLE NONE 20
AM9 C11 N6 DOUBLE NONE 21
AM9 C12 N5 SINGLE NONE 22
AM9 N5 C19 SINGLE NONE 23
AM9 O1 C12 DOUBLE NONE 24
AM9 C15 C13 DOUBLE NONE 25
AM9 C13 C14 SINGLE NONE 26
AM9 N6 C14 SINGLE NONE 27
AM9 C14 C18 DOUBLE NONE 28
AM9 C15 C16 SINGLE NONE 29
AM9 C16 C17 DOUBLE NONE 30
AM9 C17 C18 SINGLE NONE 31
AM9 C24 C19 SINGLE NONE 32
AM9 C19 C20 DOUBLE NONE 33
AM9 C20 C26 SINGLE NONE 34
AM9 C20 C21 SINGLE NONE 35
AM9 C22 C21 DOUBLE NONE 36
AM9 C23 C22 SINGLE NONE 37
AM9 C24 C23 DOUBLE NONE 38
AM9 C25 C24 SINGLE NONE 39
AM9 C27 N7 SINGLE NONE 40
AM9 N7 C30 SINGLE NONE 41
AM9 C27 C28 SINGLE NONE 42
AM9 C28 N8 SINGLE NONE 43
AM9 N8 C31 SINGLE NONE 44
AM9 N8 C29 SINGLE NONE 45
AM9 C30 C29 SINGLE NONE 46
#
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
AM9 MurckoScaffold S1 scaffold O=c1c2cnc(Nc3ccc(N4CCNCC4)cc3)nc2n2c3ccccc3nc2n1-c1ccccc1 InChI=1S/C28H24N8O/c37-26-22-18-30-27(31-19-10-12-20(13-11-19)34-16-14-29-15-17-34)33-25(22)36-24-9-5-4-8-23(24)32-28(36)35(26)21-6-2-1-3-7-21/h1-13,18,29H,14-17H2,(H,30,31,33) ZYMYNSPBQKPZGY-UHFFFAOYSA-N
AM9 benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
AM9 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
AM9 phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
AM9 piperazine F4 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-UHFFFAOYSA-N
AM9 pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
AM9 Z54628578 F6 fragment CNc1ncccn1 InChI=1S/C5H7N3/c1-6-5-7-3-2-4-8-5/h2-4H,1H3,(H,6,7,8) BQNXHDSGGRTFNX-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
AM9 C1 S1 1
AM9 N1 S1 1
AM9 C2 S1 1
AM9 C3 S1 1
AM9 C4 S1 1
AM9 N2 S1 1
AM9 N3 S1 1
AM9 C5 S1 1
AM9 C6 S1 1
AM9 C7 S1 1
AM9 C8 S1 1
AM9 C9 S1 1
AM9 C10 S1 1
AM9 N4 S1 1
AM9 C11 S1 1
AM9 N5 S1 1
AM9 C12 S1 1
AM9 C13 S1 1
AM9 C14 S1 1
AM9 N6 S1 1
AM9 C15 S1 1
AM9 C16 S1 1
AM9 C17 S1 1
AM9 C18 S1 1
AM9 O1 S1 1
AM9 C19 S1 1
AM9 C20 S1 1
AM9 C21 S1 1
AM9 C22 S1 1
AM9 C23 S1 1
AM9 C24 S1 1
AM9 N7 S1 1
AM9 C27 S1 1
AM9 C28 S1 1
AM9 N8 S1 1
AM9 C29 S1 1
AM9 C30 S1 1
AM9 C13 F1 1
AM9 N4 F1 1
AM9 C11 F1 1
AM9 N6 F1 1
AM9 C14 F1 1
AM9 C18 F1 1
AM9 C17 F1 1
AM9 C16 F1 1
AM9 C15 F1 1
AM9 C13 F2 1
AM9 C14 F2 1
AM9 N6 F2 1
AM9 C11 F2 1
AM9 N4 F2 1
AM9 C5 F3 1
AM9 C10 F3 1
AM9 C9 F3 1
AM9 C8 F3 1
AM9 C7 F3 1
AM9 C6 F3 1
AM9 C13 F3 2
AM9 C15 F3 2
AM9 C16 F3 2
AM9 C17 F3 2
AM9 C18 F3 2
AM9 C14 F3 2
AM9 C19 F3 3
AM9 C24 F3 3
AM9 C23 F3 3
AM9 C22 F3 3
AM9 C21 F3 3
AM9 C20 F3 3
AM9 N7 F4 1
AM9 C27 F4 1
AM9 C28 F4 1
AM9 N8 F4 1
AM9 C29 F4 1
AM9 C30 F4 1
AM9 C3 F5 1
AM9 C2 F5 1
AM9 N1 F5 1
AM9 C1 F5 1
AM9 N2 F5 1
AM9 C4 F5 1
AM9 C3 F5 2
AM9 C2 F5 2
AM9 N4 F5 2
AM9 C11 F5 2
AM9 N5 F5 2
AM9 C12 F5 2
AM9 C5 F6 1
AM9 N3 F6 1
AM9 C1 F6 1
AM9 N2 F6 1
AM9 C4 F6 1
AM9 C3 F6 1
AM9 C2 F6 1
AM9 N1 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AM9
_pdbe_chem_comp_rdkit_properties.exactmw 530.254
_pdbe_chem_comp_rdkit_properties.amw 530.636
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 70
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.226
_pdbe_chem_comp_rdkit_properties.NumRings 7
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 6
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_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 273.103
_pdbe_chem_comp_rdkit_properties.tpsa 83.590
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.081
_pdbe_chem_comp_rdkit_properties.CrippenMR 151.228
_pdbe_chem_comp_rdkit_properties.chi0v 19.486
_pdbe_chem_comp_rdkit_properties.chi1v 10.926
_pdbe_chem_comp_rdkit_properties.chi2v 5.463
_pdbe_chem_comp_rdkit_properties.chi3v 5.463
_pdbe_chem_comp_rdkit_properties.chi4v 3.792
_pdbe_chem_comp_rdkit_properties.chi0n 49.486
_pdbe_chem_comp_rdkit_properties.chi1n 25.873
_pdbe_chem_comp_rdkit_properties.chi2n 5.463
_pdbe_chem_comp_rdkit_properties.chi3n 5.463
_pdbe_chem_comp_rdkit_properties.chi4n 3.792
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -4.760
_pdbe_chem_comp_rdkit_properties.kappa1 8.141
_pdbe_chem_comp_rdkit_properties.kappa2 9.460
_pdbe_chem_comp_rdkit_properties.kappa3 3.974
_pdbe_chem_comp_rdkit_properties.Phi 1.925
#
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
AM9 UniChem ChEMBL CHEMBL410295
AM9 UniChem PDBe AM9
AM9 UniChem ZINC ZINC000053214756
AM9 UniChem SureChEMBL SCHEMBL5235694
AM9 UniChem 'PubChem TPHARMA' 16896334
AM9 UniChem PubChem 11785878
AM9 UniChem BindingDb 50374608
AM9 UniChem MedChemExpress HY-12072
AM9 UniChem 'Probes And Drugs' PD013011
#
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
AM9 C1 0.061 -0.872 -0.123 ETKDGv3 1
AM9 N1 -1.110 -1.373 -0.395 ETKDGv3 2
AM9 C2 -2.316 -0.646 -0.113 ETKDGv3 3
AM9 C3 -2.250 0.575 0.457 ETKDGv3 4
AM9 C4 -0.912 1.118 0.774 ETKDGv3 5
AM9 N2 0.153 0.424 0.497 ETKDGv3 6
AM9 N3 1.240 -1.643 -0.392 ETKDGv3 7
AM9 C5 2.577 -1.120 -0.334 ETKDGv3 8
AM9 C6 2.867 0.121 -0.767 ETKDGv3 9
AM9 C7 4.258 0.620 -0.727 ETKDGv3 10
AM9 C8 5.253 -0.169 -0.282 ETKDGv3 11
AM9 C9 4.934 -1.545 0.172 ETKDGv3 12
AM9 C10 3.674 -1.994 0.141 ETKDGv3 13
AM9 N4 -3.597 -1.199 -0.427 ETKDGv3 14
AM9 C11 -4.818 -0.516 -0.149 ETKDGv3 15
AM9 N5 -4.788 0.784 0.446 ETKDGv3 16
AM9 C12 -3.494 1.343 0.760 ETKDGv3 17
AM9 C13 -4.014 -2.431 -0.981 ETKDGv3 18
AM9 C14 -5.450 -2.398 -1.000 ETKDGv3 19
AM9 N6 -5.910 -1.161 -0.459 ETKDGv3 20
AM9 C15 -3.309 -3.474 -1.425 ETKDGv3 21
AM9 C16 -4.081 -4.633 -1.954 ETKDGv3 22
AM9 C17 -5.434 -4.607 -1.974 ETKDGv3 23
AM9 C18 -6.174 -3.417 -1.465 ETKDGv3 24
AM9 O1 -3.413 2.484 1.290 ETKDGv3 25
AM9 C19 -6.002 1.487 0.756 ETKDGv3 26
AM9 C20 -6.610 2.254 -0.177 ETKDGv3 27
AM9 C21 -7.864 2.966 0.167 ETKDGv3 28
AM9 C22 -8.385 2.865 1.394 ETKDGv3 29
AM9 C23 -7.719 2.037 2.416 ETKDGv3 30
AM9 C24 -6.592 1.367 2.121 ETKDGv3 31
AM9 C25 -5.907 0.534 3.168 ETKDGv3 32
AM9 C26 -6.044 2.390 -1.564 ETKDGv3 33
AM9 N7 6.613 0.304 -0.244 ETKDGv3 34
AM9 C27 6.917 1.676 0.178 ETKDGv3 35
AM9 C28 8.258 1.711 0.914 ETKDGv3 36
AM9 N8 9.309 1.076 0.094 ETKDGv3 37
AM9 C29 8.977 -0.341 -0.152 ETKDGv3 38
AM9 C30 7.666 -0.448 -0.933 ETKDGv3 39
AM9 C31 10.607 1.175 0.778 ETKDGv3 40
AM9 H4 -0.807 2.089 1.238 ETKDGv3 41
AM9 HN3 1.124 -2.670 -0.547 ETKDGv3 42
AM9 H6 2.099 0.762 -1.179 ETKDGv3 43
AM9 H7 4.462 1.621 -1.083 ETKDGv3 44
AM9 H9 5.720 -2.189 0.545 ETKDGv3 45
AM9 H10 3.454 -2.998 0.479 ETKDGv3 46
AM9 H15 -2.229 -3.488 -1.406 ETKDGv3 47
AM9 H16 -3.552 -5.502 -2.325 ETKDGv3 48
AM9 H17 -5.986 -5.454 -2.360 ETKDGv3 49
AM9 H18 -7.255 -3.382 -1.472 ETKDGv3 50
AM9 H21 -8.365 3.577 -0.573 ETKDGv3 51
AM9 H22 -9.298 3.390 1.640 ETKDGv3 52
AM9 H23 -8.158 1.978 3.405 ETKDGv3 53
AM9 H25 -6.552 0.377 4.059 ETKDGv3 54
AM9 H25A -4.973 1.040 3.490 ETKDGv3 55
AM9 H25B -5.653 -0.464 2.752 ETKDGv3 56
AM9 H26 -6.619 3.128 -2.162 ETKDGv3 57
AM9 H26A -6.085 1.410 -2.085 ETKDGv3 58
AM9 H26B -4.989 2.735 -1.514 ETKDGv3 59
AM9 H27 6.126 2.059 0.860 ETKDGv3 60
AM9 H27A 6.964 2.335 -0.717 ETKDGv3 61
AM9 H28 8.154 1.193 1.895 ETKDGv3 62
AM9 H28A 8.519 2.774 1.109 ETKDGv3 63
AM9 H29 8.882 -0.900 0.807 ETKDGv3 64
AM9 H29A 9.780 -0.821 -0.756 ETKDGv3 65
AM9 H30 7.806 -0.028 -1.952 ETKDGv3 66
AM9 H30A 7.394 -1.520 -1.039 ETKDGv3 67
AM9 H31 11.406 0.727 0.149 ETKDGv3 68
AM9 H31A 10.875 2.242 0.937 ETKDGv3 69
AM9 H31B 10.586 0.655 1.762 ETKDGv3 70
#