data_XB7
#
_chem_comp.id XB7
_chem_comp.name "1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C28 H31 F N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-08
_chem_comp.pdbx_modified_date 2021-02-19
_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 458.570
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XB7
_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 7KXT
_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.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
XB7 C1 C1 C 0 1 N N N -3.601 -15.151 -34.319 -10.718 -0.766 -1.415 C1 XB7 1
XB7 C10 C2 C 0 1 N N N -11.319 -12.529 -26.198 0.305 0.803 0.688 C10 XB7 2
XB7 C11 C3 C 0 1 N N N -11.369 -11.838 -27.532 -0.080 0.117 -0.625 C11 XB7 3
XB7 C12 C4 C 0 1 N N N -10.613 -12.639 -28.567 -1.532 0.460 -0.967 C12 XB7 4
XB7 C13 C5 C 0 1 Y N N -13.360 -12.056 -24.856 2.741 1.134 0.533 C13 XB7 5
XB7 C14 C6 C 0 1 Y N N -15.312 -12.947 -24.724 3.886 2.610 -0.594 C14 XB7 6
XB7 C15 C7 C 0 1 Y N N -16.441 -13.738 -24.854 4.353 3.646 -1.406 C15 XB7 7
XB7 C16 C8 C 0 1 Y N N -17.557 -13.382 -24.133 5.708 3.863 -1.527 C16 XB7 8
XB7 C17 C9 C 0 1 Y N N -17.566 -12.266 -23.297 6.612 3.059 -0.849 C17 XB7 9
XB7 C18 C10 C 0 1 Y N N -16.454 -11.465 -23.154 6.167 2.032 -0.043 C18 XB7 10
XB7 C19 C11 C 0 1 Y N N -15.336 -11.831 -23.882 4.807 1.799 0.091 C19 XB7 11
XB7 C2 C12 C 0 1 Y N N -4.846 -15.361 -32.281 -8.818 0.045 -0.239 C2 XB7 12
XB7 C20 C13 C 0 1 N N N -13.621 -10.056 -23.287 4.574 -0.177 1.675 C20 XB7 13
XB7 C21 C14 C 0 1 Y N N -13.726 -8.856 -24.199 4.802 -1.431 0.871 C21 XB7 14
XB7 C22 C15 C 0 1 Y N N -14.927 -8.533 -24.796 6.026 -1.651 0.267 C22 XB7 15
XB7 C23 C16 C 0 1 Y N N -15.042 -7.443 -25.643 6.236 -2.800 -0.471 C23 XB7 16
XB7 C24 C17 C 0 1 Y N N -13.926 -6.700 -25.885 5.221 -3.732 -0.605 C24 XB7 17
XB7 C25 C18 C 0 1 Y N N -12.712 -6.987 -25.328 3.996 -3.511 0.001 C25 XB7 18
XB7 C26 C19 C 0 1 Y N N -12.622 -8.079 -24.480 3.789 -2.363 0.742 C26 XB7 19
XB7 C27 C20 C 0 1 Y N N -5.878 -15.481 -30.122 -6.852 0.782 0.918 C27 XB7 20
XB7 C28 C21 C 0 1 Y N N -5.197 -16.096 -31.160 -8.181 0.962 0.585 C28 XB7 21
XB7 C3 C22 C 0 1 Y N N -5.177 -14.015 -32.352 -8.120 -1.049 -0.726 C3 XB7 22
XB7 C4 C23 C 0 1 Y N N -5.859 -13.421 -31.302 -6.791 -1.224 -0.390 C4 XB7 23
XB7 C5 C24 C 0 1 Y N N -6.220 -14.139 -30.171 -6.158 -0.310 0.431 C5 XB7 24
XB7 C6 C25 C 0 1 N N N -6.958 -13.478 -29.030 -4.709 -0.503 0.796 C6 XB7 25
XB7 C7 C26 C 0 1 N N N -8.466 -13.520 -29.229 -3.825 0.198 -0.238 C7 XB7 26
XB7 C8 C27 C 0 1 N N N -9.143 -13.536 -26.895 -2.091 0.690 1.379 C8 XB7 27
XB7 C9 C28 C 0 1 N N N -9.896 -12.795 -25.791 -0.657 0.354 1.792 C9 XB7 28
XB7 F1 F1 F 0 1 N N N -14.024 -5.627 -26.722 5.426 -4.856 -1.326 F1 XB7 29
XB7 N1 N1 N 0 1 N N N -9.216 -12.820 -28.178 -2.412 0.010 0.118 N1 XB7 30
XB7 N2 N2 N 0 1 N N N -12.053 -11.776 -25.189 1.675 0.431 1.052 N2 XB7 31
XB7 N3 N3 N 0 1 Y N N -14.061 -13.070 -25.329 2.644 2.152 -0.286 N3 XB7 32
XB7 N4 N4 N 0 1 Y N N -14.073 -11.266 -23.969 4.056 0.877 0.800 N4 XB7 33
XB7 O1 O1 O 0 1 N N N -4.157 -15.973 -33.296 -10.127 0.217 -0.563 O1 XB7 34
XB7 H1 H1 H 0 1 N N N -3.083 -15.782 -35.056 -10.182 -0.794 -2.364 H1 XB7 35
XB7 H2 H2 H 0 1 N N N -4.406 -14.591 -34.817 -10.661 -1.744 -0.937 H2 XB7 36
XB7 H3 H3 H 0 1 N N N -2.885 -14.445 -33.873 -11.762 -0.511 -1.595 H3 XB7 37
XB7 H4 H4 H 0 1 N N N -11.813 -13.505 -26.316 0.242 1.884 0.568 H4 XB7 38
XB7 H5 H5 H 0 1 N N N -10.914 -10.841 -27.441 0.575 0.465 -1.424 H5 XB7 39
XB7 H6 H6 H 0 1 N N N -12.418 -11.735 -27.848 0.023 -0.963 -0.515 H6 XB7 40
XB7 H7 H7 H 0 1 N N N -10.652 -12.108 -29.530 -1.630 1.539 -1.091 H7 XB7 41
XB7 H8 H8 H 0 1 N N N -11.087 -13.626 -28.673 -1.814 -0.038 -1.895 H8 XB7 42
XB7 H9 H9 H 0 1 N N N -16.445 -14.604 -25.499 3.654 4.275 -1.937 H9 XB7 43
XB7 H10 H10 H 0 1 N N N -18.450 -13.983 -24.217 6.068 4.664 -2.155 H10 XB7 44
XB7 H11 H11 H 0 1 N N N -18.465 -12.024 -22.749 7.672 3.239 -0.953 H11 XB7 45
XB7 H12 H12 H 0 1 N N N -16.455 -10.599 -22.509 6.877 1.409 0.481 H12 XB7 46
XB7 H13 H13 H 0 1 N N N -12.573 -10.185 -22.980 3.852 -0.380 2.467 H13 XB7 47
XB7 H14 H14 H 0 1 N N N -14.246 -9.889 -22.397 5.516 0.148 2.117 H14 XB7 48
XB7 H15 H15 H 0 1 N N N -15.796 -9.143 -24.599 6.818 -0.924 0.371 H15 XB7 49
XB7 H16 H16 H 0 1 N N N -15.988 -7.190 -26.098 7.193 -2.972 -0.943 H16 XB7 50
XB7 H17 H17 H 0 1 N N N -11.846 -6.379 -25.543 3.203 -4.237 -0.103 H17 XB7 51
XB7 H18 H18 H 0 1 N N N -11.671 -8.326 -24.031 2.833 -2.190 1.215 H18 XB7 52
XB7 H19 H19 H 0 1 N N N -6.149 -16.062 -29.253 -6.356 1.496 1.558 H19 XB7 53
XB7 H20 H20 H 0 1 N N N -4.941 -17.143 -31.096 -8.723 1.815 0.965 H20 XB7 54
XB7 H21 H21 H 0 1 N N N -4.905 -13.434 -33.221 -8.614 -1.765 -1.367 H21 XB7 55
XB7 H22 H22 H 0 1 N N N -6.116 -12.374 -31.366 -6.246 -2.077 -0.769 H22 XB7 56
XB7 H23 H23 H 0 1 N N N -6.708 -14.000 -28.095 -4.522 -0.078 1.782 H23 XB7 57
XB7 H24 H24 H 0 1 N N N -6.638 -12.428 -28.960 -4.476 -1.568 0.810 H24 XB7 58
XB7 H25 H25 H 0 1 N N N -8.703 -13.052 -30.196 -4.011 -0.227 -1.224 H25 XB7 59
XB7 H26 H26 H 0 1 N N N -8.786 -14.572 -29.243 -4.057 1.263 -0.252 H26 XB7 60
XB7 H27 H27 H 0 1 N N N -9.585 -14.536 -27.019 -2.780 0.359 2.156 H27 XB7 61
XB7 H28 H28 H 0 1 N N N -8.087 -13.635 -26.602 -2.187 1.768 1.244 H28 XB7 62
XB7 H29 H29 H 0 1 N N N -9.891 -13.408 -24.878 -0.564 -0.722 1.939 H29 XB7 63
XB7 H30 H30 H 0 1 N N N -9.393 -11.837 -25.592 -0.414 0.871 2.720 H30 XB7 64
XB7 H32 H32 H 0 1 N N N -11.527 -11.862 -24.343 1.832 -0.311 1.657 H32 XB7 65
# #
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
XB7 C1 O1 SING N N 1
XB7 O1 C2 SING N N 2
XB7 C3 C2 DOUB Y N 3
XB7 C3 C4 SING Y N 4
XB7 C2 C28 SING Y N 5
XB7 C4 C5 DOUB Y N 6
XB7 C28 C27 DOUB Y N 7
XB7 C5 C27 SING Y N 8
XB7 C5 C6 SING N N 9
XB7 C7 C6 SING N N 10
XB7 C7 N1 SING N N 11
XB7 C12 N1 SING N N 12
XB7 C12 C11 SING N N 13
XB7 N1 C8 SING N N 14
XB7 C11 C10 SING N N 15
XB7 C8 C9 SING N N 16
XB7 F1 C24 SING N N 17
XB7 C10 C9 SING N N 18
XB7 C10 N2 SING N N 19
XB7 C24 C23 DOUB Y N 20
XB7 C24 C25 SING Y N 21
XB7 C23 C22 SING Y N 22
XB7 N3 C13 DOUB Y N 23
XB7 N3 C14 SING Y N 24
XB7 C25 C26 DOUB Y N 25
XB7 N2 C13 SING N N 26
XB7 C13 N4 SING Y N 27
XB7 C15 C14 DOUB Y N 28
XB7 C15 C16 SING Y N 29
XB7 C22 C21 DOUB Y N 30
XB7 C14 C19 SING Y N 31
XB7 C26 C21 SING Y N 32
XB7 C21 C20 SING N N 33
XB7 C16 C17 DOUB Y N 34
XB7 N4 C19 SING Y N 35
XB7 N4 C20 SING N N 36
XB7 C19 C18 DOUB Y N 37
XB7 C17 C18 SING Y N 38
XB7 C1 H1 SING N N 39
XB7 C1 H2 SING N N 40
XB7 C1 H3 SING N N 41
XB7 C10 H4 SING N N 42
XB7 C11 H5 SING N N 43
XB7 C11 H6 SING N N 44
XB7 C12 H7 SING N N 45
XB7 C12 H8 SING N N 46
XB7 C15 H9 SING N N 47
XB7 C16 H10 SING N N 48
XB7 C17 H11 SING N N 49
XB7 C18 H12 SING N N 50
XB7 C20 H13 SING N N 51
XB7 C20 H14 SING N N 52
XB7 C22 H15 SING N N 53
XB7 C23 H16 SING N N 54
XB7 C25 H17 SING N N 55
XB7 C26 H18 SING N N 56
XB7 C27 H19 SING N N 57
XB7 C28 H20 SING N N 58
XB7 C3 H21 SING N N 59
XB7 C4 H22 SING N N 60
XB7 C6 H23 SING N N 61
XB7 C6 H24 SING N N 62
XB7 C7 H25 SING N N 63
XB7 C7 H26 SING N N 64
XB7 C8 H27 SING N N 65
XB7 C8 H28 SING N N 66
XB7 C9 H29 SING N N 67
XB7 C9 H30 SING N N 68
XB7 N2 H32 SING N N 69
# #
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
XB7 SMILES ACDLabs 12.01 "COc1ccc(cc1)CCN2CCC(CC2)Nc4n(c3c(cccc3)n4)Cc5ccc(cc5)F"
XB7 InChI InChI 1.03 "InChI=1S/C28H31FN4O/c1-34-25-12-8-21(9-13-25)14-17-32-18-15-24(16-19-32)30-28-31-26-4-2-3-5-27(26)33(28)20-22-6-10-23(29)11-7-22/h2-13,24H,14-20H2,1H3,(H,30,31)"
XB7 InChIKey InChI 1.03 GXDALQBWZGODGZ-UHFFFAOYSA-N
XB7 SMILES_CANONICAL CACTVS 3.385 "COc1ccc(CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(F)cc5)cc1"
XB7 SMILES CACTVS 3.385 "COc1ccc(CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(F)cc5)cc1"
XB7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1)CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(cc5)F"
XB7 SMILES "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1)CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(cc5)F"
# #
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
XB7 "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine"
XB7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(4-fluorophenyl)methyl]-~{N}-[1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl]benzimidazol-2-amine"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XB7 "Create component" 2020-12-08 RCSB
XB7 "Initial release" 2021-02-24 RCSB
##