data_V9W
#
_chem_comp.id V9W
_chem_comp.name
(3~{R})-3-[[5-[(4,4-dimethylpiperidin-1-yl)methyl]-1~{H}-benzimidazol-2-yl]methyl]-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-ol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C32 H41 N7 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-05-03
_chem_comp.pdbx_modified_date 2021-10-15
_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 539.714
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code V9W
_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 7OEI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
V9W C10 C1 C 0 1 Y N N N N N 45.636 -30.794 23.053 4.930 -1.688 1.866 C10 V9W 1
V9W C13 C2 C 0 1 Y N N N N N 44.769 -31.516 24.023 3.763 -1.553 1.127 C13 V9W 2
V9W C15 C3 C 0 1 Y N N N N N 43.908 -32.872 25.653 1.821 -1.682 0.084 C15 V9W 3
V9W C17 C4 C 0 1 N N R N N N 43.681 -35.383 26.345 -0.603 -1.184 -0.069 C17 V9W 4
V9W C20 C5 C 0 1 N N N N N N 43.516 -37.727 24.467 -3.053 -0.535 1.333 C20 V9W 5
V9W C21 C6 C 0 1 N N N N N N 42.372 -35.871 25.666 -1.968 -1.761 -0.454 C21 V9W 6
V9W C01 C7 C 0 1 N N N N N N 41.928 -23.929 24.552 11.071 0.828 -2.423 C01 V9W 7
V9W C02 C8 C 0 1 N N N N N N 42.561 -24.828 23.458 10.228 1.068 -1.170 C02 V9W 8
V9W C03 C9 C 0 1 N N N N N N 43.737 -24.142 22.746 11.148 1.236 0.041 C03 V9W 9
V9W C04 C10 C 0 1 N N N N N N 43.098 -26.057 24.130 9.388 2.335 -1.353 C04 V9W 10
V9W C05 C11 C 0 1 N N N N N N 43.559 -27.078 23.096 8.502 2.536 -0.122 C05 V9W 11
V9W C07 C12 C 0 1 N N N N N N 42.886 -28.512 21.280 6.667 1.585 1.140 C07 V9W 12
V9W C08 C13 C 0 1 Y N N N N N 43.585 -29.585 22.205 5.638 0.484 1.130 C08 V9W 13
V9W C09 C14 C 0 1 Y N N N N N 45.036 -29.836 22.156 5.861 -0.671 1.864 C09 V9W 14
V9W C11 C15 C 0 1 Y N N N N N 42.781 -30.290 23.151 4.495 0.635 0.396 C11 V9W 15
V9W C12 C16 C 0 1 Y N N N N N 43.396 -31.267 24.060 3.538 -0.383 0.383 C12 V9W 16
V9W C16 C17 C 0 1 N N N N N N 43.773 -33.919 26.800 0.493 -2.198 -0.406 C16 V9W 17
V9W C18 C18 C 0 1 N N N N N N 44.816 -35.699 25.394 -0.583 -0.891 1.433 C18 V9W 18
V9W C19 C19 C 0 1 N N N N N N 44.880 -37.154 24.923 -1.720 0.078 1.771 C19 V9W 19
V9W C23 C20 C 0 1 Y N N N N N 41.319 -38.360 25.848 -4.258 -1.231 -0.564 C23 V9W 20
V9W C25 C21 C 0 1 Y N N N N N 39.962 -39.318 27.577 -5.544 -2.814 -1.636 C25 V9W 21
V9W C27 C22 C 0 1 Y N N N N N 39.823 -40.303 25.342 -6.615 -0.942 -0.824 C27 V9W 22
V9W C29 C23 C 0 1 N N N N N N 39.890 -41.948 23.076 -7.734 1.071 0.067 C29 V9W 23
V9W C30 C24 C 0 1 Y N N N N N 41.481 -42.621 23.127 -9.122 1.654 0.137 C30 V9W 24
V9W C31 C25 C 0 1 Y N N N N N 41.996 -43.197 24.345 -9.942 1.359 1.210 C31 V9W 25
V9W C32 C26 C 0 1 Y N N N N N 43.331 -43.767 24.412 -11.215 1.893 1.275 C32 V9W 26
V9W C33 C27 C 0 1 Y N N N N N 44.170 -43.768 23.246 -11.668 2.724 0.267 C33 V9W 27
V9W C34 C28 C 0 1 Y N N N N N 43.662 -43.195 22.022 -10.848 3.020 -0.806 C34 V9W 28
V9W C35 C29 C 0 1 Y N N N N N 42.331 -42.627 21.960 -9.573 2.489 -0.868 C35 V9W 29
V9W C36 C30 C 0 1 Y N N N N N 40.804 -39.311 24.921 -5.398 -0.462 -0.350 C36 V9W 30
V9W C39 C31 C 0 1 N N N N N N 41.960 -26.260 21.400 8.413 0.146 0.276 C39 V9W 31
V9W C40 C32 C 0 1 N N N N N N 41.492 -25.193 22.414 9.297 -0.126 -0.943 C40 V9W 32
V9W N06 N1 N 0 1 N N N N N N 42.409 -27.430 22.190 7.628 1.368 0.050 N06 V9W 33
V9W N14 N2 N 0 1 Y N N N N N 45.063 -32.516 25.022 2.659 -2.356 0.917 N14 V9W 34
V9W N22 N3 N 0 1 N N N N N N 42.342 -37.351 25.361 -3.022 -0.797 -0.111 N22 V9W 35
V9W N24 N4 N 0 1 Y N N N N N 40.902 -38.369 27.168 -4.373 -2.392 -1.207 N24 V9W 36
V9W N26 N5 N 0 1 Y N N N N N 39.435 -40.268 26.679 -6.646 -2.116 -1.452 N26 V9W 37
V9W N28 N6 N 0 1 N N N N N N 39.263 -41.328 24.374 -7.779 -0.214 -0.636 N28 V9W 38
V9W N38 N7 N 0 1 Y N N N N N 42.855 -32.118 25.080 2.334 -0.528 -0.229 N38 V9W 39
V9W O37 O1 O 0 1 N N N N N N 43.860 -36.222 27.492 -0.374 0.025 -0.796 O37 V9W 40
V9W H1 H1 H 0 1 N N N N N N 46.699 -30.984 23.021 5.106 -2.584 2.443 H1 V9W 41
V9W H2 H2 H 0 1 N N N N N N 43.309 -37.355 23.453 -3.215 -1.471 1.869 H2 V9W 42
V9W H3 H3 H 0 1 N N N N N N 43.594 -38.824 24.446 -3.863 0.158 1.559 H3 V9W 43
V9W H4 H4 H 0 1 N N N N N N 41.530 -35.640 26.336 -1.990 -1.958 -1.525 H4 V9W 44
V9W H5 H5 H 0 1 N N N N N N 42.249 -35.322 24.721 -2.135 -2.691 0.090 H5 V9W 45
V9W H6 H6 H 0 1 N N N N N N 41.094 -24.464 25.030 11.668 -0.075 -2.293 H6 V9W 46
V9W H7 H7 H 0 1 N N N N N N 42.687 -23.683 25.309 10.415 0.709 -3.286 H7 V9W 47
V9W H8 H8 H 0 1 N N N N N N 41.554 -23.002 24.093 11.733 1.679 -2.585 H8 V9W 48
V9W H9 H9 H 0 1 N N N N N N 44.149 -24.818 21.983 11.809 2.087 -0.120 H9 V9W 49
V9W H10 H10 H 0 1 N N N N N N 43.385 -23.217 22.265 10.546 1.406 0.934 H10 V9W 50
V9W H11 H11 H 0 1 N N N N N N 44.519 -23.899 23.481 11.744 0.333 0.172 H11 V9W 51
V9W H12 H12 H 0 1 N N N N N N 43.950 -25.777 24.766 10.047 3.195 -1.472 H12 V9W 52
V9W H13 H13 H 0 1 N N N N N N 42.308 -26.504 24.751 8.761 2.231 -2.239 H13 V9W 53
V9W H14 H14 H 0 1 N N N N N N 44.378 -26.651 22.499 9.129 2.654 0.762 H14 V9W 54
V9W H15 H15 H 0 1 N N N N N N 43.913 -27.985 23.609 7.891 3.429 -0.255 H15 V9W 55
V9W H16 H16 H 0 1 N N N N N N 43.605 -28.109 20.552 6.173 2.547 1.002 H16 V9W 56
V9W H17 H17 H 0 1 N N N N N N 42.037 -28.963 20.746 7.194 1.581 2.095 H17 V9W 57
V9W H18 H18 H 0 1 N N N N N N 45.652 -29.302 21.447 6.769 -0.774 2.439 H18 V9W 58
V9W H19 H19 H 0 1 N N N N N N 41.718 -30.105 23.199 4.332 1.538 -0.173 H19 V9W 59
V9W H20 H20 H 0 1 N N N N N N 44.652 -33.821 27.455 0.535 -2.342 -1.486 H20 V9W 60
V9W H21 H21 H 0 1 N N N N N N 42.863 -33.683 27.370 0.270 -3.148 0.079 H21 V9W 61
V9W H22 H22 H 0 1 N N N N N N 44.706 -35.058 24.507 -0.719 -1.819 1.988 H22 V9W 62
V9W H23 H23 H 0 1 N N N N N N 45.763 -35.463 25.902 0.371 -0.440 1.704 H23 V9W 63
V9W H24 H24 H 0 1 N N N N N N 45.254 -37.771 25.753 -1.564 1.020 1.247 H24 V9W 64
V9W H25 H25 H 0 1 N N N N N N 45.581 -37.214 24.077 -1.738 0.257 2.846 H25 V9W 65
V9W H26 H26 H 0 1 N N N N N N 39.631 -39.324 28.605 -5.603 -3.760 -2.153 H26 V9W 66
V9W H27 H27 H 0 1 N N N N N N 39.214 -42.752 22.749 -7.079 1.756 -0.471 H27 V9W 67
V9W H28 H28 H 0 1 N N N N N N 39.906 -41.151 22.318 -7.352 0.920 1.077 H28 V9W 68
V9W H29 H29 H 0 1 N N N N N N 41.375 -43.205 25.228 -9.588 0.710 1.998 H29 V9W 69
V9W H30 H30 H 0 1 N N N N N N 43.692 -44.190 25.338 -11.856 1.662 2.113 H30 V9W 70
V9W H31 H31 H 0 1 N N N N N N 45.163 -44.190 23.284 -12.663 3.141 0.317 H31 V9W 71
V9W H32 H32 H 0 1 N N N N N N 44.284 -43.190 21.139 -11.202 3.668 -1.593 H32 V9W 72
V9W H33 H33 H 0 1 N N N N N N 41.972 -42.205 21.033 -8.931 2.723 -1.704 H33 V9W 73
V9W H34 H34 H 0 1 N N N N N N 41.144 -39.297 23.896 -5.339 0.482 0.171 H34 V9W 74
V9W H35 H35 H 0 1 N N N N N N 41.128 -26.545 20.739 7.739 -0.696 0.432 H35 V9W 75
V9W H36 H36 H 0 1 N N N N N N 42.792 -25.869 20.795 9.041 0.276 1.158 H36 V9W 76
V9W H37 H37 H 0 1 N N N N N N 40.607 -25.579 22.942 8.669 -0.270 -1.823 H37 V9W 77
V9W H38 H38 H 0 1 N N N N N N 41.221 -24.282 21.860 9.891 -1.023 -0.769 H38 V9W 78
V9W H40 H40 H 0 1 N N N N N N 45.970 -32.888 25.220 2.509 -3.237 1.294 H40 V9W 79
V9W H41 H41 H 0 1 N N N N N N 39.063 -42.121 24.949 -8.624 -0.555 -0.969 H41 V9W 80
V9W H43 H43 H 0 1 N N N N N N 44.652 -35.968 27.950 0.474 0.446 -0.601 H43 V9W 81
#
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
V9W C10 C13 DOUB Y N 1
V9W C10 C09 SING Y N 2
V9W C13 C12 SING Y N 3
V9W C13 N14 SING Y N 4
V9W C15 C16 SING N N 5
V9W C15 N14 SING Y N 6
V9W C15 N38 DOUB Y N 7
V9W C17 C21 SING N N 8
V9W C17 C16 SING N N 9
V9W C17 C18 SING N N 10
V9W C17 O37 SING N N 11
V9W C20 C19 SING N N 12
V9W C20 N22 SING N N 13
V9W C21 N22 SING N N 14
V9W C01 C02 SING N N 15
V9W C02 C03 SING N N 16
V9W C02 C04 SING N N 17
V9W C02 C40 SING N N 18
V9W C04 C05 SING N N 19
V9W C05 N06 SING N N 20
V9W C07 C08 SING N N 21
V9W C07 N06 SING N N 22
V9W C08 C09 DOUB Y N 23
V9W C08 C11 SING Y N 24
V9W C11 C12 DOUB Y N 25
V9W C12 N38 SING Y N 26
V9W C18 C19 SING N N 27
V9W C23 C36 DOUB Y N 28
V9W C23 N22 SING N N 29
V9W C23 N24 SING Y N 30
V9W C25 N24 DOUB Y N 31
V9W C25 N26 SING Y N 32
V9W C27 C36 SING Y N 33
V9W C27 N26 DOUB Y N 34
V9W C27 N28 SING N N 35
V9W C29 N28 SING N N 36
V9W C30 C31 DOUB Y N 37
V9W C30 C35 SING Y N 38
V9W C31 C32 SING Y N 39
V9W C32 C33 DOUB Y N 40
V9W C33 C34 SING Y N 41
V9W C34 C35 DOUB Y N 42
V9W C39 C40 SING N N 43
V9W C39 N06 SING N N 44
V9W C29 C30 SING N N 45
V9W C10 H1 SING N N 46
V9W C20 H2 SING N N 47
V9W C20 H3 SING N N 48
V9W C21 H4 SING N N 49
V9W C21 H5 SING N N 50
V9W C01 H6 SING N N 51
V9W C01 H7 SING N N 52
V9W C01 H8 SING N N 53
V9W C03 H9 SING N N 54
V9W C03 H10 SING N N 55
V9W C03 H11 SING N N 56
V9W C04 H12 SING N N 57
V9W C04 H13 SING N N 58
V9W C05 H14 SING N N 59
V9W C05 H15 SING N N 60
V9W C07 H16 SING N N 61
V9W C07 H17 SING N N 62
V9W C09 H18 SING N N 63
V9W C11 H19 SING N N 64
V9W C16 H20 SING N N 65
V9W C16 H21 SING N N 66
V9W C18 H22 SING N N 67
V9W C18 H23 SING N N 68
V9W C19 H24 SING N N 69
V9W C19 H25 SING N N 70
V9W C25 H26 SING N N 71
V9W C29 H27 SING N N 72
V9W C29 H28 SING N N 73
V9W C31 H29 SING N N 74
V9W C32 H30 SING N N 75
V9W C33 H31 SING N N 76
V9W C34 H32 SING N N 77
V9W C35 H33 SING N N 78
V9W C36 H34 SING N N 79
V9W C39 H35 SING N N 80
V9W C39 H36 SING N N 81
V9W C40 H37 SING N N 82
V9W C40 H38 SING N N 83
V9W N14 H40 SING N N 84
V9W N28 H41 SING N N 85
V9W O37 H43 SING N N 86
#
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
V9W InChI InChI 1.03 InChI=1S/C32H41N7O/c1-31(2)12-15-38(16-13-31)21-25-9-10-26-27(17-25)37-29(36-26)19-32(40)11-6-14-39(22-32)30-18-28(34-23-35-30)33-20-24-7-4-3-5-8-24/h3-5,7-10,17-18,23,40H,6,11-16,19-22H2,1-2H3,(H,36,37)(H,33,34,35)/t32-/m1/s1
V9W InChIKey InChI 1.03 YTMRIXJBQMOKPZ-JGCGQSQUSA-N
V9W SMILES_CANONICAL CACTVS 3.385 CC1(C)CCN(CC1)Cc2ccc3[nH]c(C[C@]4(O)CCCN(C4)c5cc(NCc6ccccc6)ncn5)nc3c2
V9W SMILES CACTVS 3.385 CC1(C)CCN(CC1)Cc2ccc3[nH]c(C[C]4(O)CCCN(C4)c5cc(NCc6ccccc6)ncn5)nc3c2
V9W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC1(CCN(CC1)Cc2ccc3c(c2)nc([nH]3)C[C@@]4(CCCN(C4)c5cc(ncn5)NCc6ccccc6)O)C
V9W SMILES "OpenEye OEToolkits" 2.0.7 CC1(CCN(CC1)Cc2ccc3c(c2)nc([nH]3)CC4(CCCN(C4)c5cc(ncn5)NCc6ccccc6)O)C
#
_pdbx_chem_comp_identifier.comp_id V9W
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
(3~{R})-3-[[5-[(4,4-dimethylpiperidin-1-yl)methyl]-1~{H}-benzimidazol-2-yl]methyl]-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
V9W 'Create component' 2021-05-03 PDBE
V9W 'Initial release' 2021-10-20 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
V9W C10 C 10.995 0.729 1
V9W C13 C 12.294 1.479 2
V9W C15 C 14.589 2.229 3
V9W C17 C 16.839 0.930 4
V9W C20 C 16.839 -2.070 5
V9W C21 C 18.138 0.180 6
V9W C01 C 3.000 1.479 7
V9W C02 C 4.500 1.479 8
V9W C03 C 3.750 0.180 9
V9W C04 C 4.500 2.979 10
V9W C05 C 5.799 3.729 11
V9W C07 C 8.397 3.729 12
V9W C08 C 9.696 2.979 13
V9W C09 C 9.696 1.479 14
V9W C11 C 10.995 3.729 15
V9W C12 C 12.294 2.979 16
V9W C16 C 16.089 2.229 17
V9W C18 C 15.540 0.180 18
V9W C19 C 15.540 -1.320 19
V9W C23 C 19.437 -2.070 20
V9W C25 C 20.736 -4.320 21
V9W C27 C 22.035 -2.070 22
V9W C29 C 24.633 -2.070 23
V9W C30 C 25.932 -1.320 24
V9W C31 C 25.932 0.180 25
V9W C32 C 27.231 0.930 26
V9W C33 C 28.530 0.180 27
V9W C34 C 28.530 -1.320 28
V9W C35 C 27.231 -2.070 29
V9W C36 C 20.736 -1.320 30
V9W C39 C 7.098 1.479 31
V9W C40 C 5.799 0.729 32
V9W N06 N 7.098 2.979 33
V9W N14 N 13.714 1.022 34
V9W N22 N 18.138 -1.320 35
V9W N24 N 19.437 -3.570 36
V9W N26 N 22.035 -3.570 37
V9W N28 N 23.334 -1.320 38
V9W N38 N 13.714 3.436 39
V9W O37 O 17.589 2.229 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
V9W C10 C13 DOUBLE NONE 1
V9W C10 C09 SINGLE NONE 2
V9W C13 C12 SINGLE NONE 3
V9W C13 N14 SINGLE NONE 4
V9W C15 C16 SINGLE NONE 5
V9W C15 N14 SINGLE NONE 6
V9W C15 N38 DOUBLE NONE 7
V9W C17 C21 SINGLE NONE 8
V9W C17 C16 SINGLE NONE 9
V9W C17 C18 SINGLE NONE 10
V9W C17 O37 SINGLE BEGINDASH 11
V9W C20 C19 SINGLE NONE 12
V9W C20 N22 SINGLE NONE 13
V9W C21 N22 SINGLE NONE 14
V9W C01 C02 SINGLE NONE 15
V9W C02 C03 SINGLE NONE 16
V9W C02 C04 SINGLE NONE 17
V9W C02 C40 SINGLE NONE 18
V9W C04 C05 SINGLE NONE 19
V9W C05 N06 SINGLE NONE 20
V9W C07 C08 SINGLE NONE 21
V9W C07 N06 SINGLE NONE 22
V9W C08 C09 DOUBLE NONE 23
V9W C08 C11 SINGLE NONE 24
V9W C11 C12 DOUBLE NONE 25
V9W C12 N38 SINGLE NONE 26
V9W C18 C19 SINGLE NONE 27
V9W C23 C36 DOUBLE NONE 28
V9W C23 N22 SINGLE NONE 29
V9W C23 N24 SINGLE NONE 30
V9W C25 N24 DOUBLE NONE 31
V9W C25 N26 SINGLE NONE 32
V9W C27 C36 SINGLE NONE 33
V9W C27 N26 DOUBLE NONE 34
V9W C27 N28 SINGLE NONE 35
V9W C29 N28 SINGLE NONE 36
V9W C30 C31 DOUBLE NONE 37
V9W C30 C35 SINGLE NONE 38
V9W C31 C32 SINGLE NONE 39
V9W C32 C33 DOUBLE NONE 40
V9W C33 C34 SINGLE NONE 41
V9W C34 C35 DOUBLE NONE 42
V9W C39 C40 SINGLE NONE 43
V9W C39 N06 SINGLE NONE 44
V9W C29 C30 SINGLE NONE 45
#
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
V9W MurckoScaffold S1 scaffold 'c1ccc(CNc2cc(N3CCCC(Cc4nc5cc(CN6CCCCC6)ccc5[nH]4)C3)ncn2)cc1' InChI=1S/C30H37N7/c1-3-8-23(9-4-1)19-31-28-18-30(33-22-32-28)37-15-7-10-24(21-37)17-29-34-26-12-11-25(16-27(26)35-29)20-36-13-5-2-6-14-36/h1,3-4,8-9,11-12,16,18,22,24H,2,5-7,10,13-15,17,19-21H2,(H,34,35)(H,31,32,33) NPKVWRDYTZUYGR-UHFFFAOYSA-N
V9W 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
V9W imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
V9W phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
V9W pyrimidine F4 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
V9W C10 S1 1
V9W C13 S1 1
V9W C15 S1 1
V9W C17 S1 1
V9W C20 S1 1
V9W C21 S1 1
V9W C02 S1 1
V9W C04 S1 1
V9W C05 S1 1
V9W C07 S1 1
V9W C08 S1 1
V9W C09 S1 1
V9W C11 S1 1
V9W C12 S1 1
V9W C16 S1 1
V9W C18 S1 1
V9W C19 S1 1
V9W C23 S1 1
V9W C25 S1 1
V9W C27 S1 1
V9W C29 S1 1
V9W C30 S1 1
V9W C31 S1 1
V9W C32 S1 1
V9W C33 S1 1
V9W C34 S1 1
V9W C35 S1 1
V9W C36 S1 1
V9W C39 S1 1
V9W C40 S1 1
V9W N06 S1 1
V9W N14 S1 1
V9W N22 S1 1
V9W N24 S1 1
V9W N26 S1 1
V9W N28 S1 1
V9W N38 S1 1
V9W C13 F1 1
V9W N14 F1 1
V9W C15 F1 1
V9W N38 F1 1
V9W C12 F1 1
V9W C11 F1 1
V9W C08 F1 1
V9W C09 F1 1
V9W C10 F1 1
V9W C13 F2 1
V9W C12 F2 1
V9W N38 F2 1
V9W C15 F2 1
V9W N14 F2 1
V9W C10 F3 1
V9W C13 F3 1
V9W C12 F3 1
V9W C11 F3 1
V9W C08 F3 1
V9W C09 F3 1
V9W C30 F3 2
V9W C31 F3 2
V9W C32 F3 2
V9W C33 F3 2
V9W C34 F3 2
V9W C35 F3 2
V9W C36 F4 1
V9W C23 F4 1
V9W N24 F4 1
V9W C25 F4 1
V9W N26 F4 1
V9W C27 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id V9W
_pdbe_chem_comp_rdkit_properties.exactmw 539.337
_pdbe_chem_comp_rdkit_properties.amw 539.728
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 81
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.469
_pdbe_chem_comp_rdkit_properties.NumRings 6
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 294.228
_pdbe_chem_comp_rdkit_properties.tpsa 93.200
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.807
_pdbe_chem_comp_rdkit_properties.CrippenMR 155.635
_pdbe_chem_comp_rdkit_properties.chi0v 19.539
_pdbe_chem_comp_rdkit_properties.chi1v 10.782
_pdbe_chem_comp_rdkit_properties.chi2v 4.627
_pdbe_chem_comp_rdkit_properties.chi3v 4.627
_pdbe_chem_comp_rdkit_properties.chi4v 2.964
_pdbe_chem_comp_rdkit_properties.chi0n 60.539
_pdbe_chem_comp_rdkit_properties.chi1n 31.085
_pdbe_chem_comp_rdkit_properties.chi2n 4.627
_pdbe_chem_comp_rdkit_properties.chi3n 4.627
_pdbe_chem_comp_rdkit_properties.chi4n 2.964
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.490
_pdbe_chem_comp_rdkit_properties.kappa1 6.762
_pdbe_chem_comp_rdkit_properties.kappa2 11.178
_pdbe_chem_comp_rdkit_properties.kappa3 6.450
_pdbe_chem_comp_rdkit_properties.Phi 1.890
#
_pdbe_chem_comp_external_mappings.comp_id V9W
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id V9W
#
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
V9W C10 -3.590 -2.438 1.056 ETKDGv3 1
V9W C13 -2.791 -1.427 1.389 ETKDGv3 2
V9W C15 -1.383 0.029 2.325 ETKDGv3 3
V9W C17 0.946 -0.008 3.323 ETKDGv3 4
V9W C20 3.685 -0.666 3.191 ETKDGv3 5
V9W C21 1.631 0.167 1.942 ETKDGv3 6
V9W C01 -7.427 1.743 0.002 ETKDGv3 7
V9W C02 -7.695 0.820 -1.207 ETKDGv3 8
V9W C03 -9.210 0.839 -1.505 ETKDGv3 9
V9W C04 -7.248 -0.631 -0.846 ETKDGv3 10
V9W C05 -6.787 -1.410 -2.087 ETKDGv3 11
V9W C07 -4.351 -1.468 -2.624 ETKDGv3 12
V9W C08 -3.805 -1.462 -1.212 ETKDGv3 13
V9W C09 -4.125 -2.452 -0.334 ETKDGv3 14
V9W C11 -2.869 -0.374 -0.784 ETKDGv3 15
V9W C12 -2.426 -0.398 0.472 ETKDGv3 16
V9W C16 -0.456 0.659 3.321 ETKDGv3 17
V9W C18 1.837 0.662 4.399 ETKDGv3 18
V9W C19 3.249 0.045 4.481 ETKDGv3 19
V9W C23 3.875 0.269 0.841 ETKDGv3 20
V9W C25 3.993 0.296 -1.546 ETKDGv3 21
V9W C27 5.843 1.133 -0.295 ETKDGv3 22
V9W C29 7.973 1.987 -1.392 ETKDGv3 23
V9W C30 8.498 0.701 -1.970 ETKDGv3 24
V9W C31 8.041 0.229 -3.144 ETKDGv3 25
V9W C32 8.552 -1.050 -3.681 ETKDGv3 26
V9W C33 9.469 -1.746 -2.999 ETKDGv3 27
V9W C34 9.971 -1.238 -1.706 ETKDGv3 28
V9W C35 9.512 -0.079 -1.217 ETKDGv3 29
V9W C36 5.093 0.829 0.941 ETKDGv3 30
V9W C39 -5.537 0.708 -2.568 ETKDGv3 31
V9W C40 -6.923 1.351 -2.455 ETKDGv3 32
V9W N06 -5.642 -0.756 -2.769 ETKDGv3 33
V9W N14 -2.124 -1.174 2.607 ETKDGv3 34
V9W N22 3.088 -0.025 2.011 ETKDGv3 35
V9W N24 3.326 0.017 -0.466 ETKDGv3 36
V9W N26 5.304 0.874 -1.452 ETKDGv3 37
V9W N28 7.153 1.713 -0.214 ETKDGv3 38
V9W N38 -1.526 0.495 1.112 ETKDGv3 39
V9W O37 0.814 -1.386 3.595 ETKDGv3 40
V9W H1 -3.837 -3.219 1.764 ETKDGv3 41
V9W H2 3.356 -1.727 3.223 ETKDGv3 42
V9W H3 4.794 -0.688 3.138 ETKDGv3 43
V9W H4 1.435 1.195 1.563 ETKDGv3 44
V9W H5 1.199 -0.552 1.212 ETKDGv3 45
V9W H6 -7.791 2.774 -0.200 ETKDGv3 46
V9W H7 -7.948 1.361 0.907 ETKDGv3 47
V9W H8 -6.340 1.797 0.223 ETKDGv3 48
V9W H9 -9.456 0.148 -2.339 ETKDGv3 49
V9W H10 -9.793 0.525 -0.612 ETKDGv3 50
V9W H11 -9.538 1.862 -1.792 ETKDGv3 51
V9W H12 -8.070 -1.188 -0.344 ETKDGv3 52
V9W H13 -6.400 -0.611 -0.127 ETKDGv3 53
V9W H14 -6.559 -2.459 -1.807 ETKDGv3 54
V9W H15 -7.632 -1.471 -2.805 ETKDGv3 55
V9W H16 -3.604 -1.007 -3.306 ETKDGv3 56
V9W H17 -4.465 -2.515 -2.981 ETKDGv3 57
V9W H18 -4.763 -3.272 -0.631 ETKDGv3 58
V9W H19 -2.557 0.407 -1.466 ETKDGv3 59
V9W H20 -0.364 1.745 3.101 ETKDGv3 60
V9W H21 -0.915 0.571 4.330 ETKDGv3 61
V9W H22 1.353 0.594 5.398 ETKDGv3 62
V9W H23 1.936 1.745 4.160 ETKDGv3 63
V9W H24 3.978 0.851 4.718 ETKDGv3 64
V9W H25 3.284 -0.687 5.318 ETKDGv3 65
V9W H26 3.560 0.095 -2.516 ETKDGv3 66
V9W H27 8.837 2.621 -1.097 ETKDGv3 67
V9W H28 7.383 2.566 -2.136 ETKDGv3 68
V9W H29 7.293 0.773 -3.708 ETKDGv3 69
V9W H30 8.182 -1.422 -4.628 ETKDGv3 70
V9W H31 9.843 -2.683 -3.391 ETKDGv3 71
V9W H32 10.710 -1.805 -1.156 ETKDGv3 72
V9W H33 9.882 0.287 -0.268 ETKDGv3 73
V9W H34 5.517 1.086 1.902 ETKDGv3 74
V9W H35 -4.968 0.953 -1.648 ETKDGv3 75
V9W H36 -5.001 1.155 -3.432 ETKDGv3 76
V9W H37 -7.478 1.115 -3.391 ETKDGv3 77
V9W H38 -6.818 2.457 -2.419 ETKDGv3 78
V9W H40 -2.138 -1.739 3.484 ETKDGv3 79
V9W H41 7.543 1.951 0.726 ETKDGv3 80
V9W H43 0.413 -1.481 4.499 ETKDGv3 81
#