data_VG3
#
_chem_comp.id VG3
_chem_comp.name
N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-2-hydroxypropyl]-3-(pentylsulfonyl)benzamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type ?
_chem_comp.formula "C31 H45 N3 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-12-06
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 571.771
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VG3
_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 2VIY
_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
VG3 C1 C1 C 0 1 N N N N N N 30.547 1.245 34.359 30.547 1.245 34.359 C1 VG3 1
VG3 N2 N2 N 0 1 N N N N N N 29.360 1.456 33.717 29.360 1.456 33.717 N2 VG3 2
VG3 C3 C3 C 0 1 N N S N N N 29.202 2.345 32.550 29.202 2.345 32.550 C3 VG3 3
VG3 C4 C4 C 0 1 N N R N N N 28.337 3.524 33.019 28.337 3.524 33.019 C4 VG3 4
VG3 C5 C5 C 0 1 N N N N N N 28.560 1.564 31.376 28.560 1.564 31.376 C5 VG3 5
VG3 O6 O6 O 0 1 N N N N N N 31.504 2.017 34.224 31.504 2.017 34.224 O6 VG3 6
VG3 C7 C7 C 0 1 Y N N N N N 30.572 0.047 35.215 30.572 0.047 35.215 C7 VG3 7
VG3 C8 C8 C 0 1 Y N N N N N 30.153 -1.229 34.731 30.153 -1.229 34.731 C8 VG3 8
VG3 C9 C9 C 0 1 Y N N N N N 30.176 -2.361 35.583 30.176 -2.361 35.583 C9 VG3 9
VG3 C10 C10 C 0 1 Y N N N N N 30.611 -2.234 36.921 30.611 -2.234 36.921 C10 VG3 10
VG3 C11 C11 C 0 1 Y N N N N N 31.029 -0.973 37.410 31.029 -0.973 37.410 C11 VG3 11
VG3 C12 C12 C 0 1 Y N N N N N 31.011 0.168 36.565 31.011 0.168 36.565 C12 VG3 12
VG3 C13 C13 C 0 1 Y N N N N N 29.209 0.224 31.102 29.209 0.224 31.102 C13 VG3 13
VG3 C14 C14 C 0 1 Y N N N N N 28.428 -0.965 31.089 28.428 -0.965 31.089 C14 VG3 14
VG3 C15 C15 C 0 1 Y N N N N N 29.035 -2.220 30.835 29.035 -2.220 30.835 C15 VG3 15
VG3 C16 C16 C 0 1 Y N N N N N 30.427 -2.296 30.593 30.427 -2.296 30.593 C16 VG3 16
VG3 C17 C17 C 0 1 Y N N N N N 31.214 -1.117 30.605 31.214 -1.117 30.605 C17 VG3 17
VG3 C18 C18 C 0 1 Y N N N N N 30.609 0.136 30.857 30.609 0.136 30.857 C18 VG3 18
VG3 O19 O19 O 0 1 N N N N N N 28.098 4.450 31.987 28.098 4.450 31.987 O19 VG3 19
VG3 C20 C20 C 0 1 N N S N N N 28.956 6.745 34.890 28.956 6.745 34.890 C20 VG3 20
VG3 C21 C21 C 0 1 N N N N N N 28.993 4.282 34.186 28.993 4.282 34.186 C21 VG3 21
VG3 N22 N22 N 0 1 N N N N N N 28.273 5.524 34.425 28.273 5.524 34.425 N22 VG3 22
VG3 S23 S23 S 0 1 N N N N N N 31.555 -0.833 39.100 31.555 -0.833 39.100 S23 VG3 23
VG3 C24 C24 C 0 1 N N N N N N 29.526 6.525 36.307 29.526 6.525 36.307 C24 VG3 24
VG3 C38 C38 C 0 1 N N N N N N 30.091 7.154 33.904 30.091 7.154 33.904 C38 VG3 25
VG3 N39 N39 N 0 1 N N N N N N 29.635 7.931 32.904 29.635 7.931 32.904 N39 VG3 26
VG3 C40 C40 C 0 1 N N N N N N 30.479 8.402 31.803 30.479 8.402 31.803 C40 VG3 27
VG3 O41 O41 O 0 1 N N N N N N 31.256 6.777 34.042 31.256 6.777 34.042 O41 VG3 28
VG3 C43 C43 C 0 1 N N N N N N 30.895 9.865 32.078 30.895 9.865 32.078 C43 VG3 29
VG3 C44 C44 C 0 1 N N N N N N 31.780 10.403 30.884 31.780 10.403 30.884 C44 VG3 30
VG3 C45 C45 C 0 1 N N N N N N 31.086 10.244 29.507 31.086 10.244 29.507 C45 VG3 31
VG3 C46 C46 C 0 1 N N N N N N 30.568 8.798 29.279 30.568 8.798 29.279 C46 VG3 32
VG3 C47 C47 C 0 1 N N N N N N 29.707 8.295 30.468 29.707 8.295 30.468 C47 VG3 33
VG3 C60 C60 C 0 1 N N N N N N 32.995 -1.891 39.170 32.995 -1.891 39.170 C60 VG3 34
VG3 C61 C61 C 0 1 N N N N N N 33.553 -1.884 40.600 33.553 -1.884 40.600 C61 VG3 35
VG3 C64 C64 C 0 1 N N N N N N 34.787 -2.779 40.776 34.787 -2.779 40.776 C64 VG3 36
VG3 C67 C67 C 0 1 N N N N N N 35.316 -2.755 42.218 35.316 -2.755 42.218 C67 VG3 37
VG3 C70 C70 C 0 1 N N N N N N 36.549 -3.650 42.402 36.549 -3.650 42.402 C70 VG3 38
VG3 O76 O76 O 0 1 N N N N N N 30.530 -1.417 39.924 30.530 -1.417 39.924 O76 VG3 39
VG3 O77 O77 O 0 1 N N N N N N 31.930 0.525 39.343 31.930 0.525 39.343 O77 VG3 40
VG3 H2 H2 H 0 1 N N N N N N 28.550 0.980 34.058 28.550 0.980 34.058 H2 VG3 41
VG3 H3 H3 H 0 1 N N N N N N 30.166 2.720 32.175 30.166 2.720 32.175 H3 VG3 42
VG3 H4 H4 H 0 1 N N N N N N 27.385 3.079 33.345 27.385 3.079 33.345 H4 VG3 43
VG3 H5C1 1H5C H 0 0 N N N N N N 27.503 1.386 31.624 27.503 1.386 31.624 H5C1 VG3 44
VG3 H5C2 2H5C H 0 0 N N N N N N 28.693 2.176 30.472 28.693 2.176 30.472 H5C2 VG3 45
VG3 H19 H19 H 0 1 N N N N N N 28.044 5.325 32.352 28.044 5.325 32.353 H19 VG3 46
VG3 H211 1H21 H 0 0 N N N N N N 28.960 3.659 35.092 28.960 3.659 35.092 H211 VG3 47
VG3 H212 2H21 H 0 0 N N N N N N 30.040 4.508 33.934 30.039 4.508 33.934 H212 VG3 48
VG3 H8 H8 H 0 1 N N N N N N 29.817 -1.332 33.710 29.817 -1.332 33.710 H8 VG3 49
VG3 H12 H12 H 0 1 N N N N N N 31.330 1.127 36.945 31.330 1.127 36.945 H12 VG3 50
VG3 H9 H9 H 0 1 N N N N N N 29.860 -3.323 35.208 29.860 -3.323 35.208 H9 VG3 51
VG3 H10 H10 H 0 1 N N N N N N 30.625 -3.097 37.570 30.625 -3.097 37.570 H10 VG3 52
VG3 H14 H14 H 0 1 N N N N N N 27.365 -0.911 31.274 27.365 -0.911 31.274 H14 VG3 53
VG3 H18 H18 H 0 1 N N N N N N 31.212 1.032 30.864 31.212 1.032 30.864 H18 VG3 54
VG3 H15 H15 H 0 1 N N N N N N 28.435 -3.118 30.826 28.435 -3.118 30.826 H15 VG3 55
VG3 H16 H16 H 0 1 N N N N N N 30.890 -3.252 30.399 30.890 -3.252 30.399 H16 VG3 56
VG3 H17 H17 H 0 1 N N N N N N 32.277 -1.176 30.421 32.277 -1.176 30.421 H17 VG3 57
VG3 H20 H20 H 0 1 N N N N N N 28.222 7.564 34.925 28.222 7.564 34.925 H20 VG3 58
VG3 H22 H22 H 0 1 N N N N N N 27.598 5.310 35.131 27.598 5.310 35.131 H22 VG3 59
VG3 H241 1H24 H 0 0 N N N N N N 30.624 6.473 36.257 30.624 6.473 36.257 H241 VG3 60
VG3 H242 2H24 H 0 0 N N N N N N 29.228 7.362 36.956 29.228 7.362 36.956 H242 VG3 61
VG3 H243 3H24 H 0 0 N N N N N N 29.133 5.584 36.718 29.133 5.584 36.718 H243 VG3 62
VG3 H601 1H60 H 0 0 N N N N N N 32.714 -2.916 38.888 32.714 -2.917 38.889 H601 VG3 63
VG3 H602 2H60 H 0 0 N N N N N N 33.760 -1.522 38.471 33.761 -1.522 38.471 H602 VG3 64
VG3 H39 H39 H 0 1 N N N N N N 28.672 8.200 32.913 28.672 8.200 32.913 H39 VG3 65
VG3 H40 H40 H 0 1 N N N N N N 31.383 7.779 31.729 31.383 7.779 31.729 H40 VG3 66
VG3 H431 1H43 H 0 0 N N N N N N 29.994 10.489 32.174 29.994 10.489 32.174 H431 VG3 67
VG3 H432 2H43 H 0 0 N N N N N N 31.477 9.908 33.010 31.477 9.908 33.010 H432 VG3 68
VG3 H471 1H47 H 0 0 N N N N N N 29.440 7.242 30.294 29.440 7.242 30.294 H471 VG3 69
VG3 H472 2H47 H 0 0 N N N N N N 28.805 8.921 30.535 28.805 8.921 30.535 H472 VG3 70
VG3 H441 1H44 H 0 0 N N N N N N 31.978 11.472 31.052 31.978 11.472 31.052 H441 VG3 71
VG3 H442 2H44 H 0 0 N N N N N N 32.707 9.811 30.862 32.707 9.811 30.862 H442 VG3 72
VG3 H451 1H45 H 0 0 N N N N N N 30.231 10.935 29.463 30.231 10.934 29.463 H451 VG3 73
VG3 H452 2H45 H 0 0 N N N N N N 31.826 10.468 28.725 31.826 10.468 28.725 H452 VG3 74
VG3 H461 1H46 H 0 0 N N N N N N 29.951 8.785 28.368 29.951 8.785 28.368 H461 VG3 75
VG3 H462 2H46 H 0 0 N N N N N N 31.440 8.134 29.184 31.440 8.134 29.184 H462 VG3 76
VG3 H611 1H61 H 0 0 N N N N N N 33.838 -0.852 40.852 33.838 -0.852 40.852 H611 VG3 77
VG3 H612 2H61 H 0 0 N N N N N N 32.766 -2.278 41.260 32.766 -2.278 41.260 H612 VG3 78
VG3 H641 1H64 H 0 0 N N N N N N 34.511 -3.813 40.520 34.511 -3.813 40.521 H641 VG3 79
VG3 H642 2H64 H 0 0 N N N N N N 35.580 -2.399 40.116 35.580 -2.399 40.116 H642 VG3 80
VG3 H671 1H67 H 0 0 N N N N N N 35.594 -1.721 42.471 35.594 -1.721 42.471 H671 VG3 81
VG3 H672 2H67 H 0 0 N N N N N N 34.521 -3.136 42.876 34.521 -3.136 42.876 H672 VG3 82
VG3 H701 1H70 H 0 0 N N N N N N 36.997 -3.864 41.420 36.997 -3.864 41.421 H701 VG3 83
VG3 H702 2H70 H 0 0 N N N N N N 37.285 -3.134 43.036 37.285 -3.134 43.036 H702 VG3 84
VG3 H703 3H70 H 0 0 N N N N N N 36.249 -4.593 42.881 36.249 -4.593 42.881 H703 VG3 85
#
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
VG3 C1 N2 SING N N 1
VG3 C1 O6 DOUB N N 2
VG3 C1 C7 SING N N 3
VG3 N2 C3 SING N N 4
VG3 C3 C4 SING N N 5
VG3 C3 C5 SING N N 6
VG3 C4 O19 SING N N 7
VG3 C4 C21 SING N N 8
VG3 C5 C13 SING N N 9
VG3 C7 C8 SING Y N 10
VG3 C7 C12 DOUB Y N 11
VG3 C8 C9 DOUB Y N 12
VG3 C9 C10 SING Y N 13
VG3 C10 C11 DOUB Y N 14
VG3 C11 C12 SING Y N 15
VG3 C11 S23 SING N N 16
VG3 C13 C14 SING Y N 17
VG3 C13 C18 DOUB Y N 18
VG3 C14 C15 DOUB Y N 19
VG3 C15 C16 SING Y N 20
VG3 C16 C17 DOUB Y N 21
VG3 C17 C18 SING Y N 22
VG3 C20 N22 SING N N 23
VG3 C20 C24 SING N N 24
VG3 C20 C38 SING N N 25
VG3 C21 N22 SING N N 26
VG3 S23 C60 SING N N 27
VG3 S23 O76 DOUB N N 28
VG3 S23 O77 DOUB N N 29
VG3 C38 N39 SING N N 30
VG3 C38 O41 DOUB N N 31
VG3 N39 C40 SING N N 32
VG3 C40 C43 SING N N 33
VG3 C40 C47 SING N N 34
VG3 C43 C44 SING N N 35
VG3 C44 C45 SING N N 36
VG3 C45 C46 SING N N 37
VG3 C46 C47 SING N N 38
VG3 C60 C61 SING N N 39
VG3 C61 C64 SING N N 40
VG3 C64 C67 SING N N 41
VG3 C67 C70 SING N N 42
VG3 N2 H2 SING N N 43
VG3 C3 H3 SING N N 44
VG3 C4 H4 SING N N 45
VG3 C5 H5C1 SING N N 46
VG3 C5 H5C2 SING N N 47
VG3 O19 H19 SING N N 48
VG3 C21 H211 SING N N 49
VG3 C21 H212 SING N N 50
VG3 C8 H8 SING N N 51
VG3 C12 H12 SING N N 52
VG3 C9 H9 SING N N 53
VG3 C10 H10 SING N N 54
VG3 C14 H14 SING N N 55
VG3 C18 H18 SING N N 56
VG3 C15 H15 SING N N 57
VG3 C16 H16 SING N N 58
VG3 C17 H17 SING N N 59
VG3 C20 H20 SING N N 60
VG3 N22 H22 SING N N 61
VG3 C24 H241 SING N N 62
VG3 C24 H242 SING N N 63
VG3 C24 H243 SING N N 64
VG3 C60 H601 SING N N 65
VG3 C60 H602 SING N N 66
VG3 N39 H39 SING N N 67
VG3 C40 H40 SING N N 68
VG3 C43 H431 SING N N 69
VG3 C43 H432 SING N N 70
VG3 C47 H471 SING N N 71
VG3 C47 H472 SING N N 72
VG3 C44 H441 SING N N 73
VG3 C44 H442 SING N N 74
VG3 C45 H451 SING N N 75
VG3 C45 H452 SING N N 76
VG3 C46 H461 SING N N 77
VG3 C46 H462 SING N N 78
VG3 C61 H611 SING N N 79
VG3 C61 H612 SING N N 80
VG3 C64 H641 SING N N 81
VG3 C64 H642 SING N N 82
VG3 C67 H671 SING N N 83
VG3 C67 H672 SING N N 84
VG3 C70 H701 SING N N 85
VG3 C70 H702 SING N N 86
VG3 C70 H703 SING N N 87
#
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
VG3 SMILES ACDLabs 10.04 O=C(NC1CCCCC1)C(NCC(O)C(NC(=O)c2cccc(c2)S(=O)(=O)CCCCC)Cc3ccccc3)C
VG3 SMILES_CANONICAL CACTVS 3.341 CCCCC[S](=O)(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CN[C@@H](C)C(=O)NC3CCCCC3
VG3 SMILES CACTVS 3.341 CCCCC[S](=O)(=O)c1cccc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CN[CH](C)C(=O)NC3CCCCC3
VG3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CCCCCS(=O)(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](CN[C@@H](C)C(=O)NC3CCCCC3)O
VG3 SMILES "OpenEye OEToolkits" 1.5.0 CCCCCS(=O)(=O)c1cccc(c1)C(=O)NC(Cc2ccccc2)C(CNC(C)C(=O)NC3CCCCC3)O
VG3 InChI InChI 1.03 InChI=1S/C31H45N3O5S/c1-3-4-11-19-40(38,39)27-18-12-15-25(21-27)31(37)34-28(20-24-13-7-5-8-14-24)29(35)22-32-23(2)30(36)33-26-16-9-6-10-17-26/h5,7-8,12-15,18,21,23,26,28-29,32,35H,3-4,6,9-11,16-17,19-20,22H2,1-2H3,(H,33,36)(H,34,37)/t23-,28-,29+/m0/s1
VG3 InChIKey InChI 1.03 FBMGVFBNGKNQCB-WTWMYVDVSA-N
#
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
VG3 "SYSTEMATIC NAME" ACDLabs 10.04 N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-2-hydroxypropyl]-3-(pentylsulfonyl)benzamide
VG3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 N-[(2S,3R)-4-[[(2S)-1-(cyclohexylamino)-1-oxo-propan-2-yl]amino]-3-hydroxy-1-phenyl-butan-2-yl]-3-pentylsulfonyl-benzamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VG3 'Create component' 2007-12-06 EBI
VG3 'Modify aromatic_flag' 2011-06-04 RCSB
VG3 '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
VG3 C1 C 9.495 1.500 1
VG3 N2 N 9.495 0.000 2
VG3 C3 C 8.196 -0.750 3
VG3 C4 C 8.196 -2.250 4
VG3 C5 C 6.897 0.000 5
VG3 O6 O 8.196 2.250 6
VG3 C7 C 10.794 2.250 7
VG3 C8 C 12.093 1.500 8
VG3 C9 C 13.392 2.250 9
VG3 C10 C 13.392 3.750 10
VG3 C11 C 12.093 4.500 11
VG3 C12 C 10.794 3.750 12
VG3 C13 C 5.598 -0.750 13
VG3 C14 C 4.299 0.000 14
VG3 C15 C 3.000 -0.750 15
VG3 C16 C 3.000 -2.250 16
VG3 C17 C 4.299 -3.000 17
VG3 C18 C 5.598 -2.250 18
VG3 O19 O 6.897 -3.000 19
VG3 C20 C 10.794 -5.250 20
VG3 C21 C 9.495 -3.000 21
VG3 N22 N 9.495 -4.500 22
VG3 S23 S 12.093 6.000 23
VG3 C24 C 12.093 -4.500 24
VG3 C38 C 10.794 -6.750 25
VG3 N39 N 12.093 -7.500 26
VG3 C40 C 12.093 -9.000 27
VG3 O41 O 9.495 -7.500 28
VG3 C43 C 10.794 -9.750 29
VG3 C44 C 10.794 -11.250 30
VG3 C45 C 12.093 -12.000 31
VG3 C46 C 13.392 -11.250 32
VG3 C47 C 13.392 -9.750 33
VG3 C60 C 12.093 7.500 34
VG3 C61 C 13.392 8.250 35
VG3 C64 C 13.392 9.750 36
VG3 C67 C 14.691 10.500 37
VG3 C70 C 14.691 12.000 38
VG3 O76 O 13.593 6.000 39
VG3 O77 O 10.593 6.000 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
VG3 C1 N2 SINGLE NONE 1
VG3 C1 O6 DOUBLE NONE 2
VG3 C1 C7 SINGLE NONE 3
VG3 N2 C3 SINGLE NONE 4
VG3 C3 C4 SINGLE NONE 5
VG3 C3 C5 SINGLE BEGINDASH 6
VG3 C4 O19 SINGLE BEGINWEDGE 7
VG3 C4 C21 SINGLE NONE 8
VG3 C5 C13 SINGLE NONE 9
VG3 C7 C8 DOUBLE NONE 10
VG3 C7 C12 SINGLE NONE 11
VG3 C8 C9 SINGLE NONE 12
VG3 C9 C10 DOUBLE NONE 13
VG3 C10 C11 SINGLE NONE 14
VG3 C11 C12 DOUBLE NONE 15
VG3 C11 S23 SINGLE NONE 16
VG3 C13 C14 DOUBLE NONE 17
VG3 C13 C18 SINGLE NONE 18
VG3 C14 C15 SINGLE NONE 19
VG3 C15 C16 DOUBLE NONE 20
VG3 C16 C17 SINGLE NONE 21
VG3 C17 C18 DOUBLE NONE 22
VG3 C20 N22 SINGLE NONE 23
VG3 C20 C24 SINGLE BEGINWEDGE 24
VG3 C20 C38 SINGLE NONE 25
VG3 C21 N22 SINGLE NONE 26
VG3 S23 C60 SINGLE NONE 27
VG3 S23 O76 DOUBLE NONE 28
VG3 S23 O77 DOUBLE NONE 29
VG3 C38 N39 SINGLE NONE 30
VG3 C38 O41 DOUBLE NONE 31
VG3 N39 C40 SINGLE NONE 32
VG3 C40 C43 SINGLE NONE 33
VG3 C40 C47 SINGLE NONE 34
VG3 C43 C44 SINGLE NONE 35
VG3 C44 C45 SINGLE NONE 36
VG3 C45 C46 SINGLE NONE 37
VG3 C46 C47 SINGLE NONE 38
VG3 C60 C61 SINGLE NONE 39
VG3 C61 C64 SINGLE NONE 40
VG3 C64 C67 SINGLE NONE 41
VG3 C67 C70 SINGLE NONE 42
#
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
VG3 MurckoScaffold S1 scaffold 'O=C(CNCC[C@H](Cc1ccccc1)NC(=O)c1ccccc1)NC1CCCCC1' InChI=1S/C25H33N3O2/c29-24(27-22-14-8-3-9-15-22)19-26-17-16-23(18-20-10-4-1-5-11-20)28-25(30)21-12-6-2-7-13-21/h1-2,4-7,10-13,22-23,26H,3,8-9,14-19H2,(H,27,29)(H,28,30)/t23-/m1/s1 WURZHSXDRRLLGZ-HSZRJFAPSA-N
VG3 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
VG3 cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
VG3 peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
VG3 phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
VG3 C1 S1 1
VG3 N2 S1 1
VG3 C3 S1 1
VG3 C4 S1 1
VG3 C5 S1 1
VG3 O6 S1 1
VG3 C7 S1 1
VG3 C8 S1 1
VG3 C9 S1 1
VG3 C10 S1 1
VG3 C11 S1 1
VG3 C12 S1 1
VG3 C13 S1 1
VG3 C14 S1 1
VG3 C15 S1 1
VG3 C16 S1 1
VG3 C17 S1 1
VG3 C18 S1 1
VG3 C20 S1 1
VG3 C21 S1 1
VG3 N22 S1 1
VG3 C38 S1 1
VG3 N39 S1 1
VG3 C40 S1 1
VG3 O41 S1 1
VG3 C43 S1 1
VG3 C44 S1 1
VG3 C45 S1 1
VG3 C46 S1 1
VG3 C47 S1 1
VG3 N2 F1 1
VG3 C1 F1 1
VG3 O6 F1 1
VG3 C7 F1 1
VG3 N39 F1 2
VG3 C38 F1 2
VG3 O41 F1 2
VG3 C20 F1 2
VG3 C40 F2 1
VG3 C43 F2 1
VG3 C44 F2 1
VG3 C45 F2 1
VG3 C46 F2 1
VG3 C47 F2 1
VG3 O41 F3 1
VG3 C38 F3 1
VG3 C20 F3 1
VG3 N22 F3 1
VG3 C7 F4 1
VG3 C8 F4 1
VG3 C9 F4 1
VG3 C10 F4 1
VG3 C11 F4 1
VG3 C12 F4 1
VG3 C13 F4 2
VG3 C14 F4 2
VG3 C15 F4 2
VG3 C16 F4 2
VG3 C17 F4 2
VG3 C18 F4 2
#
_pdbe_chem_comp_rdkit_properties.comp_id VG3
_pdbe_chem_comp_rdkit_properties.exactmw 571.308
_pdbe_chem_comp_rdkit_properties.amw 571.784
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 85
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.548
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 302.293
_pdbe_chem_comp_rdkit_properties.tpsa 124.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.562
_pdbe_chem_comp_rdkit_properties.CrippenMR 157.945
_pdbe_chem_comp_rdkit_properties.chi0v 20.108
_pdbe_chem_comp_rdkit_properties.chi1v 11.429
_pdbe_chem_comp_rdkit_properties.chi2v 4.851
_pdbe_chem_comp_rdkit_properties.chi3v 4.851
_pdbe_chem_comp_rdkit_properties.chi4v 2.837
_pdbe_chem_comp_rdkit_properties.chi0n 64.291
_pdbe_chem_comp_rdkit_properties.chi1n 32.195
_pdbe_chem_comp_rdkit_properties.chi2n 3.739
_pdbe_chem_comp_rdkit_properties.chi3n 3.739
_pdbe_chem_comp_rdkit_properties.chi4n 2.128
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.750
_pdbe_chem_comp_rdkit_properties.kappa1 6.896
_pdbe_chem_comp_rdkit_properties.kappa2 15.885
_pdbe_chem_comp_rdkit_properties.kappa3 10.017
_pdbe_chem_comp_rdkit_properties.Phi 2.739
#
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
VG3 UniChem ChEMBL CHEMBL402305
VG3 UniChem PDBe VG3
VG3 UniChem ZINC ZINC000016052614
VG3 UniChem PubChem 23657804
VG3 UniChem BindingDb 50373812
#
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
VG3 C1 -2.121 0.224 -0.506 ETKDGv3 1
VG3 N2 -0.937 0.270 -1.321 ETKDGv3 2
VG3 C3 0.380 -0.128 -0.804 ETKDGv3 3
VG3 C4 1.459 0.870 -1.317 ETKDGv3 4
VG3 C5 0.657 -1.611 -1.153 ETKDGv3 5
VG3 O6 -2.020 0.214 0.752 ETKDGv3 6
VG3 C7 -3.461 0.105 -1.117 ETKDGv3 7
VG3 C8 -3.761 0.708 -2.281 ETKDGv3 8
VG3 C9 -5.100 0.540 -2.882 ETKDGv3 9
VG3 C10 -6.020 -0.215 -2.274 ETKDGv3 10
VG3 C11 -5.707 -0.879 -0.989 ETKDGv3 11
VG3 C12 -4.493 -0.721 -0.440 ETKDGv3 12
VG3 C13 -0.461 -2.508 -0.681 ETKDGv3 13
VG3 C14 -0.549 -2.873 0.611 ETKDGv3 14
VG3 C15 -1.701 -3.670 1.083 ETKDGv3 15
VG3 C16 -2.670 -4.021 0.229 ETKDGv3 16
VG3 C17 -2.584 -3.622 -1.190 ETKDGv3 17
VG3 C18 -1.537 -2.909 -1.624 ETKDGv3 18
VG3 O19 1.442 1.022 -2.716 ETKDGv3 19
VG3 C20 4.658 -1.085 -0.763 ETKDGv3 20
VG3 C21 2.883 0.592 -0.788 ETKDGv3 21
VG3 N22 3.528 -0.513 -1.515 ETKDGv3 22
VG3 S23 -6.932 -1.880 -0.211 ETKDGv3 23
VG3 C24 5.110 -2.385 -1.433 ETKDGv3 24
VG3 C38 5.808 -0.108 -0.666 ETKDGv3 25
VG3 N39 6.095 0.543 0.581 ETKDGv3 26
VG3 C40 7.197 1.501 0.727 ETKDGv3 27
VG3 O41 6.483 0.168 -1.696 ETKDGv3 28
VG3 C43 7.006 2.374 1.993 ETKDGv3 29
VG3 C44 8.322 2.977 2.530 ETKDGv3 30
VG3 C45 9.386 3.109 1.435 ETKDGv3 31
VG3 C46 9.735 1.741 0.816 ETKDGv3 32
VG3 C47 8.544 0.760 0.779 ETKDGv3 33
VG3 C60 -8.414 -0.924 0.113 ETKDGv3 34
VG3 C61 -8.331 -0.092 1.401 ETKDGv3 35
VG3 C64 -7.341 1.080 1.289 ETKDGv3 36
VG3 C67 -7.356 1.984 2.531 ETKDGv3 37
VG3 C70 -8.587 2.889 2.590 ETKDGv3 38
VG3 O76 -6.407 -2.448 1.079 ETKDGv3 39
VG3 O77 -7.273 -3.017 -1.132 ETKDGv3 40
VG3 H2 -1.045 0.315 -2.358 ETKDGv3 41
VG3 H3 0.383 -0.046 0.306 ETKDGv3 42
VG3 H4 1.172 1.858 -0.894 ETKDGv3 43
VG3 H5C1 0.784 -1.739 -2.248 ETKDGv3 44
VG3 H5C2 1.599 -1.945 -0.669 ETKDGv3 45
VG3 H19 1.612 0.138 -3.129 ETKDGv3 46
VG3 H211 2.817 0.371 0.301 ETKDGv3 47
VG3 H212 3.494 1.516 -0.901 ETKDGv3 48
VG3 H8 -3.042 1.337 -2.789 ETKDGv3 49
VG3 H12 -4.249 -1.210 0.495 ETKDGv3 50
VG3 H9 -5.332 1.028 -3.820 ETKDGv3 51
VG3 H10 -6.997 -0.338 -2.725 ETKDGv3 52
VG3 H14 0.207 -2.567 1.324 ETKDGv3 53
VG3 H18 -1.489 -2.607 -2.663 ETKDGv3 54
VG3 H15 -1.766 -3.958 2.124 ETKDGv3 55
VG3 H16 -3.519 -4.595 0.575 ETKDGv3 56
VG3 H17 -3.373 -3.900 -1.876 ETKDGv3 57
VG3 H20 4.320 -1.364 0.260 ETKDGv3 58
VG3 H22 3.876 -0.153 -2.436 ETKDGv3 59
VG3 H241 4.268 -3.110 -1.450 ETKDGv3 60
VG3 H242 5.951 -2.837 -0.864 ETKDGv3 61
VG3 H243 5.437 -2.198 -2.478 ETKDGv3 62
VG3 H601 -8.631 -0.266 -0.755 ETKDGv3 63
VG3 H602 -9.262 -1.635 0.212 ETKDGv3 64
VG3 H39 5.461 0.356 1.391 ETKDGv3 65
VG3 H40 7.199 2.179 -0.157 ETKDGv3 66
VG3 H431 6.550 1.777 2.813 ETKDGv3 67
VG3 H432 6.296 3.195 1.752 ETKDGv3 68
VG3 H471 8.653 0.092 -0.102 ETKDGv3 69
VG3 H472 8.567 0.117 1.688 ETKDGv3 70
VG3 H441 8.120 3.977 2.973 ETKDGv3 71
VG3 H442 8.724 2.329 3.339 ETKDGv3 72
VG3 H451 10.304 3.569 1.861 ETKDGv3 73
VG3 H452 9.006 3.791 0.643 ETKDGv3 74
VG3 H461 10.108 1.907 -0.218 ETKDGv3 75
VG3 H462 10.562 1.276 1.395 ETKDGv3 76
VG3 H611 -8.051 -0.744 2.256 ETKDGv3 77
VG3 H612 -9.348 0.304 1.603 ETKDGv3 78
VG3 H641 -6.315 0.672 1.191 ETKDGv3 79
VG3 H642 -7.557 1.682 0.379 ETKDGv3 80
VG3 H671 -7.299 1.369 3.455 ETKDGv3 81
VG3 H672 -6.453 2.632 2.504 ETKDGv3 82
VG3 H701 -8.681 3.480 1.655 ETKDGv3 83
VG3 H702 -9.510 2.294 2.745 ETKDGv3 84
VG3 H703 -8.485 3.593 3.443 ETKDGv3 85
#