data_HDG
#
_chem_comp.id HDG
_chem_comp.name "(2R,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-methoxyphenyl)ethyl]hexanamide (non-preferred name)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C32 H42 N8 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(R)-SKI-72"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-06-26
_chem_comp.pdbx_modified_date 2021-03-01
_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 618.726
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HDG
_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 6DVR
_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
HDG C4 C1 C 0 1 N N S -50.912 -35.101 -23.599 -1.777 -1.920 -1.093 C4 HDG 1
HDG C3 C2 C 0 1 N N N -49.568 -35.526 -24.188 -2.066 -0.871 -2.168 C3 HDG 2
HDG C2 C3 C 0 1 N N R -49.167 -36.978 -23.996 -3.172 0.068 -1.680 C2 HDG 3
HDG C5 C4 C 0 1 N N N -51.151 -33.588 -23.821 -0.589 -2.781 -1.526 C5 HDG 4
HDG C6 C5 C 0 1 N N N -50.932 -33.109 -25.260 0.672 -1.916 -1.586 C6 HDG 5
HDG C1 C6 C 0 1 N N S -47.659 -37.225 -23.978 -3.568 1.059 -2.797 C1 HDG 6
HDG O3 O1 O 0 1 N N N -51.197 -30.137 -23.676 3.488 -1.326 -3.008 O3 HDG 7
HDG C8 C7 C 0 1 N N N -50.664 -30.644 -24.651 3.111 -1.945 -2.036 C8 HDG 8
HDG N1 N1 N 0 1 N N N -49.407 -30.385 -24.975 3.825 -1.908 -0.894 N1 HDG 9
HDG C9 C8 C 0 1 N N N -48.622 -29.473 -24.162 4.995 -1.032 -0.790 C9 HDG 10
HDG C10 C9 C 0 1 N N N -47.141 -29.671 -24.305 5.692 -1.268 0.552 C10 HDG 11
HDG C11 C10 C 0 1 Y N N -46.403 -28.913 -23.227 6.823 -0.285 0.710 C11 HDG 12
HDG C17 C11 C 0 1 Y N N -46.266 -29.448 -21.953 6.593 0.941 1.308 C17 HDG 13
HDG C16 C12 C 0 1 Y N N -45.615 -28.752 -20.949 7.628 1.844 1.454 C16 HDG 14
HDG C14 C13 C 0 1 Y N N -45.076 -27.502 -21.214 8.899 1.520 1.002 C14 HDG 15
HDG O2 O2 O 0 1 N N N -44.524 -26.875 -20.125 9.919 2.407 1.145 O2 HDG 16
HDG C15 C14 C 0 1 N N N -44.027 -25.543 -20.297 11.200 2.006 0.655 C15 HDG 17
HDG C13 C15 C 0 1 Y N N -45.179 -26.962 -22.492 9.127 0.289 0.403 C13 HDG 18
HDG C12 C16 C 0 1 Y N N -45.846 -27.665 -23.482 8.090 -0.612 0.263 C12 HDG 19
HDG C7 C17 C 0 1 N N R -51.476 -31.617 -25.489 1.842 -2.755 -2.105 C7 HDG 20
HDG N N2 N 0 1 N N N -52.885 -31.485 -25.112 1.585 -3.145 -3.497 N HDG 21
HDG C18 C18 C 0 1 N N N -51.023 -35.386 -22.106 -3.008 -2.809 -0.904 C18 HDG 22
HDG N2 N3 N 0 1 N N N -52.303 -35.161 -21.427 -2.780 -3.729 0.219 N2 HDG 23
HDG C19 C19 C 0 1 N N N -52.133 -35.547 -20.007 -3.911 -4.652 0.381 C19 HDG 24
HDG C20 C20 C 0 1 Y N N -53.087 -34.860 -19.062 -3.701 -5.493 1.614 C20 HDG 25
HDG C25 C21 C 0 1 Y N N -52.618 -34.021 -18.058 -4.264 -5.109 2.817 C25 HDG 26
HDG C24 C22 C 0 1 Y N N -53.498 -33.306 -17.272 -4.071 -5.880 3.947 C24 HDG 27
HDG C23 C23 C 0 1 Y N N -54.855 -33.422 -17.465 -3.315 -7.035 3.875 C23 HDG 28
HDG C22 C24 C 0 1 Y N N -55.336 -34.270 -18.434 -2.751 -7.419 2.673 C22 HDG 29
HDG C21 C25 C 0 1 Y N N -54.459 -34.992 -19.223 -2.949 -6.650 1.541 C21 HDG 30
HDG O1 O3 O 0 1 N N N -47.258 -37.919 -22.799 -4.746 0.609 -3.471 O1 HDG 31
HDG O4 O4 O 0 1 N N N -49.703 -37.759 -25.087 -2.687 0.900 -0.604 O4 HDG 32
HDG C26 C26 C 0 1 N N R -48.729 -38.691 -25.486 -3.583 2.032 -0.564 C26 HDG 33
HDG C C27 C 0 1 N N R -47.397 -37.981 -25.286 -3.845 2.380 -2.046 C HDG 34
HDG O O5 O 0 1 N N N -46.310 -38.894 -25.215 -5.202 2.787 -2.233 O HDG 35
HDG N3 N4 N 0 1 Y N N -49.033 -39.086 -26.859 -2.949 3.161 0.121 N3 HDG 36
HDG C31 C28 C 0 1 Y N N -49.178 -38.258 -27.942 -1.611 3.340 0.313 C31 HDG 37
HDG N7 N5 N 0 1 Y N N -49.495 -38.883 -29.053 -1.400 4.449 0.959 N7 HDG 38
HDG C30 C29 C 0 1 Y N N -49.561 -40.217 -28.673 -2.584 5.051 1.222 C30 HDG 39
HDG C27 C30 C 0 1 Y N N -49.278 -40.357 -27.324 -3.592 4.235 0.682 C27 HDG 40
HDG C29 C31 C 0 1 Y N N -49.860 -41.392 -29.388 -2.968 6.237 1.871 C29 HDG 41
HDG N6 N6 N 0 1 N N N -50.127 -41.414 -30.704 -2.019 7.084 2.417 N6 HDG 42
HDG N5 N7 N 0 1 Y N N -49.852 -42.563 -28.711 -4.263 6.526 1.949 N5 HDG 43
HDG C28 C32 C 0 1 Y N N -49.558 -42.549 -27.405 -5.175 5.724 1.431 C28 HDG 44
HDG N4 N8 N 0 1 Y N N -49.266 -41.503 -26.620 -4.862 4.607 0.808 N4 HDG 45
HDG H1 H1 H 0 1 N N N -51.709 -35.653 -24.119 -1.541 -1.422 -0.153 H1 HDG 46
HDG H2 H2 H 0 1 N N N -48.789 -34.901 -23.726 -1.162 -0.295 -2.366 H2 HDG 47
HDG H3 H3 H 0 1 N N N -49.601 -35.330 -25.270 -2.388 -1.367 -3.083 H3 HDG 48
HDG H4 H4 H 0 1 N N N -49.590 -37.335 -23.045 -4.040 -0.506 -1.356 H4 HDG 49
HDG H5 H5 H 0 1 N N N -50.463 -33.033 -23.167 -0.443 -3.587 -0.808 H5 HDG 50
HDG H6 H6 H 0 1 N N N -52.189 -33.360 -23.538 -0.786 -3.203 -2.512 H6 HDG 51
HDG H7 H7 H 0 1 N N N -51.461 -33.788 -25.944 0.504 -1.073 -2.256 H7 HDG 52
HDG H8 H8 H 0 1 N N N -49.855 -33.132 -25.481 0.906 -1.545 -0.588 H8 HDG 53
HDG H9 H9 H 0 1 N N N -47.147 -36.253 -24.031 -2.749 1.183 -3.505 H9 HDG 54
HDG H10 H10 H 0 1 N N N -48.998 -30.817 -25.779 3.565 -2.461 -0.141 H10 HDG 55
HDG H11 H11 H 0 1 N N N -48.866 -28.442 -24.459 5.687 -1.252 -1.603 H11 HDG 56
HDG H12 H12 H 0 1 N N N -48.894 -29.624 -23.107 4.677 0.009 -0.856 H12 HDG 57
HDG H13 H13 H 0 1 N N N -46.908 -30.743 -24.219 4.976 -1.132 1.362 H13 HDG 58
HDG H14 H14 H 0 1 N N N -46.820 -29.304 -25.291 6.086 -2.284 0.582 H14 HDG 59
HDG H15 H15 H 0 1 N N N -46.675 -30.425 -21.742 5.604 1.192 1.660 H15 HDG 60
HDG H16 H16 H 0 1 N N N -45.527 -29.181 -19.962 7.448 2.801 1.920 H16 HDG 61
HDG H17 H17 H 0 1 N N N -43.619 -25.177 -19.343 11.922 2.803 0.832 H17 HDG 62
HDG H18 H18 H 0 1 N N N -43.234 -25.543 -21.059 11.522 1.103 1.175 H18 HDG 63
HDG H19 H19 H 0 1 N N N -44.847 -24.885 -20.621 11.134 1.806 -0.414 H19 HDG 64
HDG H20 H20 H 0 1 N N N -44.741 -25.999 -22.711 10.115 0.035 0.049 H20 HDG 65
HDG H21 H21 H 0 1 N N N -45.935 -27.236 -24.469 8.267 -1.572 -0.199 H21 HDG 66
HDG H22 H22 H 0 1 N N N -51.349 -31.368 -26.553 1.948 -3.649 -1.491 H22 HDG 67
HDG H23 H23 H 0 1 N N N -53.186 -30.544 -25.269 1.482 -2.333 -4.087 H23 HDG 68
HDG H24 H24 H 0 1 N N N -53.438 -32.108 -25.665 2.312 -3.753 -3.843 H24 HDG 69
HDG H26 H26 H 0 1 N N N -50.764 -36.445 -21.961 -3.877 -2.186 -0.692 H26 HDG 70
HDG H27 H27 H 0 1 N N N -50.277 -34.754 -21.602 -3.185 -3.382 -1.813 H27 HDG 71
HDG H28 H28 H 0 1 N N N -52.557 -34.196 -21.490 -1.915 -4.235 0.102 H28 HDG 72
HDG H30 H30 H 0 1 N N N -52.287 -36.633 -19.924 -4.834 -4.081 0.484 H30 HDG 73
HDG H31 H31 H 0 1 N N N -51.106 -35.298 -19.702 -3.981 -5.299 -0.493 H31 HDG 74
HDG H32 H32 H 0 1 N N N -51.555 -33.928 -17.892 -4.855 -4.207 2.873 H32 HDG 75
HDG H33 H33 H 0 1 N N N -53.119 -32.652 -16.501 -4.511 -5.581 4.887 H33 HDG 76
HDG H34 H34 H 0 1 N N N -55.540 -32.849 -16.858 -3.163 -7.637 4.759 H34 HDG 77
HDG H35 H35 H 0 1 N N N -56.401 -34.373 -18.580 -2.160 -8.321 2.616 H35 HDG 78
HDG H36 H36 H 0 1 N N N -54.846 -35.666 -19.973 -2.513 -6.952 0.600 H36 HDG 79
HDG H37 H37 H 0 1 N N N -47.453 -37.387 -22.036 -5.039 1.194 -4.182 H37 HDG 80
HDG H38 H38 H 0 1 N N N -48.758 -39.576 -24.834 -4.515 1.760 -0.068 H38 HDG 81
HDG H39 H39 H 0 1 N N N -47.245 -37.256 -26.099 -3.163 3.162 -2.381 H39 HDG 82
HDG H40 H40 H 0 1 N N N -45.500 -38.414 -25.090 -5.421 3.018 -3.146 H40 HDG 83
HDG H41 H41 H 0 1 N N N -49.044 -37.188 -27.887 -0.841 2.660 -0.021 H41 HDG 84
HDG H42 H42 H 0 1 N N N -50.289 -42.357 -30.996 -2.296 7.900 2.862 H42 HDG 85
HDG H43 H43 H 0 1 N N N -50.941 -40.864 -30.888 -1.077 6.862 2.353 H43 HDG 86
HDG H44 H44 H 0 1 N N N -49.556 -43.513 -26.917 -6.216 5.997 1.517 H44 HDG 87
# #
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
HDG N6 C29 SING N N 1
HDG C29 N5 DOUB Y N 2
HDG C29 C30 SING Y N 3
HDG N7 C30 SING Y N 4
HDG N7 C31 DOUB Y N 5
HDG N5 C28 SING Y N 6
HDG C30 C27 DOUB Y N 7
HDG C31 N3 SING Y N 8
HDG C28 N4 DOUB Y N 9
HDG C27 N3 SING Y N 10
HDG C27 N4 SING Y N 11
HDG N3 C26 SING N N 12
HDG C7 C6 SING N N 13
HDG C7 N SING N N 14
HDG C7 C8 SING N N 15
HDG C26 C SING N N 16
HDG C26 O4 SING N N 17
HDG C O SING N N 18
HDG C C1 SING N N 19
HDG C6 C5 SING N N 20
HDG O4 C2 SING N N 21
HDG N1 C8 SING N N 22
HDG N1 C9 SING N N 23
HDG C8 O3 DOUB N N 24
HDG C10 C9 SING N N 25
HDG C10 C11 SING N N 26
HDG C3 C2 SING N N 27
HDG C3 C4 SING N N 28
HDG C2 C1 SING N N 29
HDG C1 O1 SING N N 30
HDG C5 C4 SING N N 31
HDG C4 C18 SING N N 32
HDG C12 C11 DOUB Y N 33
HDG C12 C13 SING Y N 34
HDG C11 C17 SING Y N 35
HDG C13 C14 DOUB Y N 36
HDG C18 N2 SING N N 37
HDG C17 C16 DOUB Y N 38
HDG N2 C19 SING N N 39
HDG C14 C16 SING Y N 40
HDG C14 O2 SING N N 41
HDG C15 O2 SING N N 42
HDG C19 C20 SING N N 43
HDG C21 C20 DOUB Y N 44
HDG C21 C22 SING Y N 45
HDG C20 C25 SING Y N 46
HDG C22 C23 DOUB Y N 47
HDG C25 C24 DOUB Y N 48
HDG C23 C24 SING Y N 49
HDG C4 H1 SING N N 50
HDG C3 H2 SING N N 51
HDG C3 H3 SING N N 52
HDG C2 H4 SING N N 53
HDG C5 H5 SING N N 54
HDG C5 H6 SING N N 55
HDG C6 H7 SING N N 56
HDG C6 H8 SING N N 57
HDG C1 H9 SING N N 58
HDG N1 H10 SING N N 59
HDG C9 H11 SING N N 60
HDG C9 H12 SING N N 61
HDG C10 H13 SING N N 62
HDG C10 H14 SING N N 63
HDG C17 H15 SING N N 64
HDG C16 H16 SING N N 65
HDG C15 H17 SING N N 66
HDG C15 H18 SING N N 67
HDG C15 H19 SING N N 68
HDG C13 H20 SING N N 69
HDG C12 H21 SING N N 70
HDG C7 H22 SING N N 71
HDG N H23 SING N N 72
HDG N H24 SING N N 73
HDG C18 H26 SING N N 74
HDG C18 H27 SING N N 75
HDG N2 H28 SING N N 76
HDG C19 H30 SING N N 77
HDG C19 H31 SING N N 78
HDG C25 H32 SING N N 79
HDG C24 H33 SING N N 80
HDG C23 H34 SING N N 81
HDG C22 H35 SING N N 82
HDG C21 H36 SING N N 83
HDG O1 H37 SING N N 84
HDG C26 H38 SING N N 85
HDG C H39 SING N N 86
HDG O H40 SING N N 87
HDG C31 H41 SING N N 88
HDG N6 H42 SING N N 89
HDG N6 H43 SING N N 90
HDG C28 H44 SING N N 91
# #
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
HDG SMILES ACDLabs 12.01 "C(CNCc1ccccc1)(CC2C(O)C(C(O2)n3cnc4c3ncnc4N)O)CCC(C(=O)NCCc5ccc(OC)cc5)N"
HDG InChI InChI 1.03 "InChI=1S/C32H42N8O5/c1-44-23-10-7-20(8-11-23)13-14-36-31(43)24(33)12-9-22(17-35-16-21-5-3-2-4-6-21)15-25-27(41)28(42)32(45-25)40-19-39-26-29(34)37-18-38-30(26)40/h2-8,10-11,18-19,22,24-25,27-28,32,35,41-42H,9,12-17,33H2,1H3,(H,36,43)(H2,34,37,38)/t22-,24+,25+,27+,28+,32+/m0/s1"
HDG InChIKey InChI 1.03 ZLHYSNFCYFOANJ-DVTMEHRLSA-N
HDG SMILES_CANONICAL CACTVS 3.385 "COc1ccc(CCNC(=O)[C@H](N)CC[C@H](CNCc2ccccc2)C[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)cc1"
HDG SMILES CACTVS 3.385 "COc1ccc(CCNC(=O)[CH](N)CC[CH](CNCc2ccccc2)C[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)cc1"
HDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "COc1ccc(cc1)CCNC(=O)[C@@H](CC[C@@H](C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)CNCc5ccccc5)N"
HDG SMILES "OpenEye OEToolkits" 2.0.6 "COc1ccc(cc1)CCNC(=O)C(CCC(CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)CNCc5ccccc5)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
HDG "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-methoxyphenyl)ethyl]hexanamide (non-preferred name)"
HDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R},5~{S})-5-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-2-azanyl-~{N}-[2-(4-methoxyphenyl)ethyl]-6-[(phenylmethyl)amino]hexanamide"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HDG "Create component" 2018-06-26 RCSB
HDG "Initial release" 2018-07-25 RCSB
HDG "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HDG
_pdbx_chem_comp_synonyms.name "(R)-SKI-72"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##