data_V6D
#
_chem_comp.id V6D
_chem_comp.name "(3S,6Z,8E,11S,15R)-15-amino-3-[(1E,3E,5E)-7-(dimethylamino)-2,5-dimethylhepta-1,3,5-trien-1-yl]-9,11-dimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C30 H43 N3 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "des-methyl Pateamine A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-07-07
_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 541.745
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code V6D
_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 6XKI
_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
V6D C10 C1 C 0 1 N N N -22.231 -49.983 -33.564 -3.939 3.697 -0.900 C10 V6D 1
V6D C13 C2 C 0 1 N N N -22.125 -46.671 -31.919 -2.116 1.890 -3.489 C13 V6D 2
V6D C17 C3 C 0 1 N N S -23.449 -43.426 -33.035 0.037 -0.856 -2.308 C17 V6D 3
V6D C21 C4 C 0 1 Y N N -26.825 -45.733 -30.913 -1.000 -3.816 0.503 C21 V6D 4
V6D C22 C5 C 0 1 Y N N -25.990 -46.071 -29.905 -0.235 -4.880 0.241 C22 V6D 5
V6D C24 C6 C 0 1 N N N -22.691 -42.193 -33.530 1.531 -0.654 -2.323 C24 V6D 6
V6D C26 C7 C 0 1 N N N -23.613 -42.476 -35.818 1.437 -0.410 0.124 C26 V6D 7
V6D C28 C8 C 0 1 N N N -21.894 -39.989 -36.334 4.274 0.140 -0.062 C28 V6D 8
V6D C01 C9 C 0 1 N N N -28.177 -46.366 -31.247 -1.752 -3.649 1.797 C01 V6D 9
V6D C02 C10 C 0 1 N N N -28.107 -47.239 -32.497 -1.788 -2.167 2.176 C02 V6D 10
V6D C03 C11 C 0 1 N N R -27.260 -48.494 -32.296 -3.222 -1.764 2.529 C03 V6D 11
V6D C04 C12 C 0 1 N N N -26.270 -48.607 -33.451 -3.224 -0.347 3.108 C04 V6D 12
V6D C05 C13 C 0 1 N N N -25.564 -49.956 -33.488 -4.159 0.518 2.293 C05 V6D 13
V6D O06 O1 O 0 1 N N N -25.442 -50.580 -32.489 -5.247 0.097 1.982 O06 V6D 14
V6D O07 O2 O 0 1 N N N -25.081 -50.438 -34.710 -3.778 1.750 1.925 O07 V6D 15
V6D C08 C14 C 0 1 N N S -24.022 -51.352 -34.656 -4.721 2.530 1.144 C08 V6D 16
V6D C09 C15 C 0 1 N N N -22.694 -50.628 -34.868 -4.026 3.782 0.603 C09 V6D 17
V6D C11 C16 C 0 1 N N N -22.312 -48.664 -33.435 -3.046 2.884 -1.467 C11 V6D 18
V6D C12 C17 C 0 1 N N N -21.863 -47.948 -32.155 -2.955 2.790 -2.924 C12 V6D 19
V6D C14 C18 C 0 1 N N N -22.899 -45.784 -32.894 -1.357 1.023 -2.663 C14 V6D 20
V6D O15 O3 O 0 1 N N N -23.812 -46.197 -33.526 -1.410 1.142 -1.454 O15 V6D 21
V6D O16 O4 O 0 1 N N N -22.489 -44.445 -33.004 -0.577 0.068 -3.210 O16 V6D 22
V6D C18 C19 C 0 1 N N N -24.009 -43.122 -31.646 -0.289 -2.285 -2.744 C18 V6D 23
V6D C19 C20 C 0 1 Y N N -24.898 -44.233 -31.095 -0.361 -3.177 -1.532 C19 V6D 24
V6D N20 N1 N 0 1 Y N N -26.176 -44.652 -31.609 -1.043 -2.924 -0.466 N20 V6D 25
V6D S23 S1 S 0 1 Y N N -24.578 -45.219 -29.767 0.451 -4.673 -1.369 S23 V6D 26
V6D C25 C21 C 0 1 N N N -22.746 -41.759 -34.780 2.180 -0.402 -1.186 C25 V6D 27
V6D C27 C22 C 0 1 N N N -21.910 -40.511 -35.120 3.617 -0.116 -1.212 C27 V6D 28
V6D C29 C23 C 0 1 N N N -21.064 -38.743 -36.689 5.711 0.425 -0.088 C29 V6D 29
V6D C30 C24 C 0 1 N N N -21.141 -38.318 -37.941 6.360 0.678 1.048 C30 V6D 30
V6D C31 C25 C 0 1 N N N -20.366 -37.094 -38.446 7.807 1.097 1.012 C31 V6D 31
V6D N32 N2 N 0 1 N N N -21.024 -36.494 -39.607 7.970 2.362 1.740 N32 V6D 32
V6D C33 C26 C 0 1 N N N -20.272 -35.323 -40.013 7.693 2.184 3.172 C33 V6D 33
V6D C34 C27 C 0 1 N N N -21.114 -37.411 -40.738 9.311 2.923 1.528 C34 V6D 34
V6D C35 C28 C 0 1 N N N -20.192 -38.012 -35.663 6.454 0.433 -1.399 C35 V6D 35
V6D C36 C29 C 0 1 N N N -21.688 -50.898 -32.459 -4.862 4.524 -1.756 C36 V6D 36
V6D C37 C30 C 0 1 N N N -24.212 -52.382 -35.769 -5.898 2.944 2.031 C37 V6D 37
V6D N38 N3 N 0 1 N N N -28.121 -49.663 -32.273 -3.764 -2.700 3.523 N38 V6D 38
V6D H131 H1 H 0 0 N N N -21.775 -46.236 -30.994 -2.038 1.822 -4.563 H131 V6D 39
V6D H171 H2 H 0 0 N N N -24.272 -43.661 -33.726 -0.343 -0.687 -1.300 H171 V6D 40
V6D H221 H3 H 0 0 N N N -26.235 -46.866 -29.216 -0.066 -5.718 0.900 H221 V6D 41
V6D H241 H4 H 0 0 N N N -22.080 -41.649 -32.825 2.075 -0.715 -3.254 H241 V6D 42
V6D H263 H5 H 0 0 N N N -24.114 -43.335 -35.348 1.382 -1.430 0.504 H263 V6D 43
V6D H261 H6 H 0 0 N N N -24.369 -41.779 -36.208 1.962 0.218 0.844 H261 V6D 44
V6D H262 H7 H 0 0 N N N -22.979 -42.829 -36.644 0.429 -0.024 -0.027 H262 V6D 45
V6D H281 H8 H 0 0 N N N -22.487 -40.455 -37.107 3.742 0.133 0.877 H281 V6D 46
V6D H011 H9 H 0 0 N N N -28.912 -45.565 -31.414 -2.770 -4.019 1.676 H011 V6D 47
V6D H012 H10 H 0 0 N N N -28.498 -46.987 -30.398 -1.252 -4.214 2.584 H012 V6D 48
V6D H022 H11 H 0 0 N N N -27.670 -46.647 -33.315 -1.141 -1.996 3.036 H022 V6D 49
V6D H021 H12 H 0 0 N N N -29.128 -47.544 -32.770 -1.439 -1.569 1.335 H021 V6D 50
V6D H031 H13 H 0 0 N N N -26.706 -48.410 -31.350 -3.838 -1.790 1.630 H031 V6D 51
V6D H041 H14 H 0 0 N N N -25.513 -47.816 -33.345 -3.565 -0.378 4.143 H041 V6D 52
V6D H042 H15 H 0 0 N N N -26.815 -48.468 -34.397 -2.214 0.062 3.070 H042 V6D 53
V6D H081 H16 H 0 0 N N N -23.999 -51.870 -33.686 -5.088 1.930 0.312 H081 V6D 54
V6D H092 H17 H 0 0 N N N -21.936 -51.350 -35.205 -3.022 3.850 1.022 H092 V6D 55
V6D H091 H18 H 0 0 N N N -22.823 -49.848 -35.633 -4.598 4.666 0.885 H091 V6D 56
V6D H111 H19 H 0 0 N N N -22.705 -48.079 -34.254 -2.378 2.303 -0.848 H111 V6D 57
V6D H121 H20 H 0 0 N N N -21.310 -48.508 -31.415 -3.553 3.436 -3.547 H121 V6D 58
V6D H182 H21 H 0 0 N N N -23.166 -42.975 -30.955 -1.249 -2.297 -3.261 H182 V6D 59
V6D H181 H22 H 0 0 N N N -24.602 -42.197 -31.704 0.489 -2.647 -3.415 H181 V6D 60
V6D H271 H23 H 0 0 N N N -21.319 -40.049 -34.343 4.149 -0.110 -2.152 H271 V6D 61
V6D H301 H24 H 0 0 N N N -21.774 -38.854 -38.633 5.850 0.582 1.995 H301 V6D 62
V6D H311 H25 H 0 0 N N N -19.350 -37.405 -38.730 8.421 0.326 1.480 H311 V6D 63
V6D H312 H26 H 0 0 N N N -20.309 -36.348 -37.640 8.121 1.231 -0.024 H312 V6D 64
V6D H332 H28 H 0 0 N N N -20.197 -34.623 -39.168 8.385 1.450 3.587 H332 V6D 65
V6D H333 H29 H 0 0 N N N -19.263 -35.627 -40.328 7.821 3.135 3.688 H333 V6D 66
V6D H331 H30 H 0 0 N N N -20.785 -34.831 -40.852 6.670 1.833 3.304 H331 V6D 67
V6D H341 H31 H 0 0 N N N -21.683 -38.305 -40.442 9.462 3.110 0.465 H341 V6D 68
V6D H343 H32 H 0 0 N N N -21.625 -36.912 -41.575 9.403 3.859 2.079 H343 V6D 69
V6D H342 H33 H 0 0 N N N -20.102 -37.708 -41.051 10.061 2.217 1.884 H342 V6D 70
V6D H351 H34 H 0 0 N N N -20.266 -38.520 -34.690 6.509 1.453 -1.779 H351 V6D 71
V6D H352 H35 H 0 0 N N N -19.145 -38.018 -36.001 7.462 0.047 -1.247 H352 V6D 72
V6D H353 H36 H 0 0 N N N -20.539 -36.973 -35.561 5.929 -0.195 -2.118 H353 V6D 73
V6D H362 H37 H 0 0 N N N -21.397 -50.291 -31.589 -5.403 3.871 -2.441 H362 V6D 74
V6D H361 H38 H 0 0 N N N -22.467 -51.615 -32.161 -5.572 5.052 -1.120 H361 V6D 75
V6D H363 H39 H 0 0 N N N -20.810 -51.445 -32.834 -4.278 5.246 -2.327 H363 V6D 76
V6D H373 H40 H 0 0 N N N -25.167 -52.908 -35.623 -5.531 3.544 2.864 H373 V6D 77
V6D H371 H41 H 0 0 N N N -24.220 -51.872 -36.743 -6.606 3.530 1.445 H371 V6D 78
V6D H372 H42 H 0 0 N N N -23.386 -53.108 -35.742 -6.394 2.053 2.415 H372 V6D 79
V6D H2 H43 H 0 1 N N N -28.769 -49.586 -31.515 -4.710 -2.455 3.772 H2 V6D 80
V6D H382 H44 H 0 0 N N N -28.623 -49.724 -33.136 -3.713 -3.651 3.189 H382 V6D 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
V6D C34 N32 SING N N 1
V6D C33 N32 SING N N 2
V6D N32 C31 SING N N 3
V6D C31 C30 SING N N 4
V6D C30 C29 DOUB N E 5
V6D C29 C28 SING N N 6
V6D C29 C35 SING N N 7
V6D C28 C27 DOUB N E 8
V6D C26 C25 SING N N 9
V6D C37 C08 SING N N 10
V6D C27 C25 SING N N 11
V6D C09 C08 SING N N 12
V6D C09 C10 SING N N 13
V6D C25 C24 DOUB N E 14
V6D O07 C08 SING N N 15
V6D O07 C05 SING N N 16
V6D C10 C11 DOUB N E 17
V6D C10 C36 SING N N 18
V6D C24 C17 SING N N 19
V6D O15 C14 DOUB N N 20
V6D C05 C04 SING N N 21
V6D C05 O06 DOUB N N 22
V6D C04 C03 SING N N 23
V6D C11 C12 SING N N 24
V6D C17 O16 SING N N 25
V6D C17 C18 SING N N 26
V6D O16 C14 SING N N 27
V6D C14 C13 SING N N 28
V6D C02 C03 SING N N 29
V6D C02 C01 SING N N 30
V6D C03 N38 SING N N 31
V6D C12 C13 DOUB N Z 32
V6D C18 C19 SING N N 33
V6D N20 C19 DOUB Y N 34
V6D N20 C21 SING Y N 35
V6D C01 C21 SING N N 36
V6D C19 S23 SING Y N 37
V6D C21 C22 DOUB Y N 38
V6D C22 S23 SING Y N 39
V6D C13 H131 SING N N 40
V6D C17 H171 SING N N 41
V6D C22 H221 SING N N 42
V6D C24 H241 SING N N 43
V6D C26 H263 SING N N 44
V6D C26 H261 SING N N 45
V6D C26 H262 SING N N 46
V6D C28 H281 SING N N 47
V6D C01 H011 SING N N 48
V6D C01 H012 SING N N 49
V6D C02 H022 SING N N 50
V6D C02 H021 SING N N 51
V6D C03 H031 SING N N 52
V6D C04 H041 SING N N 53
V6D C04 H042 SING N N 54
V6D C08 H081 SING N N 55
V6D C09 H092 SING N N 56
V6D C09 H091 SING N N 57
V6D C11 H111 SING N N 58
V6D C12 H121 SING N N 59
V6D C18 H182 SING N N 60
V6D C18 H181 SING N N 61
V6D C27 H271 SING N N 62
V6D C30 H301 SING N N 63
V6D C31 H311 SING N N 64
V6D C31 H312 SING N N 65
V6D C33 H332 SING N N 66
V6D C33 H333 SING N N 67
V6D C33 H331 SING N N 68
V6D C34 H341 SING N N 69
V6D C34 H343 SING N N 70
V6D C34 H342 SING N N 71
V6D C35 H351 SING N N 72
V6D C35 H352 SING N N 73
V6D C35 H353 SING N N 74
V6D C36 H362 SING N N 75
V6D C36 H361 SING N N 76
V6D C36 H363 SING N N 77
V6D C37 H373 SING N N 78
V6D C37 H371 SING N N 79
V6D C37 H372 SING N N 80
V6D N38 H2 SING N N 81
V6D N38 H382 SING N N 82
# #
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
V6D SMILES ACDLabs 12.01 "C1(=CC=CC(=O)OC(Cc2scc(CCC(N)CC(=O)OC(C1)C)n2)[C@H]=C(C)C=[C@H]C(C)=[C@H]CN(C)C)C"
V6D InChI InChI 1.03 "InChI=1S/C30H43N3O4S/c1-21(14-15-33(5)6)10-11-23(3)17-27-19-28-32-26(20-38-28)13-12-25(31)18-30(35)36-24(4)16-22(2)8-7-9-29(34)37-27/h7-11,14,17,20,24-25,27H,12-13,15-16,18-19,31H2,1-6H3/b9-7-,11-10+,21-14+,22-8+,23-17+/t24-,25+,27+/m0/s1"
V6D InChIKey InChI 1.03 OKCOLQKYUABEJR-GFYARHHKSA-N
V6D SMILES_CANONICAL CACTVS 3.385 "C[C@H]1C\C(=C\C=C/C(=O)O[C@@H](Cc2scc(CC[C@@H](N)CC(=O)O1)n2)/C=C(C)/C=C/C(C)=C/CN(C)C)C"
V6D SMILES CACTVS 3.385 "C[CH]1CC(=CC=CC(=O)O[CH](Cc2scc(CC[CH](N)CC(=O)O1)n2)C=C(C)C=CC(C)=CCN(C)C)C"
V6D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1C/C(=C/C=C\C(=O)O[C@@H](Cc2nc(cs2)CC[C@H](CC(=O)O1)N)/C=C(\C)/C=C/C(=C/CN(C)C)/C)/C"
V6D SMILES "OpenEye OEToolkits" 2.0.7 "CC1CC(=CC=CC(=O)OC(Cc2nc(cs2)CCC(CC(=O)O1)N)C=C(C)C=CC(=CCN(C)C)C)C"
# #
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
V6D "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,6Z,8E,11S,15R)-15-amino-3-[(1E,3E,5E)-7-(dimethylamino)-2,5-dimethylhepta-1,3,5-trien-1-yl]-9,11-dimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione"
V6D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S},6~{Z},8~{E},11~{S},15~{R})-15-azanyl-3-[(1~{E},3~{E},5~{E})-7-(dimethylamino)-2,5-dimethyl-hepta-1,3,5-trienyl]-9,11-dimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
V6D "Create component" 2020-07-07 RCSB
V6D "Modify synonyms" 2020-07-07 RCSB
V6D "Initial release" 2021-01-06 RCSB
V6D "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id V6D
_pdbx_chem_comp_synonyms.name "des-methyl Pateamine A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##