data_YTA
#
_chem_comp.id YTA
_chem_comp.name "yatakemycin-adenine nucleobase adduct"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C40 H34 N10 O8 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-02-20
_chem_comp.pdbx_modified_date 2017-07-14
_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 814.825
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YTA
_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 5UUF
_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
YTA N1 N1 N 0 1 Y N N 40.492 -2.558 18.634 -5.551 3.353 1.258 N1 YTA 1
YTA C2 C1 C 0 1 Y N N 40.283 -1.257 18.507 -4.706 2.360 1.365 C2 YTA 2
YTA N3 N2 N 0 1 Y N N 40.556 -0.522 17.398 -3.488 2.388 0.799 N3 YTA 3
YTA C3M C2 C 0 1 N N N 40.259 0.927 17.325 -2.581 1.247 0.950 C3M YTA 4
YTA C4 C3 C 0 1 Y N N 41.124 -1.201 16.363 -3.095 3.491 0.077 C4 YTA 5
YTA C5 C4 C 0 1 Y N N 41.348 -2.602 16.453 -3.998 4.570 -0.045 C5 YTA 6
YTA C6 C5 C 0 1 Y N N 41.038 -3.283 17.624 -5.254 4.463 0.576 C6 YTA 7
YTA N6 N3 N 0 1 N N N 41.211 -4.594 17.820 -6.165 5.486 0.484 N6 YTA 8
YTA N7 N4 N 0 1 Y N N 41.899 -2.998 15.275 -3.377 5.503 -0.786 N7 YTA 9
YTA C8 C6 C 0 1 Y N N 41.951 -1.867 14.555 -2.183 5.048 -1.102 C8 YTA 10
YTA N9 N5 N 0 1 Y N N 41.492 -0.722 15.171 -2.003 3.837 -0.588 N9 YTA 11
YTA C01 C7 C 0 1 Y N N 36.634 -0.850 10.692 -9.937 -2.807 -0.097 C01 YTA 12
YTA N01 N6 N 0 1 Y N N 37.487 2.464 11.670 -6.816 -1.074 -0.067 N01 YTA 13
YTA O01 O1 O 0 1 N N N 36.310 0.484 7.298 -11.444 0.491 -0.438 O01 YTA 14
YTA C02 C8 C 0 1 Y N N 36.913 1.662 9.374 -9.163 -0.128 -0.272 C02 YTA 15
YTA O02 O2 O 0 1 N N N 36.076 -1.792 8.566 -12.204 -2.147 -0.276 O02 YTA 16
YTA C03 C9 C 0 1 Y N N 36.422 -0.721 9.336 -10.885 -1.818 -0.227 C03 YTA 17
YTA C04 C10 C 0 1 Y N N 37.006 0.298 11.416 -8.577 -2.466 -0.046 C04 YTA 18
YTA C05 C11 C 0 1 Y N N 37.140 1.534 10.748 -8.191 -1.114 -0.134 C05 YTA 19
YTA C06 C12 C 0 1 Y N N 36.561 0.536 8.687 -10.499 -0.476 -0.310 C06 YTA 20
YTA C07 C13 C 0 1 Y N N 37.569 1.868 12.943 -6.341 -2.364 0.077 C07 YTA 21
YTA C08 C14 C 0 1 Y N N 37.278 0.519 12.801 -7.392 -3.227 0.086 C08 YTA 22
YTA C09 C15 C 0 1 N N N 37.891 2.852 13.995 -4.927 -2.743 0.199 C09 YTA 23
YTA C33 C16 C 0 1 N N N 36.453 1.768 6.617 -10.984 1.842 -0.517 C33 YTA 24
YTA O03 O3 O 0 1 N N N 37.808 4.075 13.710 -4.624 -3.901 0.418 O03 YTA 25
YTA N02 N7 N 0 1 N N N 38.153 2.464 15.290 -3.966 -1.807 0.069 N02 YTA 26
YTA C10 C17 C 0 1 N N N 38.140 1.045 15.741 -4.207 -0.371 -0.092 C10 YTA 27
YTA C11 C18 C 0 1 Y N N 38.184 3.330 16.411 -2.589 -2.065 0.073 C11 YTA 28
YTA C12 C19 C 0 1 Y N N 37.999 4.737 16.483 -1.922 -3.292 0.206 C12 YTA 29
YTA C13 C20 C 0 1 Y N N 38.473 2.588 17.546 -1.855 -0.909 -0.079 C13 YTA 30
YTA C14 C21 C 0 1 N N R 38.704 1.134 17.194 -2.809 0.259 -0.196 C14 YTA 31
YTA C15 C22 C 0 1 Y N N 38.047 5.380 17.697 -0.547 -3.357 0.188 C15 YTA 32
YTA C16 C23 C 0 1 Y N N 38.344 4.632 18.859 0.207 -2.192 0.034 C16 YTA 33
YTA C17 C24 C 0 1 Y N N 38.540 3.223 18.783 -0.453 -0.957 -0.101 C17 YTA 34
YTA C18 C25 C 0 1 Y N N 38.746 3.889 20.942 1.756 -0.586 -0.187 C18 YTA 35
YTA C19 C26 C 0 1 Y N N 38.799 2.772 20.127 0.548 0.034 -0.238 C19 YTA 36
YTA C20 C27 C 0 1 N N N 38.873 4.128 22.385 3.062 0.080 -0.292 C20 YTA 37
YTA N03 N8 N 0 1 Y N N 38.475 5.012 20.186 1.561 -1.943 -0.020 N03 YTA 38
YTA O O4 O 0 1 N N N 37.875 6.740 17.852 0.079 -4.557 0.319 O YTA 39
YTA O04 O5 O 0 1 N N N 38.453 5.199 22.821 3.120 1.287 -0.436 O04 YTA 40
YTA N04 N9 N 0 1 N N N 39.391 3.123 23.160 4.196 -0.645 -0.227 N04 YTA 41
YTA O05 O6 O 0 1 N N N 40.868 0.998 30.879 11.766 -2.260 0.089 O05 YTA 42
YTA C21 C28 C 0 1 N N N 40.129 1.895 22.706 4.256 -2.109 -0.175 C21 YTA 43
YTA C22 C29 C 0 1 N N N 41.096 1.656 23.888 5.755 -2.444 -0.111 C22 YTA 44
YTA C23 C30 C 0 1 Y N N 39.262 3.020 24.601 5.492 -0.112 -0.207 C23 YTA 45
YTA C24 C31 C 0 1 Y N N 40.259 2.162 25.053 6.447 -1.100 -0.134 C24 YTA 46
YTA C25 C32 C 0 1 Y N N 40.354 1.857 26.418 7.811 -0.767 -0.098 C25 YTA 47
YTA C26 C33 C 0 1 Y N N 38.326 3.615 25.465 5.895 1.237 -0.246 C26 YTA 48
YTA C27 C34 C 0 1 Y N N 38.398 3.319 26.829 7.233 1.578 -0.217 C27 YTA 49
YTA C28 C35 C 0 1 Y N N 39.398 2.469 27.285 8.206 0.583 -0.131 C28 YTA 50
YTA C29 C36 C 0 1 Y N N 41.204 1.033 27.220 8.993 -1.543 -0.030 C29 YTA 51
YTA C30 C37 C 0 1 Y N N 40.762 1.178 28.524 10.050 -0.688 -0.023 C30 YTA 52
YTA C31 C38 C 0 1 N N N 41.191 0.582 29.771 11.465 -1.082 0.039 C31 YTA 53
YTA C32 C39 C 0 1 N N N 41.324 -2.149 30.643 14.194 -0.902 0.126 C32 YTA 54
YTA N N10 N 0 1 Y N N 39.669 2.041 28.561 9.583 0.611 -0.084 N YTA 55
YTA O47 O7 O 0 1 N N N 37.345 4.456 25.042 4.953 2.216 -0.315 O47 YTA 56
YTA O48 O8 O 0 1 N N N 37.452 3.919 27.709 7.601 2.887 -0.257 O48 YTA 57
YTA C49 C40 C 0 1 N N N 38.015 5.122 28.361 7.736 3.562 0.995 C49 YTA 58
YTA S S1 S 0 1 N N N 42.178 -0.954 29.466 12.724 0.150 0.040 S YTA 59
YTA H21 H1 H 0 1 N N N 39.861 -0.738 19.355 -4.998 1.486 1.928 H21 YTA 60
YTA H3M2 H2 H 0 0 N N N 40.763 1.362 16.449 -1.549 1.598 0.928 H3M2 YTA 61
YTA H3M1 H3 H 0 0 N N N 40.620 1.422 18.238 -2.776 0.751 1.901 H3M1 YTA 62
YTA H63 H4 H 0 1 N N N 40.890 -4.840 18.735 -5.943 6.289 -0.013 H63 YTA 63
YTA H62 H5 H 0 1 N N N 40.691 -5.105 17.136 -7.030 5.406 0.915 H62 YTA 64
YTA H82 H6 H 0 1 N N N 42.333 -1.854 13.545 -1.456 5.582 -1.695 H82 YTA 65
YTA H012 H7 H 0 0 N N N 36.518 -1.804 11.184 -10.239 -3.842 -0.029 H012 YTA 66
YTA H013 H8 H 0 0 N N N 37.659 3.430 11.475 -6.272 -0.272 -0.103 H013 YTA 67
YTA H021 H9 H 0 0 N N N 37.012 2.615 8.876 -8.873 0.910 -0.340 H021 YTA 68
YTA H023 H10 H 0 0 N N N 36.015 -2.568 9.111 -12.635 -2.173 0.589 H023 YTA 69
YTA H081 H11 H 0 0 N N N 37.260 -0.222 13.587 -7.332 -4.301 0.178 H081 YTA 70
YTA H331 H12 H 0 0 N N N 36.242 1.641 5.545 -10.332 1.954 -1.383 H331 YTA 71
YTA H333 H13 H 0 0 N N N 35.745 2.492 7.047 -11.839 2.512 -0.617 H333 YTA 72
YTA H332 H14 H 0 0 N N N 37.480 2.139 6.746 -10.432 2.091 0.389 H332 YTA 73
YTA H101 H15 H 0 0 N N N 37.118 0.638 15.738 -4.776 -0.182 -1.002 H101 YTA 74
YTA H102 H16 H 0 0 N N N 38.785 0.422 15.104 -4.736 0.023 0.776 H102 YTA 75
YTA H121 H17 H 0 0 N N N 37.820 5.303 15.581 -2.496 -4.199 0.325 H121 YTA 76
YTA H141 H18 H 0 0 N N N 38.160 0.459 17.871 -2.688 0.759 -1.157 H141 YTA 77
YTA H191 H19 H 0 0 N N N 38.997 1.757 20.438 0.382 1.094 -0.361 H191 YTA 78
YTA H033 H20 H 0 0 N N N 38.388 5.944 20.537 2.261 -2.611 0.047 H033 YTA 79
YTA HO1 H21 H 0 1 N N N 37.948 6.966 18.772 0.243 -5.009 -0.520 HO1 YTA 80
YTA H211 H22 H 0 0 N N N 39.445 1.044 22.569 3.748 -2.477 0.716 H211 YTA 81
YTA H212 H23 H 0 0 N N N 40.677 2.080 21.770 3.809 -2.538 -1.071 H212 YTA 82
YTA H221 H24 H 0 0 N N N 41.342 0.590 24.000 5.987 -2.976 0.812 H221 YTA 83
YTA H222 H25 H 0 0 N N N 42.024 2.236 23.775 6.049 -3.038 -0.977 H222 YTA 84
YTA H292 H26 H 0 0 N N N 42.025 0.421 26.878 9.046 -2.621 0.009 H292 YTA 85
YTA H321 H27 H 0 0 N N N 41.807 -3.135 30.579 14.159 -1.501 1.037 H321 YTA 86
YTA H323 H28 H 0 0 N N N 41.402 -1.769 31.672 14.220 -1.561 -0.741 H323 YTA 87
YTA H322 H29 H 0 0 N N N 40.263 -2.241 30.366 15.087 -0.278 0.136 H322 YTA 88
YTA HN1 H30 H 0 1 N N N 39.164 2.306 29.383 10.132 1.411 -0.093 HN1 YTA 89
YTA H471 H31 H 0 0 N N N 37.591 4.836 24.207 4.653 2.533 0.548 H471 YTA 90
YTA H492 H32 H 0 0 N N N 37.263 5.562 29.033 8.033 4.596 0.821 H492 YTA 91
YTA H493 H33 H 0 0 N N N 38.906 4.841 28.942 6.783 3.542 1.524 H493 YTA 92
YTA H491 H34 H 0 0 N N N 38.295 5.858 27.593 8.495 3.062 1.597 H491 YTA 93
#
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
YTA C33 O01 SING N N 1
YTA O01 C06 SING N N 2
YTA O02 C03 SING N N 3
YTA C06 C03 DOUB Y N 4
YTA C06 C02 SING Y N 5
YTA C03 C01 SING Y N 6
YTA C02 C05 DOUB Y N 7
YTA C01 C04 DOUB Y N 8
YTA C05 C04 SING Y N 9
YTA C05 N01 SING Y N 10
YTA C04 C08 SING Y N 11
YTA N01 C07 SING Y N 12
YTA C08 C07 DOUB Y N 13
YTA C07 C09 SING N N 14
YTA O03 C09 DOUB N N 15
YTA C09 N02 SING N N 16
YTA C8 N9 SING Y N 17
YTA C8 N7 DOUB Y N 18
YTA N9 C4 DOUB Y N 19
YTA N7 C5 SING Y N 20
YTA N02 C10 SING N N 21
YTA N02 C11 SING N N 22
YTA C10 C14 SING N N 23
YTA C4 C5 SING Y N 24
YTA C4 N3 SING Y N 25
YTA C11 C12 DOUB Y N 26
YTA C11 C13 SING Y N 27
YTA C5 C6 DOUB Y N 28
YTA C12 C15 SING Y N 29
YTA C14 C3M SING N N 30
YTA C14 C13 SING N N 31
YTA C3M N3 SING N N 32
YTA N3 C2 SING Y N 33
YTA C13 C17 DOUB Y N 34
YTA C6 N6 SING N N 35
YTA C6 N1 SING Y N 36
YTA C15 O SING N N 37
YTA C15 C16 DOUB Y N 38
YTA C2 N1 DOUB Y N 39
YTA C17 C16 SING Y N 40
YTA C17 C19 SING Y N 41
YTA C16 N03 SING Y N 42
YTA C19 C18 DOUB Y N 43
YTA N03 C18 SING Y N 44
YTA C18 C20 SING N N 45
YTA C20 O04 DOUB N N 46
YTA C20 N04 SING N N 47
YTA C21 N04 SING N N 48
YTA C21 C22 SING N N 49
YTA N04 C23 SING N N 50
YTA C22 C24 SING N N 51
YTA C23 C24 DOUB Y N 52
YTA C23 C26 SING Y N 53
YTA O47 C26 SING N N 54
YTA C24 C25 SING Y N 55
YTA C26 C27 DOUB Y N 56
YTA C25 C29 SING Y N 57
YTA C25 C28 DOUB Y N 58
YTA C27 C28 SING Y N 59
YTA C27 O48 SING N N 60
YTA C29 C30 DOUB Y N 61
YTA C28 N SING Y N 62
YTA O48 C49 SING N N 63
YTA C30 N SING Y N 64
YTA C30 C31 SING N N 65
YTA S C31 SING N N 66
YTA S C32 SING N N 67
YTA C31 O05 DOUB N N 68
YTA C2 H21 SING N N 69
YTA C3M H3M2 SING N N 70
YTA C3M H3M1 SING N N 71
YTA N6 H63 SING N N 72
YTA N6 H62 SING N N 73
YTA C8 H82 SING N N 74
YTA C01 H012 SING N N 75
YTA N01 H013 SING N N 76
YTA C02 H021 SING N N 77
YTA O02 H023 SING N N 78
YTA C08 H081 SING N N 79
YTA C33 H331 SING N N 80
YTA C33 H333 SING N N 81
YTA C33 H332 SING N N 82
YTA C10 H101 SING N N 83
YTA C10 H102 SING N N 84
YTA C12 H121 SING N N 85
YTA C14 H141 SING N N 86
YTA C19 H191 SING N N 87
YTA N03 H033 SING N N 88
YTA O HO1 SING N N 89
YTA C21 H211 SING N N 90
YTA C21 H212 SING N N 91
YTA C22 H221 SING N N 92
YTA C22 H222 SING N N 93
YTA C29 H292 SING N N 94
YTA C32 H321 SING N N 95
YTA C32 H323 SING N N 96
YTA C32 H322 SING N N 97
YTA N HN1 SING N N 98
YTA O47 H471 SING N N 99
YTA C49 H492 SING N N 100
YTA C49 H493 SING N N 101
YTA C49 H491 SING N N 102
#
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
YTA SMILES ACDLabs 12.01 "N9=CN(CC7CN(C(c1nc2cc(OC)c(cc2c1)O)=O)c6cc(O)c8nc(C(=O)N3c5c(CC3)c4cc(nc4c(c5O)OC)C(=O)SC)cc8c67)C=%10C(=C9N)N=CN=%10"
YTA InChI InChI 1.03
;InChI=1S/C40H34N10O8S/c1-57-28-10-21-16(7-26(28)51)6-22(45-21)39(55)50-13-17(12-48-15-44-36(41)32-37(48)43-14-42-32)29-20-9-23(46-30(20)27(52)11-25(29)50)38(54)49-5-4-18-19-8-24(40(56)59-3)47-31(19)35(58-2)34(53)33(18)49/h6-11,14-15,17,45-47,51-53H,4-5,12-13,41H2,1-3H3/t17-/m1/s1
;
YTA InChIKey InChI 1.03 FJMCEQLVMJYVHU-QGZVFWFLSA-N
YTA SMILES_CANONICAL CACTVS 3.385 "COc1cc2[nH]c(cc2cc1O)C(=O)N3C[C@@H](Cn4cnc(N)c5ncnc45)c6c3cc(O)c7[nH]c(cc67)C(=O)N8CCc9c%10cc([nH]c%10c(OC)c(O)c89)C(=O)SC"
YTA SMILES CACTVS 3.385 "COc1cc2[nH]c(cc2cc1O)C(=O)N3C[CH](Cn4cnc(N)c5ncnc45)c6c3cc(O)c7[nH]c(cc67)C(=O)N8CCc9c%10cc([nH]c%10c(OC)c(O)c89)C(=O)SC"
YTA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "COc1cc2c(cc1O)cc([nH]2)C(=O)N3C[C@H](c4c3cc(c5c4cc([nH]5)C(=O)N6CCc7c6c(c(c8c7cc([nH]8)C(=O)SC)OC)O)O)Cn9cnc(c-1ncnc91)N"
YTA SMILES "OpenEye OEToolkits" 2.0.6 "COc1cc2c(cc1O)cc([nH]2)C(=O)N3CC(c4c3cc(c5c4cc([nH]5)C(=O)N6CCc7c6c(c(c8c7cc([nH]8)C(=O)SC)OC)O)O)Cn9cnc(c-1ncnc91)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
YTA "SYSTEMATIC NAME" ACDLabs 12.01
"S-methyl 6-[(8R)-8-[(6-amino-3H-purin-3-yl)methyl]-4-hydroxy-6-(5-hydroxy-6-methoxy-1H-indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carbonyl]-5-hydroxy-4-methoxy-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carbothioate"
YTA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6
"~{S}-methyl 6-[[(8~{R})-8-[(6-azanylpurin-3-yl)methyl]-6-[(6-methoxy-5-oxidanyl-1~{H}-indol-2-yl)carbonyl]-4-oxidanyl-7,8-dihydro-3~{H}-pyrrolo[3,2-e]indol-2-yl]carbonyl]-4-methoxy-5-oxidanyl-7,8-dihydro-3~{H}-pyrrolo[3,2-e]indole-2-carbothioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YTA "Create component" 2017-02-20 RCSB
YTA "Initial release" 2017-07-19 RCSB
#