data_NMY
#
_chem_comp.id NMY
_chem_comp.name NEOMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C23 H46 N6 O13"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-07-25
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 614.644
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NMY
_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 2FCY
_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
NMY C1 C1 C 0 1 N N R 104.276 0.115 -32.524 -3.390 -1.005 1.254 C1 NMY 1
NMY O1 O1 O 0 1 N N N 104.629 1.518 -32.489 -3.227 -0.159 0.113 O1 NMY 2
NMY C2 C2 C 0 1 N N R 103.917 -0.403 -31.104 -2.598 -2.298 1.048 C2 NMY 3
NMY N2 N2 N 0 1 N N N 102.858 0.442 -30.486 -1.183 -1.975 0.816 N2 NMY 4
NMY C3 C3 C 0 1 N N R 105.215 -0.461 -30.188 -3.158 -3.043 -0.167 C3 NMY 5
NMY O3 O3 O 0 1 N N N 104.894 -0.961 -28.869 -2.473 -4.287 -0.323 O3 NMY 6
NMY C4 C4 C 0 1 N N S 106.290 -1.377 -30.859 -4.651 -3.305 0.053 C4 NMY 7
NMY O4 O4 O 0 1 N N N 107.453 -1.449 -30.037 -5.201 -3.936 -1.105 O4 NMY 8
NMY C5 C5 C 0 1 N N R 106.646 -0.818 -32.284 -5.365 -1.973 0.297 C5 NMY 9
NMY O5 O5 O 0 1 N N N 105.379 -0.747 -33.081 -4.774 -1.317 1.421 O5 NMY 10
NMY C6 C6 C 0 1 N N N 107.696 -1.735 -32.995 -6.846 -2.231 0.577 C6 NMY 11
NMY C7 C7 C 0 1 N N R 105.142 4.812 -35.306 -3.486 4.021 -0.496 C7 NMY 12
NMY N7 N7 N 0 1 N N N 105.472 5.559 -36.552 -3.615 5.454 -0.201 N7 NMY 13
NMY C12 C12 C 0 1 N N S 103.964 3.779 -35.506 -2.244 3.466 0.205 C12 NMY 14
NMY C11 C11 C 0 1 N N R 103.654 3.009 -34.206 -2.110 1.973 -0.103 C11 NMY 15
NMY O11 O11 O 0 1 N N N 102.578 2.070 -34.457 -0.950 1.454 0.551 O11 NMY 16
NMY C10 C10 C 0 1 N N R 104.916 2.234 -33.743 -3.352 1.235 0.400 C10 NMY 17
NMY C9 C9 C 0 1 N N S 106.111 3.231 -33.545 -4.594 1.790 -0.300 C9 NMY 18
NMY N9 N9 N 0 1 N N N 107.328 2.508 -33.132 -5.787 1.082 0.183 N9 NMY 19
NMY C8 C8 C 0 1 N N N 106.422 4.029 -34.859 -4.728 3.283 0.007 C8 NMY 20
NMY C13 C13 C 0 1 N N S 101.316 2.275 -33.781 0.241 1.525 -0.235 C13 NMY 21
NMY C14 C14 C 0 1 N N R 100.144 1.838 -34.629 1.460 1.061 0.592 C14 NMY 22
NMY C15 C15 C 0 1 N N S 99.120 1.259 -33.570 2.334 0.293 -0.424 C15 NMY 23
NMY C16 C16 C 0 1 N N R 99.951 0.868 -32.356 1.539 0.384 -1.746 C16 NMY 24
NMY O16 O16 O 0 1 N N N 101.272 1.498 -32.547 0.170 0.597 -1.339 O16 NMY 25
NMY C17 C17 C 0 1 N N N 100.127 -0.630 -32.196 1.664 -0.922 -2.533 C17 NMY 26
NMY C21 C21 C 0 1 N N S 94.411 2.307 -32.243 7.235 -0.711 0.730 C21 NMY 27
NMY C20 C20 C 0 1 N N R 95.337 3.560 -32.475 6.933 0.723 1.175 C20 NMY 28
NMY C19 C19 C 0 1 N N R 96.054 3.478 -33.839 5.846 1.309 0.268 C19 NMY 29
NMY C18 C18 C 0 1 N N R 96.899 2.185 -33.920 4.608 0.411 0.324 C18 NMY 30
NMY O18 O18 O 0 1 N N N 98.070 2.205 -33.124 3.610 0.921 -0.563 O18 NMY 31
NMY C22 C22 C 0 1 N N S 95.219 0.976 -32.310 5.943 -1.531 0.767 C22 NMY 32
NMY O22 O22 O 0 1 N N N 96.003 0.984 -33.593 4.964 -0.915 -0.072 O22 NMY 33
NMY C23 C23 C 0 1 N N N 96.157 0.778 -31.048 6.224 -2.950 0.267 C23 NMY 34
NMY N6 N6 N 0 1 N N N 108.053 -1.233 -34.326 -7.531 -0.952 0.811 N6 NMY 35
NMY O14 O14 O 0 1 N N N 99.695 2.910 -35.467 2.170 2.187 1.113 O14 NMY 36
NMY O20 O20 O 0 1 N N N 94.572 4.728 -32.420 6.475 0.717 2.528 O20 NMY 37
NMY O21 O21 O 0 1 N N N 93.682 2.321 -30.989 7.754 -0.699 -0.601 O21 NMY 38
NMY O17 O17 O 0 1 N N N 99.917 -0.906 -30.822 1.021 -0.778 -3.801 O17 NMY 39
NMY O12 O12 O 0 1 N N N 102.782 4.457 -35.892 -1.084 4.155 -0.266 O12 NMY 40
NMY N19 N19 N 0 1 N N N 96.920 -0.508 -31.135 4.984 -3.736 0.303 N19 NMY 41
NMY N23 N23 N 0 1 N N N 96.915 4.690 -34.105 6.343 1.377 -1.113 N23 NMY 42
NMY H1 H1 H 0 1 N N N 103.404 0.040 -33.190 -3.023 -0.491 2.142 H1 NMY 43
NMY H2 H2 H 0 1 N N N 103.519 -1.425 -31.195 -2.688 -2.925 1.935 H2 NMY 44
NMY HN21 1HN2 H 0 0 N N N 103.096 0.631 -29.533 -0.792 -1.479 1.603 HN21 NMY 45
NMY HN22 2HN2 H 0 0 N N N 102.784 1.303 -30.988 -0.651 -2.809 0.614 HN22 NMY 46
NMY H3 H3 H 0 1 N N N 105.615 0.558 -30.081 -3.022 -2.436 -1.062 H3 NMY 47
NMY HO3 HO3 H 0 1 N N N 104.824 -1.908 -28.897 -2.777 -4.813 -1.075 HO3 NMY 48
NMY H4 H4 H 0 1 N N N 105.885 -2.394 -30.972 -4.784 -3.954 0.919 H4 NMY 49
NMY HO4 HO4 H 0 1 N N N 108.229 -1.465 -30.585 -4.792 -4.785 -1.323 HO4 NMY 50
NMY H5 H5 H 0 1 N N N 107.095 0.182 -32.195 -5.266 -1.341 -0.586 H5 NMY 51
NMY H61 1H6 H 0 1 N N N 108.606 -1.772 -32.378 -7.296 -2.733 -0.280 H61 NMY 52
NMY H62 2H6 H 0 1 N N N 107.250 -2.733 -33.116 -6.945 -2.863 1.460 H62 NMY 53
NMY H7 H7 H 0 1 N N N 104.815 5.541 -34.550 -3.390 3.879 -1.572 H7 NMY 54
NMY H71 1H7 H 0 1 N N N 105.546 6.535 -36.346 -4.428 5.845 -0.652 H71 NMY 55
NMY H72 2H7 H 0 1 N N N 106.342 5.229 -36.918 -3.641 5.618 0.795 H72 NMY 56
NMY H12 H12 H 0 1 N N N 104.287 3.072 -36.284 -2.340 3.608 1.281 H12 NMY 57
NMY H11 H11 H 0 1 N N N 103.356 3.719 -33.420 -2.014 1.831 -1.179 H11 NMY 58
NMY H10 H10 H 0 1 N N N 105.195 1.499 -34.513 -3.448 1.377 1.477 H10 NMY 59
NMY H9 H9 H 0 1 N N N 105.810 3.940 -32.759 -4.498 1.648 -1.377 H9 NMY 60
NMY H91 1H9 H 0 1 N N N 107.906 2.344 -33.931 -6.603 1.344 -0.349 H91 NMY 61
NMY H92 2H9 H 0 1 N N N 107.831 3.056 -32.464 -5.647 0.083 0.162 H92 NMY 62
NMY H81 1H8 H 0 1 N N N 106.720 3.328 -35.653 -4.824 3.425 1.084 H81 NMY 63
NMY H82 2H8 H 0 1 N N N 107.241 4.739 -34.673 -5.613 3.679 -0.492 H82 NMY 64
NMY H13 H13 H 0 1 N N N 101.241 3.353 -33.577 0.394 2.540 -0.600 H13 NMY 65
NMY H14 H14 H 0 1 N N N 100.358 1.060 -35.377 1.144 0.403 1.402 H14 NMY 66
NMY H15 H15 H 0 1 N N N 98.581 0.428 -34.048 2.452 -0.746 -0.118 H15 NMY 67
NMY H16 H16 H 0 1 N N N 99.435 1.205 -31.445 1.893 1.224 -2.344 H16 NMY 68
NMY H171 1H17 H 0 0 N N N 99.399 -1.174 -32.816 2.718 -1.156 -2.685 H171 NMY 69
NMY H172 2H17 H 0 0 N N N 101.127 -0.952 -32.521 1.189 -1.730 -1.975 H172 NMY 70
NMY H21 H21 H 0 1 N N N 93.678 2.366 -33.061 7.968 -1.155 1.404 H21 NMY 71
NMY H20 H20 H 0 1 N N N 96.100 3.574 -31.682 7.838 1.327 1.097 H20 NMY 72
NMY H19 H19 H 0 1 N N N 95.279 3.455 -34.619 5.587 2.311 0.611 H19 NMY 73
NMY H18 H18 H 0 1 N N N 97.277 2.102 -34.950 4.216 0.394 1.341 H18 NMY 74
NMY H22 H22 H 0 1 N N N 94.527 0.121 -32.294 5.569 -1.574 1.790 H22 NMY 75
NMY H231 1H23 H 0 0 N N N 96.871 1.613 -31.001 6.597 -2.907 -0.756 H231 NMY 76
NMY H232 2H23 H 0 0 N N N 95.527 0.750 -30.147 6.971 -3.419 0.907 H232 NMY 77
NMY HN61 1HN6 H 0 0 N N N 108.134 -0.237 -34.296 -7.545 -0.392 -0.028 HN61 NMY 78
NMY HN62 2HN6 H 0 0 N N N 108.926 -1.630 -34.609 -8.465 -1.101 1.163 HN62 NMY 79
NMY HO41 1HO4 H 0 0 N N N 99.596 3.699 -34.947 1.647 2.739 1.711 HO41 NMY 80
NMY HO22 2HO2 H 0 0 N N N 94.398 4.951 -31.513 7.112 0.352 3.158 HO22 NMY 81
NMY HO21 1HO2 H 0 0 N N N 94.297 2.324 -30.265 8.572 -0.192 -0.700 HO21 NMY 82
NMY H17 H17 H 0 1 N N N 99.870 -1.846 -30.691 1.061 -1.569 -4.355 H17 NMY 83
NMY HO12 2HO1 H 0 0 N N N 102.239 4.609 -35.127 -1.101 5.108 -0.104 HO12 NMY 84
NMY H191 1H19 H 0 0 N N N 97.090 -0.731 -32.095 5.143 -4.678 -0.023 H191 NMY 85
NMY H192 2H19 H 0 0 N N N 97.792 -0.411 -30.656 4.583 -3.737 1.229 H192 NMY 86
NMY HN31 1HN3 H 0 0 N N N 97.105 5.160 -33.243 5.643 1.760 -1.730 HN31 NMY 87
NMY HN32 2HN3 H 0 0 N N N 97.776 4.402 -34.524 7.200 1.907 -1.163 HN32 NMY 88
# #
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
NMY C1 O5 SING N N 1
NMY C1 O1 SING N N 2
NMY C1 C2 SING N N 3
NMY C1 H1 SING N N 4
NMY O1 C10 SING N N 5
NMY C2 N2 SING N N 6
NMY C2 C3 SING N N 7
NMY C2 H2 SING N N 8
NMY N2 HN21 SING N N 9
NMY N2 HN22 SING N N 10
NMY C3 C4 SING N N 11
NMY C3 O3 SING N N 12
NMY C3 H3 SING N N 13
NMY O3 HO3 SING N N 14
NMY C4 C5 SING N N 15
NMY C4 O4 SING N N 16
NMY C4 H4 SING N N 17
NMY O4 HO4 SING N N 18
NMY C5 O5 SING N N 19
NMY C5 C6 SING N N 20
NMY C5 H5 SING N N 21
NMY C6 N6 SING N N 22
NMY C6 H61 SING N N 23
NMY C6 H62 SING N N 24
NMY C7 N7 SING N N 25
NMY C7 C12 SING N N 26
NMY C7 C8 SING N N 27
NMY C7 H7 SING N N 28
NMY N7 H71 SING N N 29
NMY N7 H72 SING N N 30
NMY C12 O12 SING N N 31
NMY C12 C11 SING N N 32
NMY C12 H12 SING N N 33
NMY C11 O11 SING N N 34
NMY C11 C10 SING N N 35
NMY C11 H11 SING N N 36
NMY O11 C13 SING N N 37
NMY C10 C9 SING N N 38
NMY C10 H10 SING N N 39
NMY C9 C8 SING N N 40
NMY C9 N9 SING N N 41
NMY C9 H9 SING N N 42
NMY N9 H91 SING N N 43
NMY N9 H92 SING N N 44
NMY C8 H81 SING N N 45
NMY C8 H82 SING N N 46
NMY C13 C14 SING N N 47
NMY C13 O16 SING N N 48
NMY C13 H13 SING N N 49
NMY C14 O14 SING N N 50
NMY C14 C15 SING N N 51
NMY C14 H14 SING N N 52
NMY C15 O18 SING N N 53
NMY C15 C16 SING N N 54
NMY C15 H15 SING N N 55
NMY C16 O16 SING N N 56
NMY C16 C17 SING N N 57
NMY C16 H16 SING N N 58
NMY C17 O17 SING N N 59
NMY C17 H171 SING N N 60
NMY C17 H172 SING N N 61
NMY C21 C20 SING N N 62
NMY C21 C22 SING N N 63
NMY C21 O21 SING N N 64
NMY C21 H21 SING N N 65
NMY C20 C19 SING N N 66
NMY C20 O20 SING N N 67
NMY C20 H20 SING N N 68
NMY C19 N23 SING N N 69
NMY C19 C18 SING N N 70
NMY C19 H19 SING N N 71
NMY C18 O22 SING N N 72
NMY C18 O18 SING N N 73
NMY C18 H18 SING N N 74
NMY C22 O22 SING N N 75
NMY C22 C23 SING N N 76
NMY C22 H22 SING N N 77
NMY C23 N19 SING N N 78
NMY C23 H231 SING N N 79
NMY C23 H232 SING N N 80
NMY N6 HN61 SING N N 81
NMY N6 HN62 SING N N 82
NMY O14 HO41 SING N N 83
NMY O20 HO22 SING N N 84
NMY O21 HO21 SING N N 85
NMY O17 H17 SING N N 86
NMY O12 HO12 SING N N 87
NMY N19 H191 SING N N 88
NMY N19 H192 SING N N 89
NMY N23 HN31 SING N N 90
NMY N23 HN32 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
NMY SMILES ACDLabs 10.04 "O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C4OC(C(OC3OC(CN)C(O)C(O)C3N)C4O)CO"
NMY SMILES_CANONICAL CACTVS 3.341 "NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O[C@H]4O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]4N)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O"
NMY SMILES CACTVS 3.341 "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CN)[CH](O)[CH](O)[CH]4N)[CH]3O)[CH](N)[CH](O)[CH]1O"
NMY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)O)O)N"
NMY SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)O)O)N)O)O)N"
NMY InChI InChI 1.03 "InChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1"
NMY InChIKey InChI 1.03 PGBHMTALBVVCIT-VCIWKGPPSA-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
NMY "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside"
NMY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxy-oxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-cyclohexyl]oxy-oxane-3,4-diol"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NMY "Create component" 2007-07-25 RCSB
NMY "Modify descriptor" 2011-06-04 RCSB
NMY "Modify synonyms" 2020-06-05 PDBE
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 NMY MYCIFRADIN ? ?
2 NMY NEOMAS ? ?
3 NMY PIMAVECORT ? ?
4 NMY VONAMYCIN ? ?
##