data_LLL
#
_chem_comp.id LLL
_chem_comp.name
;(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR
OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H39 N5 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "GENTAMICIN C1A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-11-02
_chem_comp.pdbx_modified_date 2020-06-17
_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 449.542
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LLL
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
LLL C11 C11 C 0 1 N N R 0.932 -7.120 29.442 -3.040 1.340 -0.079 C11 LLL 1
LLL O11 O11 O 0 1 N N N 0.006 -8.231 29.322 -2.774 0.350 0.917 O11 LLL 2
LLL C21 C21 C 0 1 N N R 0.327 -5.869 28.796 -3.764 2.525 0.562 C21 LLL 3
LLL N21 N21 N 0 1 N N N -0.937 -5.604 29.411 -2.909 3.122 1.597 N21 LLL 4
LLL C31 C31 C 0 1 N N N 0.193 -6.064 27.247 -5.068 2.032 1.196 C31 LLL 5
LLL C41 C41 C 0 1 N N N 1.620 -6.317 26.667 -5.873 1.274 0.135 C41 LLL 6
LLL C51 C51 C 0 1 N N S 2.235 -7.603 27.376 -4.990 0.182 -0.475 C51 LLL 7
LLL O51 O51 O 0 1 N N N 2.241 -7.483 28.833 -3.855 0.774 -1.104 O51 LLL 8
LLL C61 C61 C 0 1 N N N 3.617 -7.974 26.892 -5.796 -0.601 -1.513 C61 LLL 9
LLL N61 N61 N 0 1 N N N 4.559 -8.059 27.977 -4.994 -1.728 -2.007 N61 LLL 10
LLL C12 C12 C 0 1 N N R -1.402 -11.351 31.889 0.398 -2.442 0.687 C12 LLL 11
LLL N12 N12 N 0 1 N N N -1.411 -12.321 32.940 1.385 -3.367 0.114 N12 LLL 12
LLL C22 C22 C 0 1 N N N -0.254 -11.683 30.882 -1.012 -2.916 0.331 C22 LLL 13
LLL C32 C32 C 0 1 N N S -0.231 -10.616 29.727 -2.040 -1.952 0.928 C32 LLL 14
LLL N32 N32 N 0 1 N N N 0.849 -10.924 28.776 -3.394 -2.407 0.587 N32 LLL 15
LLL C42 C42 C 0 1 N N R -0.037 -9.177 30.342 -1.814 -0.550 0.360 C42 LLL 16
LLL C52 C52 C 0 1 N N S -1.208 -8.873 31.354 -0.404 -0.076 0.715 C52 LLL 17
LLL O52 O52 O 0 1 N N N -1.054 -7.575 31.919 -0.193 1.234 0.184 O52 LLL 18
LLL C62 C62 C 0 1 N N S -1.216 -9.948 32.497 0.624 -1.040 0.118 C62 LLL 19
LLL O62 O62 O 0 1 N N N -2.282 -9.661 33.394 1.941 -0.597 0.451 O62 LLL 20
LLL C13 C13 C 0 1 N N R -2.178 -9.841 34.838 2.789 -0.970 -0.637 C13 LLL 21
LLL C23 C23 C 0 1 N N R -3.623 -10.040 35.346 4.252 -0.863 -0.202 C23 LLL 22
LLL O23 O23 O 0 1 N N N -4.176 -11.175 34.718 4.495 -1.754 0.888 O23 LLL 23
LLL C33 C33 C 0 1 N N R -4.442 -8.726 35.015 4.538 0.577 0.239 C33 LLL 24
LLL N33 N33 N 0 1 N N N -5.876 -8.853 35.435 5.973 0.734 0.511 N33 LLL 25
LLL C43 C43 C 0 1 N N R -3.764 -7.446 35.740 4.120 1.530 -0.886 C43 LLL 26
LLL O43 O43 O 0 1 N N N -3.785 -7.581 37.146 4.967 1.325 -2.019 O43 LLL 27
LLL C53 C53 C 0 1 N N N -2.272 -7.340 35.297 2.668 1.239 -1.273 C53 LLL 28
LLL O53 O53 O 0 1 N N N -1.567 -8.650 35.496 2.549 -0.102 -1.743 O53 LLL 29
LLL C83 C83 C 0 1 N N N -4.432 -6.084 35.507 4.243 2.979 -0.409 C83 LLL 30
LLL C93 C93 C 0 1 N N N -6.770 -9.616 34.548 6.190 0.302 1.898 C93 LLL 31
LLL H11 H11 H 0 1 N N N 1.113 -6.892 30.518 -2.099 1.680 -0.511 H11 LLL 32
LLL H21 H21 H 0 1 N N N 0.995 -4.990 28.955 -3.989 3.271 -0.200 H21 LLL 33
LLL H211 1H21 H 0 0 N N N -0.869 -5.526 30.426 -3.428 3.891 1.994 H211 LLL 34
LLL H212 2H21 H 0 0 N N N -1.340 -4.771 28.981 -2.812 2.432 2.326 H212 LLL 35
LLL H311 1H31 H 0 0 N N N -0.330 -5.215 26.749 -5.646 2.884 1.554 H311 LLL 36
LLL H312 2H31 H 0 0 N N N -0.532 -6.866 26.975 -4.841 1.366 2.028 H312 LLL 37
LLL H411 1H41 H 0 0 N N N 2.281 -5.424 26.754 -6.189 1.966 -0.646 H411 LLL 38
LLL H412 2H41 H 0 0 N N N 1.621 -6.400 25.555 -6.749 0.819 0.597 H412 LLL 39
LLL H51 H51 H 0 1 N N N 1.550 -8.431 27.079 -4.657 -0.495 0.312 H51 LLL 40
LLL H611 1H61 H 0 0 N N N 3.972 -7.273 26.101 -6.710 -0.979 -1.054 H611 LLL 41
LLL H612 2H61 H 0 0 N N N 3.599 -8.916 26.296 -6.052 0.055 -2.345 H612 LLL 42
LLL H11A 1H1 H 0 0 N N N 4.235 -8.700 28.701 -4.870 -2.358 -1.229 H11A LLL 43
LLL H12A 2H1 H 0 0 N N N 5.492 -8.309 27.650 -5.563 -2.213 -2.685 H12A LLL 44
LLL H12 H12 H 0 1 N N N -2.370 -11.374 31.336 0.510 -2.417 1.771 H12 LLL 45
LLL H121 1H12 H 0 0 N N N -0.504 -12.398 33.401 1.199 -4.274 0.515 H121 LLL 46
LLL H122 2H12 H 0 0 N N N -2.160 -12.104 33.597 1.178 -3.438 -0.871 H122 LLL 47
LLL H221 1H22 H 0 0 N N N -0.329 -12.724 30.489 -1.125 -2.941 -0.753 H221 LLL 48
LLL H222 2H22 H 0 0 N N N 0.735 -11.773 31.389 -1.173 -3.915 0.736 H222 LLL 49
LLL H32 H32 H 0 1 N N N -1.200 -10.644 29.177 -1.928 -1.927 2.012 H32 LLL 50
LLL H321 1H32 H 0 0 N N N 0.780 -11.876 28.415 -3.458 -3.372 0.876 H321 LLL 51
LLL H322 2H32 H 0 0 N N N 0.864 -10.232 28.027 -4.031 -1.887 1.171 H322 LLL 52
LLL H42 H42 H 0 1 N N N 0.928 -9.131 30.899 -1.927 -0.575 -0.724 H42 LLL 53
LLL H52 H52 H 0 1 N N N -2.175 -8.911 30.801 -0.292 -0.051 1.799 H52 LLL 54
LLL H3 H3 H 0 1 N N N -1.759 -7.392 32.529 0.647 1.550 0.544 H3 LLL 55
LLL H62 H62 H 0 1 N N N -0.247 -9.921 33.049 0.511 -1.065 -0.965 H62 LLL 56
LLL H13 H13 H 0 1 N N N -1.523 -10.711 35.079 2.572 -1.998 -0.930 H13 LLL 57
LLL H23 H23 H 0 1 N N N -3.652 -10.212 36.447 4.901 -1.124 -1.038 H23 LLL 58
LLL H2 H2 H 0 1 N N N -5.065 -11.297 35.030 4.304 -2.646 0.568 H2 LLL 59
LLL H1 H1 H 0 1 N N N -4.418 -8.579 33.910 3.968 0.803 1.140 H1 LLL 60
LLL H33 H33 H 0 1 N N N -6.267 -7.924 35.594 6.167 1.723 0.482 H33 LLL 61
LLL H43 H43 H 0 1 N N N -3.387 -6.830 37.571 4.666 1.935 -2.707 H43 LLL 62
LLL H531 1H53 H 0 0 N N N -1.745 -6.504 35.814 2.357 1.928 -2.058 H531 LLL 63
LLL H532 2H53 H 0 0 N N N -2.177 -6.974 34.248 2.029 1.375 -0.400 H532 LLL 64
LLL H831 1H83 H 0 0 N N N -5.509 -6.144 35.787 3.599 3.131 0.457 H831 LLL 65
LLL H832 2H83 H 0 0 N N N -3.965 -5.203 36.006 5.277 3.185 -0.135 H832 LLL 66
LLL H833 3H83 H 0 0 N N N -4.515 -5.892 34.412 3.939 3.652 -1.211 H833 LLL 67
LLL H931 1H93 H 0 0 N N N -6.343 -10.631 34.375 7.246 0.400 2.149 H931 LLL 68
LLL H932 2H93 H 0 0 N N N -7.836 -9.710 34.860 5.598 0.924 2.569 H932 LLL 69
LLL H933 3H93 H 0 0 N N N -6.721 -9.192 33.518 5.886 -0.740 2.006 H933 LLL 70
# #
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
LLL C11 O11 SING N N 1
LLL C11 C21 SING N N 2
LLL C11 O51 SING N N 3
LLL C11 H11 SING N N 4
LLL O11 C42 SING N N 5
LLL C21 N21 SING N N 6
LLL C21 C31 SING N N 7
LLL C21 H21 SING N N 8
LLL N21 H211 SING N N 9
LLL N21 H212 SING N N 10
LLL C31 C41 SING N N 11
LLL C31 H311 SING N N 12
LLL C31 H312 SING N N 13
LLL C41 C51 SING N N 14
LLL C41 H411 SING N N 15
LLL C41 H412 SING N N 16
LLL C51 O51 SING N N 17
LLL C51 C61 SING N N 18
LLL C51 H51 SING N N 19
LLL C61 N61 SING N N 20
LLL C61 H611 SING N N 21
LLL C61 H612 SING N N 22
LLL N61 H11A SING N N 23
LLL N61 H12A SING N N 24
LLL C12 N12 SING N N 25
LLL C12 C22 SING N N 26
LLL C12 C62 SING N N 27
LLL C12 H12 SING N N 28
LLL N12 H121 SING N N 29
LLL N12 H122 SING N N 30
LLL C22 C32 SING N N 31
LLL C22 H221 SING N N 32
LLL C22 H222 SING N N 33
LLL C32 N32 SING N N 34
LLL C32 C42 SING N N 35
LLL C32 H32 SING N N 36
LLL N32 H321 SING N N 37
LLL N32 H322 SING N N 38
LLL C42 C52 SING N N 39
LLL C42 H42 SING N N 40
LLL C52 O52 SING N N 41
LLL C52 C62 SING N N 42
LLL C52 H52 SING N N 43
LLL O52 H3 SING N N 44
LLL C62 O62 SING N N 45
LLL C62 H62 SING N N 46
LLL O62 C13 SING N N 47
LLL C13 C23 SING N N 48
LLL C13 O53 SING N N 49
LLL C13 H13 SING N N 50
LLL C23 O23 SING N N 51
LLL C23 C33 SING N N 52
LLL C23 H23 SING N N 53
LLL O23 H2 SING N N 54
LLL C33 N33 SING N N 55
LLL C33 C43 SING N N 56
LLL C33 H1 SING N N 57
LLL N33 C93 SING N N 58
LLL N33 H33 SING N N 59
LLL C43 O43 SING N N 60
LLL C43 C53 SING N N 61
LLL C43 C83 SING N N 62
LLL O43 H43 SING N N 63
LLL C53 O53 SING N N 64
LLL C53 H531 SING N N 65
LLL C53 H532 SING N N 66
LLL C83 H831 SING N N 67
LLL C83 H832 SING N N 68
LLL C83 H833 SING N N 69
LLL C93 H931 SING N N 70
LLL C93 H932 SING N N 71
LLL C93 H933 SING N N 72
# #
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
LLL SMILES ACDLabs 10.04 "O(C2C(O)C(OC1OC(CN)CCC1N)C(N)CC2N)C3OCC(O)(C(NC)C3O)C"
LLL SMILES_CANONICAL CACTVS 3.341 "CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3N)[C@@H]2O"
LLL SMILES CACTVS 3.341 "CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CN)CC[CH]3N)[CH]2O"
LLL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC[C@H](O3)CN)N)N)N)O"
LLL SMILES "OpenEye OEToolkits" 1.5.0 "CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(CCC(O3)CN)N)N)N)O"
LLL InChI InChI 1.03 "InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1"
LLL InChIKey InChI 1.03 VEGXETMJINRLTH-BOZYPMBZSA-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
LLL "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside"
LLL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-5-methyl-4-methylamino-oxane-3,5-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
LLL "Create component" 2005-11-02 RCSB
LLL "Modify descriptor" 2011-06-04 RCSB
LLL "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id LLL
_pdbx_chem_comp_synonyms.name "GENTAMICIN C1A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##