data_8LM
#
_chem_comp.id 8LM
_chem_comp.name
;2,6-anhydro-3,5-dideoxy-5-[(2-methylpropanoyl)amino]-3-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-D-galacto-non-2-enoni
c acid
;
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C21 H26 N4 O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-02-15
_chem_comp.pdbx_modified_date 2020-07-17
_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 462.453
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8LM
_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 6C0M
_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
8LM C10 C10 C 0 1 N N N -2.174 30.878 -30.058 -3.022 -2.882 -0.128 C10 8LM 1
8LM C13 C13 C 0 1 N N N -0.018 29.982 -29.048 -4.080 -5.116 -0.329 C13 8LM 2
8LM C4 C4 C 0 1 N N R -5.417 31.262 -31.131 -0.405 -1.060 0.051 C4 8LM 3
8LM C3 C3 C 0 1 N N N -6.723 32.019 -31.211 0.448 0.106 -0.369 C3 8LM 4
8LM C20 C20 C 0 1 Y N N -9.835 30.376 -30.303 3.967 -0.225 -0.297 C20 8LM 5
8LM C21 C21 C 0 1 Y N N -10.979 29.992 -29.366 5.321 -0.170 0.308 C21 8LM 6
8LM C22 C22 C 0 1 Y N N -11.384 30.877 -28.379 6.438 -0.522 -0.446 C22 8LM 7
8LM C24 C24 C 0 1 Y N N -13.043 29.298 -27.658 7.847 -0.068 1.436 C24 8LM 8
8LM C26 C26 C 0 1 Y N N -11.607 28.763 -29.500 5.480 0.239 1.630 C26 8LM 9
8LM O9 O9 O 0 1 N N N -5.469 35.328 -34.539 -5.598 4.168 0.697 O9 8LM 10
8LM C9 C9 C 0 1 N N N -4.331 34.529 -34.337 -5.384 2.783 0.423 C9 8LM 11
8LM C8 C8 C 0 1 N N R -3.381 35.190 -33.323 -3.899 2.453 0.593 C8 8LM 12
8LM O8 O8 O 0 1 N N N -3.909 36.435 -32.924 -3.526 2.629 1.961 O8 8LM 13
8LM C7 C7 C 0 1 N N R -3.147 34.254 -32.133 -3.649 1.001 0.180 C7 8LM 14
8LM O7 O7 O 0 1 N N N -2.912 34.963 -30.961 -4.022 0.824 -1.189 O7 8LM 15
8LM C6 C6 C 0 1 N N R -4.392 33.310 -31.953 -2.165 0.671 0.350 C6 8LM 16
8LM C5 C5 C 0 1 N N R -4.201 32.159 -30.974 -1.880 -0.731 -0.205 C5 8LM 17
8LM N5 N5 N 0 1 N N N -2.998 31.255 -31.202 -2.730 -1.713 0.474 N5 8LM 18
8LM C11 C11 C 0 1 N N N -0.972 29.943 -30.242 -3.901 -3.889 0.567 C11 8LM 19
8LM C12 C12 C 0 1 N N N -1.457 28.514 -30.492 -3.248 -4.312 1.885 C12 8LM 20
8LM O10 O10 O 0 1 N N N -2.438 31.296 -28.975 -2.582 -3.122 -1.233 O10 8LM 21
8LM O4 O4 O 0 1 N N N -5.489 30.343 -30.000 -0.037 -2.216 -0.703 O4 8LM 22
8LM N18 N18 N 0 1 Y N N -7.966 31.277 -31.085 1.803 -0.095 -0.575 N18 8LM 23
8LM C19 C19 C 0 1 Y N N -8.714 31.214 -29.976 2.803 0.091 0.333 C19 8LM 24
8LM C23 C23 C 0 1 Y N N -12.417 30.527 -27.527 7.695 -0.469 0.121 C23 8LM 25
8LM C25 C25 C 0 1 Y N N -12.636 28.412 -28.642 6.742 0.288 2.188 C25 8LM 26
8LM N27 N27 N 0 1 Y N N -9.657 30.003 -31.575 3.687 -0.590 -1.557 N27 8LM 27
8LM N28 N28 N 0 1 Y N N -8.542 30.548 -32.029 2.418 -0.523 -1.761 N28 8LM 28
8LM C2 C2 C 0 1 N N N -6.751 33.379 -31.176 -0.059 1.329 -0.552 C2 8LM 29
8LM C1 C1 C 0 1 N N N -8.114 34.047 -31.215 0.845 2.411 -0.955 C1 8LM 30
8LM O1B O1B O 0 1 N N N -8.402 34.938 -30.374 0.389 3.678 -1.030 O1B 8LM 31
8LM O1A O1A O 0 1 N N N -8.941 33.695 -32.102 2.006 2.165 -1.222 O1A 8LM 32
8LM O6 O6 O 0 1 N N N -5.601 34.156 -31.383 -1.375 1.613 -0.380 O6 8LM 33
8LM H1 H1 H 0 1 N N N 0.321 31.015 -28.882 -3.106 -5.562 -0.533 H1 8LM 34
8LM H2 H2 H 0 1 N N N -0.539 29.619 -28.150 -4.715 -5.845 0.174 H2 8LM 35
8LM H3 H3 H 0 1 N N N 0.851 29.340 -29.252 -4.544 -4.815 -1.268 H3 8LM 36
8LM H4 H4 H 0 1 N N N -5.298 30.681 -32.057 -0.256 -1.255 1.113 H4 8LM 37
8LM H9 H9 H 0 1 N N N -10.896 31.835 -28.275 6.321 -0.836 -1.473 H9 8LM 38
8LM H10 H10 H 0 1 N N N -13.850 29.030 -26.992 8.833 -0.027 1.876 H10 8LM 39
8LM H23 H23 H 0 1 N N N -11.293 28.079 -30.274 4.618 0.517 2.218 H23 8LM 40
8LM HO9 HO9 H 0 1 N N N -6.045 34.907 -35.167 -6.519 4.449 0.608 HO9 8LM 41
8LM H91 H91 H 0 1 N N N -4.642 33.546 -33.954 -5.972 2.180 1.115 H91 8LM 42
8LM H92 H92 H 0 1 N N N -3.805 34.399 -35.294 -5.689 2.563 -0.600 H92 8LM 43
8LM H8 H8 H 0 1 N N N -2.414 35.347 -33.823 -3.305 3.117 -0.034 H8 8LM 44
8LM HO8 HO8 H 0 1 N N N -3.322 36.842 -32.298 -4.016 2.068 2.578 HO8 8LM 45
8LM H7 H7 H 0 1 N N N -2.280 33.618 -32.366 -4.243 0.337 0.807 H7 8LM 46
8LM HO7 HO7 H 0 1 N N N -2.771 34.355 -30.245 -3.532 1.385 -1.805 HO7 8LM 47
8LM H6 H6 H 0 1 N N N -4.677 32.909 -32.937 -1.899 0.709 1.406 H6 8LM 48
8LM H5 H5 H 0 1 N N N -4.170 32.555 -29.948 -2.080 -0.750 -1.276 H5 8LM 49
8LM HN5 HN5 H 0 1 N N N -2.776 30.925 -32.120 -3.082 -1.521 1.357 HN5 8LM 50
8LM H11 H11 H 0 1 N N N -0.417 30.275 -31.132 -4.874 -3.443 0.771 H11 8LM 51
8LM H20 H20 H 0 1 N N N -0.590 27.850 -30.623 -3.121 -3.438 2.524 H20 8LM 52
8LM H21 H21 H 0 1 N N N -2.053 28.174 -29.633 -3.884 -5.040 2.388 H21 8LM 53
8LM H22 H22 H 0 1 N N N -2.077 28.491 -31.400 -2.275 -4.758 1.682 H22 8LM 54
8LM HO4 HO4 H 0 1 N N N -4.675 29.857 -29.934 0.886 -2.483 -0.589 HO4 8LM 55
8LM H24 H24 H 0 1 N N N -8.515 31.695 -29.029 2.693 0.425 1.355 H24 8LM 56
8LM H25 H25 H 0 1 N N N -12.736 31.214 -26.757 8.562 -0.742 -0.463 H25 8LM 57
8LM H26 H26 H 0 1 N N N -13.119 27.451 -28.740 6.866 0.605 3.213 H26 8LM 58
8LM HO1B HO1B H 0 0 N N N -9.283 35.254 -30.536 1.023 4.357 -1.300 HO1B 8LM 59
# #
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
8LM O9 C9 SING N N 1
8LM C9 C8 SING N N 2
8LM C8 O8 SING N N 3
8LM C8 C7 SING N N 4
8LM C7 C6 SING N N 5
8LM C7 O7 SING N N 6
8LM O1A C1 DOUB N N 7
8LM N28 N27 DOUB Y N 8
8LM N28 N18 SING Y N 9
8LM C6 O6 SING N N 10
8LM C6 C5 SING N N 11
8LM N27 C20 SING Y N 12
8LM O6 C2 SING N N 13
8LM C1 C2 SING N N 14
8LM C1 O1B SING N N 15
8LM C3 C2 DOUB N N 16
8LM C3 C4 SING N N 17
8LM C3 N18 SING N N 18
8LM N5 C5 SING N N 19
8LM N5 C10 SING N N 20
8LM C4 C5 SING N N 21
8LM C4 O4 SING N N 22
8LM N18 C19 SING Y N 23
8LM C12 C11 SING N N 24
8LM C20 C19 DOUB Y N 25
8LM C20 C21 SING N N 26
8LM C11 C10 SING N N 27
8LM C11 C13 SING N N 28
8LM C10 O10 DOUB N N 29
8LM C26 C21 DOUB Y N 30
8LM C26 C25 SING Y N 31
8LM C21 C22 SING Y N 32
8LM C25 C24 DOUB Y N 33
8LM C22 C23 DOUB Y N 34
8LM C24 C23 SING Y N 35
8LM C13 H1 SING N N 36
8LM C13 H2 SING N N 37
8LM C13 H3 SING N N 38
8LM C4 H4 SING N N 39
8LM C22 H9 SING N N 40
8LM C24 H10 SING N N 41
8LM C26 H23 SING N N 42
8LM O9 HO9 SING N N 43
8LM C9 H91 SING N N 44
8LM C9 H92 SING N N 45
8LM C8 H8 SING N N 46
8LM O8 HO8 SING N N 47
8LM C7 H7 SING N N 48
8LM O7 HO7 SING N N 49
8LM C6 H6 SING N N 50
8LM C5 H5 SING N N 51
8LM N5 HN5 SING N N 52
8LM C11 H11 SING N N 53
8LM C12 H20 SING N N 54
8LM C12 H21 SING N N 55
8LM C12 H22 SING N N 56
8LM O4 HO4 SING N N 57
8LM C19 H24 SING N N 58
8LM C23 H25 SING N N 59
8LM C25 H26 SING N N 60
8LM O1B HO1B SING N N 61
# #
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
8LM SMILES ACDLabs 12.01 "C(=O)(NC1C(O)C(=C(C(O)=O)OC1C(C(CO)O)O)n3cc(c2ccccc2)nn3)C(C)C"
8LM InChI InChI 1.03 "InChI=1S/C21H26N4O8/c1-10(2)20(30)22-14-17(29)15(19(21(31)32)33-18(14)16(28)13(27)9-26)25-8-12(23-24-25)11-6-4-3-5-7-11/h3-8,10,13-14,16-18,26-29H,9H2,1-2H3,(H,22,30)(H,31,32)/t13-,14-,16-,17-,18-/m1/s1"
8LM InChIKey InChI 1.03 HLCFXRXMEMQOHX-RTKZEXODSA-N
8LM SMILES_CANONICAL CACTVS 3.385 "CC(C)C(=O)N[C@@H]1[C@@H](O)C(=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)n2cc(nn2)c3ccccc3"
8LM SMILES CACTVS 3.385 "CC(C)C(=O)N[CH]1[CH](O)C(=C(O[CH]1[CH](O)[CH](O)CO)C(O)=O)n2cc(nn2)c3ccccc3"
8LM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(C)C(=O)N[C@@H]1[C@H](C(=C(O[C@H]1[C@@H]([C@@H](CO)O)O)C(=O)O)n2cc(nn2)c3ccccc3)O"
8LM SMILES "OpenEye OEToolkits" 2.0.6 "CC(C)C(=O)NC1C(C(=C(OC1C(C(CO)O)O)C(=O)O)n2cc(nn2)c3ccccc3)O"
# #
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
8LM "SYSTEMATIC NAME" ACDLabs 12.01
;2,6-anhydro-3,5-dideoxy-5-[(2-methylpropanoyl)amino]-3-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-D-galacto-non-2-enoni
c acid
;
8LM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6
;(2~{R},3~{R},4~{R})-3-(2-methylpropanoylamino)-4-oxidanyl-5-(4-phenyl-1,2,3-triazol-1-yl)-2-[(1~{R},2~{R})-1,2,3-tris(o
xidanyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid
;
# #
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
8LM "CARBOHYDRATE ISOMER" D PDB ?
8LM "CARBOHYDRATE RING" dihydropyran PDB ?
8LM "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose PDB ?
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
8LM "Create component" 2017-02-15 RCSB
8LM "Modify name" 2018-01-29 RCSB
8LM "Initial release" 2018-06-27 RCSB
8LM "Other modification" 2020-04-12 RCSB
8LM "Other modification" 2020-07-03 RCSB
8LM "Modify name" 2020-07-17 RCSB
8LM "Modify component atom id" 2020-07-17 RCSB
##