data_Q3M
#
_chem_comp.id Q3M
_chem_comp.name "Methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H19 N O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-09-16
_chem_comp.pdbx_modified_date 2021-03-26
_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 249.327
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Q3M
_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 6U70
_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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
Q3M C01 C1 C 0 1 N N N N N N -14.051 -12.779 5.714 1.006 -3.743 -0.026 C01 Q3M 1
Q3M S02 S1 S 0 1 N N N N N N -13.686 -11.118 4.998 -0.417 -2.645 0.219 S02 Q3M 2
Q3M C03 C2 C 0 1 N N S N N N -15.216 -10.079 4.995 0.345 -1.002 0.308 C03 Q3M 3
Q3M C04 C3 C 0 1 N N N N N N -15.930 -10.185 6.324 0.986 -0.663 -1.039 C04 Q3M 4
Q3M C05 C4 C 0 1 N N R N N N -15.063 -9.572 7.423 1.630 0.723 -0.964 C05 Q3M 5
Q3M C06 C5 C 0 1 N N N N N N -15.799 -9.738 8.771 2.703 0.729 0.127 C06 Q3M 6
Q3M O07 O1 O 0 1 N N N N N N -15.873 -11.126 9.000 3.782 -0.123 -0.262 O07 Q3M 7
Q3M C08 C6 C 0 1 N N S N N N -14.738 -8.093 7.199 0.559 1.765 -0.632 C08 Q3M 8
Q3M O09 O2 O 0 1 N N N N N N -15.902 -7.312 7.296 1.160 3.059 -0.561 O09 Q3M 9
Q3M C10 C7 C 0 1 N N R N N N -14.083 -7.872 5.824 -0.082 1.426 0.716 C10 Q3M 10
Q3M O11 O3 O 0 1 N N N N N N -13.986 -6.483 5.594 0.920 1.431 1.735 O11 Q3M 11
Q3M C12 C8 C 0 1 N N R N N N -14.874 -8.579 4.711 -0.725 0.040 0.640 C12 Q3M 12
Q3M N13 N1 N 0 1 N N N N N N -14.097 -8.572 3.492 -1.752 0.034 -0.404 N13 Q3M 13
Q3M C14 C9 C 0 1 N N N N N N -14.737 -8.416 2.208 -3.001 0.457 -0.124 C14 Q3M 14
Q3M C15 C10 C 0 1 N N N N N N -13.828 -8.412 0.985 -4.057 0.451 -1.198 C15 Q3M 15
Q3M O16 O4 O 0 1 N N N N N N -15.922 -8.259 2.119 -3.274 0.841 0.994 O16 Q3M 16
Q3M H1 H1 H 0 1 N N N N N N -13.136 -13.389 5.712 0.661 -4.775 -0.095 H1 Q3M 17
Q3M H2 H2 H 0 1 N N N N N N -14.411 -12.662 6.747 1.522 -3.470 -0.946 H2 Q3M 18
Q3M H3 H3 H 0 1 N N N N N N -14.825 -13.276 5.111 1.690 -3.644 0.817 H3 Q3M 19
Q3M H4 H4 H 0 1 N N N N N N -15.855 -10.469 4.189 1.110 -0.998 1.085 H4 Q3M 20
Q3M H5 H5 H 0 1 N N N N N N -16.887 -9.646 6.269 1.749 -1.405 -1.276 H5 Q3M 21
Q3M H6 H6 H 0 1 N N N N N N -16.119 -11.244 6.555 0.222 -0.667 -1.816 H6 Q3M 22
Q3M H7 H7 H 0 1 N N N N N N -14.118 -10.132 7.475 2.086 0.965 -1.923 H7 Q3M 23
Q3M H8 H8 H 0 1 N N N N N N -15.236 -9.246 9.578 3.073 1.744 0.267 H8 Q3M 24
Q3M H9 H9 H 0 1 N N N N N N -16.809 -9.305 8.712 2.273 0.367 1.061 H9 Q3M 25
Q3M H10 H10 H 0 1 N N N N N N -16.320 -11.288 9.823 4.500 -0.168 0.384 H10 Q3M 26
Q3M H11 H11 H 0 1 N N N N N N -14.018 -7.782 7.970 -0.205 1.761 -1.409 H11 Q3M 27
Q3M H12 H12 H 0 1 N N N N N N -16.306 -7.449 8.145 0.539 3.771 -0.354 H12 Q3M 28
Q3M H13 H13 H 0 1 N N N N N N -13.075 -8.312 5.855 -0.844 2.168 0.952 H13 Q3M 29
Q3M H14 H14 H 0 1 N N N N N N -13.493 -6.079 6.298 1.371 2.280 1.839 H14 Q3M 30
Q3M H15 H15 H 0 1 N N N N N N -15.817 -8.036 4.554 -1.181 -0.202 1.600 H15 Q3M 31
Q3M H16 H16 H 0 1 N N N N N N -13.104 -8.677 3.539 -1.533 -0.273 -1.298 H16 Q3M 32
Q3M H17 H17 H 0 1 N N N N N N -14.431 -8.249 0.080 -4.576 -0.507 -1.192 H17 Q3M 33
Q3M H18 H18 H 0 1 N N N N N N -13.087 -7.605 1.082 -4.772 1.252 -1.009 H18 Q3M 34
Q3M H19 H19 H 0 1 N N N N N N -13.309 -9.379 0.911 -3.588 0.605 -2.170 H19 Q3M 35
#
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
Q3M C15 C14 SING N N 1
Q3M O16 C14 DOUB N N 2
Q3M C14 N13 SING N N 3
Q3M N13 C12 SING N N 4
Q3M C12 C03 SING N N 5
Q3M C12 C10 SING N N 6
Q3M C03 S02 SING N N 7
Q3M C03 C04 SING N N 8
Q3M S02 C01 SING N N 9
Q3M O11 C10 SING N N 10
Q3M C10 C08 SING N N 11
Q3M C04 C05 SING N N 12
Q3M C08 O09 SING N N 13
Q3M C08 C05 SING N N 14
Q3M C05 C06 SING N N 15
Q3M C06 O07 SING N N 16
Q3M C01 H1 SING N N 17
Q3M C01 H2 SING N N 18
Q3M C01 H3 SING N N 19
Q3M C03 H4 SING N N 20
Q3M C04 H5 SING N N 21
Q3M C04 H6 SING N N 22
Q3M C05 H7 SING N N 23
Q3M C06 H8 SING N N 24
Q3M C06 H9 SING N N 25
Q3M O07 H10 SING N N 26
Q3M C08 H11 SING N N 27
Q3M O09 H12 SING N N 28
Q3M C10 H13 SING N N 29
Q3M O11 H14 SING N N 30
Q3M C12 H15 SING N N 31
Q3M N13 H16 SING N N 32
Q3M C15 H17 SING N N 33
Q3M C15 H18 SING N N 34
Q3M C15 H19 SING N N 35
#
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
Q3M SMILES ACDLabs 12.01 CSC1CC(CO)C(O)C(O)C1NC(C)=O
Q3M InChI InChI 1.03 InChI=1S/C10H19NO4S/c1-5(13)11-8-7(16-2)3-6(4-12)9(14)10(8)15/h6-10,12,14-15H,3-4H2,1-2H3,(H,11,13)/t6-,7+,8+,9+,10-/m1/s1
Q3M InChIKey InChI 1.03 ZYKRTEHWXBHGOU-SQQIUAQRSA-N
Q3M SMILES_CANONICAL CACTVS 3.385 CS[C@H]1C[C@H](CO)[C@H](O)[C@H](O)[C@H]1NC(C)=O
Q3M SMILES CACTVS 3.385 CS[CH]1C[CH](CO)[CH](O)[CH](O)[CH]1NC(C)=O
Q3M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(=O)N[C@H]1[C@H](C[C@@H]([C@@H]([C@@H]1O)O)CO)SC
Q3M SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)NC1C(CC(C(C1O)O)CO)SC
#
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
Q3M "SYSTEMATIC NAME" ACDLabs 12.01 N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide
Q3M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-[(1~{R},2~{R},3~{S},4~{R},6~{S})-4-(hydroxymethyl)-6-methylsulfanyl-2,3-bis(oxidanyl)cyclohexyl]ethanamide
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id Q3M
_pdbx_chem_comp_synonyms.name N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Q3M 'Create component' 2019-09-16 RCSB
Q3M 'Modify synonyms' 2019-09-25 RCSB
Q3M 'Modify synonyms' 2020-06-05 PDBE
Q3M 'Modify linking type' 2020-07-23 RCSB
Q3M 'Initial release' 2021-03-31 RCSB
#
_pdbe_chem_comp_synonyms.comp_id Q3M
_pdbe_chem_comp_synonyms.name
'N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
Q3M C01 C 10.301 0.465 1
Q3M S02 S 9.002 1.215 2
Q3M C03 C 7.702 0.465 3
Q3M C04 C 7.702 -1.035 4
Q3M C05 C 6.404 -1.785 5
Q3M C06 C 6.404 -3.285 6
Q3M O07 O 7.702 -4.035 7
Q3M C08 C 5.104 -1.035 8
Q3M O09 O 3.805 -1.785 9
Q3M C10 C 5.104 0.465 10
Q3M O11 O 3.805 1.215 11
Q3M C12 C 6.404 1.215 12
Q3M N13 N 6.404 2.715 13
Q3M C14 C 7.702 3.465 14
Q3M C15 C 9.002 2.715 15
Q3M O16 O 7.702 4.965 16
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
Q3M C15 C14 SINGLE NONE 1
Q3M O16 C14 DOUBLE NONE 2
Q3M C14 N13 SINGLE NONE 3
Q3M C12 N13 SINGLE BEGINWEDGE 4
Q3M C12 C03 SINGLE NONE 5
Q3M C12 C10 SINGLE NONE 6
Q3M C03 S02 SINGLE BEGINWEDGE 7
Q3M C03 C04 SINGLE NONE 8
Q3M S02 C01 SINGLE NONE 9
Q3M C10 O11 SINGLE BEGINDASH 10
Q3M C10 C08 SINGLE NONE 11
Q3M C04 C05 SINGLE NONE 12
Q3M C08 O09 SINGLE BEGINDASH 13
Q3M C08 C05 SINGLE NONE 14
Q3M C05 C06 SINGLE BEGINDASH 15
Q3M C06 O07 SINGLE NONE 16
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
Q3M MurckoScaffold S1 scaffold C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
Q3M amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
Q3M cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
Q3M C03 S1 1
Q3M C04 S1 1
Q3M C05 S1 1
Q3M C08 S1 1
Q3M C10 S1 1
Q3M C12 S1 1
Q3M N13 F1 1
Q3M C14 F1 1
Q3M O16 F1 1
Q3M C15 F1 1
Q3M C03 F2 1
Q3M C12 F2 1
Q3M C10 F2 1
Q3M C08 F2 1
Q3M C05 F2 1
Q3M C04 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Q3M
_pdbe_chem_comp_rdkit_properties.exactmw 249.103
_pdbe_chem_comp_rdkit_properties.amw 249.332
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 126.248
_pdbe_chem_comp_rdkit_properties.tpsa 89.790
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.043
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.114
_pdbe_chem_comp_rdkit_properties.chi0v 8.305
_pdbe_chem_comp_rdkit_properties.chi1v 4.488
_pdbe_chem_comp_rdkit_properties.chi2v 2.019
_pdbe_chem_comp_rdkit_properties.chi3v 2.019
_pdbe_chem_comp_rdkit_properties.chi4v 1.291
_pdbe_chem_comp_rdkit_properties.chi0n 26.488
_pdbe_chem_comp_rdkit_properties.chi1n 12.844
_pdbe_chem_comp_rdkit_properties.chi2n 1.519
_pdbe_chem_comp_rdkit_properties.chi3n 1.519
_pdbe_chem_comp_rdkit_properties.chi4n 0.902
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.300
_pdbe_chem_comp_rdkit_properties.kappa1 2.818
_pdbe_chem_comp_rdkit_properties.kappa2 5.859
_pdbe_chem_comp_rdkit_properties.kappa3 2.880
_pdbe_chem_comp_rdkit_properties.Phi 1.032
#
_pdbe_chem_comp_external_mappings.comp_id Q3M
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 155818889
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
Q3M C01 1.240 2.834 0.428 ETKDGv3 1
Q3M S02 0.883 1.719 1.828 ETKDGv3 2
Q3M C03 -0.222 0.488 1.000 ETKDGv3 3
Q3M C04 -1.512 1.155 0.470 ETKDGv3 4
Q3M C05 -2.374 0.204 -0.391 ETKDGv3 5
Q3M C06 -3.152 -0.814 0.476 ETKDGv3 6
Q3M O07 -2.297 -1.778 1.027 ETKDGv3 7
Q3M C08 -1.568 -0.424 -1.582 ETKDGv3 8
Q3M O09 -1.827 -1.801 -1.715 ETKDGv3 9
Q3M C10 -0.037 -0.195 -1.481 ETKDGv3 10
Q3M O11 0.638 -1.042 -2.377 ETKDGv3 11
Q3M C12 0.470 -0.451 -0.045 ETKDGv3 12
Q3M N13 1.935 -0.370 0.017 ETKDGv3 13
Q3M C14 2.692 -0.988 1.068 ETKDGv3 14
Q3M C15 4.181 -0.879 1.075 ETKDGv3 15
Q3M O16 2.107 -1.606 1.998 ETKDGv3 16
Q3M H1 1.474 2.274 -0.494 ETKDGv3 17
Q3M H2 2.124 3.451 0.689 ETKDGv3 18
Q3M H3 0.387 3.521 0.255 ETKDGv3 19
Q3M H4 -0.535 -0.167 1.840 ETKDGv3 20
Q3M H5 -1.257 2.027 -0.163 ETKDGv3 21
Q3M H6 -2.106 1.548 1.324 ETKDGv3 22
Q3M H7 -3.162 0.847 -0.847 ETKDGv3 23
Q3M H8 -3.924 -1.316 -0.150 ETKDGv3 24
Q3M H9 -3.686 -0.278 1.293 ETKDGv3 25
Q3M H10 -2.872 -2.383 1.563 ETKDGv3 26
Q3M H11 -1.888 0.091 -2.520 ETKDGv3 27
Q3M H12 -2.687 -1.888 -2.203 ETKDGv3 28
Q3M H13 0.184 0.863 -1.752 ETKDGv3 29
Q3M H14 0.474 -0.685 -3.288 ETKDGv3 30
Q3M H15 0.186 -1.501 0.193 ETKDGv3 31
Q3M H16 2.461 0.095 -0.758 ETKDGv3 32
Q3M H17 4.586 -1.234 0.104 ETKDGv3 33
Q3M H18 4.473 0.181 1.228 ETKDGv3 34
Q3M H19 4.615 -1.495 1.892 ETKDGv3 35
#