data_D8M
#
_chem_comp.id D8M
_chem_comp.name 2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H19 N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-23
_chem_comp.pdbx_modified_date 2020-04-17
_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 281.308
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D8M
_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 5QBH
_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
D8M O3 O1 O 0 1 N N N N N N 3.202 6.490 8.994 3.348 -2.683 0.079 O3 D8M 1
D8M C4 C1 C 0 1 Y N N N N N -2.995 2.830 10.254 -4.915 -0.720 0.831 C4 D8M 2
D8M C5 C2 C 0 1 N N N N N N -2.185 4.123 8.239 -2.744 0.516 0.868 C5 D8M 3
D8M C6 C3 C 0 1 N N N N N N -0.902 6.124 8.790 -0.447 -0.154 0.409 C6 D8M 4
D8M N1 N1 N 0 1 N N N N N N -1.151 5.110 7.965 -1.753 -0.221 0.081 N1 D8M 5
D8M C7 C4 C 0 1 N N N N N N 0.112 7.133 8.296 0.573 -0.912 -0.400 C7 D8M 6
D8M C8 C5 C 0 1 N N S N N N 1.077 7.585 9.391 1.968 -0.668 0.179 C8 D8M 7
D8M N2 N2 N 0 1 N N N N N N 0.714 11.708 9.904 4.011 3.161 0.264 N2 D8M 8
D8M C9 C6 C 0 1 N N R N N N 2.532 7.743 8.986 3.026 -1.472 -0.608 C9 D8M 9
D8M C10 C7 C 0 1 N N S N N N 3.066 8.659 10.083 4.252 -0.534 -0.656 C10 D8M 10
D8M C11 C8 C 0 1 N N R N N N 1.885 9.591 10.344 3.790 0.727 0.109 C11 D8M 11
D8M C12 C9 C 0 1 N N N N N N 1.971 10.961 9.640 4.363 1.986 -0.545 C12 D8M 12
D8M O O2 O 0 1 N N N N N N -1.455 6.249 9.880 -0.094 0.515 1.357 O D8M 13
D8M C3 C10 C 0 1 Y N N N N N -1.942 3.308 9.488 -4.118 0.275 0.297 C3 D8M 14
D8M N N3 N 0 1 Y N N N N N -0.660 3.042 9.781 -4.546 1.016 -0.706 N D8M 15
D8M C2 C11 C 0 1 Y N N N N N -0.418 2.265 10.848 -5.740 0.841 -1.237 C2 D8M 16
D8M C1 C12 C 0 1 Y N N N N N -1.407 1.739 11.652 -6.592 -0.134 -0.756 C1 D8M 17
D8M C C13 C 0 1 Y N N N N N -2.712 2.032 11.347 -6.177 -0.934 0.298 C D8M 18
D8M O1 O3 O 0 1 N N N N N N 0.706 8.889 9.885 2.350 0.714 0.004 O1 D8M 19
D8M O2 O4 O 0 1 N N N N N N 3.412 7.924 11.252 5.370 -1.136 0.001 O2 D8M 20
D8M H1 H1 H 0 1 N N N N N N 4.108 6.613 8.738 4.008 -3.227 -0.371 H1 D8M 21
D8M H2 H2 H 0 1 N N N N N N -4.016 3.076 10.002 -4.557 -1.327 1.650 H2 D8M 22
D8M H3 H3 H 0 1 N N N N N N -3.144 4.649 8.351 -2.715 0.172 1.902 H3 D8M 23
D8M H4 H4 H 0 1 N N N N N N -2.242 3.435 7.383 -2.518 1.581 0.833 H4 D8M 24
D8M H5 H5 H 0 1 N N N N N N -0.610 5.023 7.129 -2.035 -0.756 -0.677 H5 D8M 25
D8M H6 H6 H 0 1 N N N N N N 0.693 6.677 7.481 0.347 -1.978 -0.365 H6 D8M 26
D8M H7 H7 H 0 1 N N N N N N -0.425 8.014 7.915 0.544 -0.569 -1.434 H7 D8M 27
D8M H8 H8 H 0 1 N N N N N N 1.026 6.857 10.214 1.992 -0.938 1.235 H8 D8M 28
D8M H9 H9 H 0 1 N N N N N N 0.755 12.600 9.453 4.331 3.053 1.215 H9 D8M 29
D8M H10 H10 H 0 1 N N N N N N -0.063 11.189 9.547 4.379 4.006 -0.147 H10 D8M 30
D8M H12 H12 H 0 1 N N N N N N 2.605 8.239 8.007 2.669 -1.689 -1.615 H12 D8M 31
D8M H13 H13 H 0 1 N N N N N N 3.922 9.237 9.704 4.503 -0.285 -1.687 H13 D8M 32
D8M H14 H14 H 0 1 N N N N N N 1.811 9.764 11.428 4.096 0.670 1.153 H14 D8M 33
D8M H15 H15 H 0 1 N N N N N N 2.095 10.814 8.557 3.947 2.096 -1.546 H15 D8M 34
D8M H16 H16 H 0 1 N N N N N N 2.828 11.527 10.033 5.448 1.901 -0.610 H16 D8M 35
D8M H17 H17 H 0 1 N N N N N N 0.610 2.039 11.091 -6.056 1.468 -2.058 H17 D8M 36
D8M H18 H18 H 0 1 N N N N N N -1.161 1.114 12.498 -7.569 -0.273 -1.196 H18 D8M 37
D8M H19 H19 H 0 1 N N N N N N -3.513 1.642 11.957 -6.820 -1.707 0.692 H19 D8M 38
D8M H20 H20 H 0 1 N N N N N N 3.740 8.519 11.915 5.663 -1.964 -0.402 H20 D8M 39
#
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
D8M N1 C5 SING N N 1
D8M N1 C6 SING N N 2
D8M C5 C3 SING N N 3
D8M C7 C6 SING N N 4
D8M C7 C8 SING N N 5
D8M C6 O DOUB N N 6
D8M C9 O3 SING N N 7
D8M C9 C8 SING N N 8
D8M C9 C10 SING N N 9
D8M C8 O1 SING N N 10
D8M C3 N DOUB Y N 11
D8M C3 C4 SING Y N 12
D8M C12 N2 SING N N 13
D8M C12 C11 SING N N 14
D8M N C2 SING Y N 15
D8M O1 C11 SING N N 16
D8M C10 C11 SING N N 17
D8M C10 O2 SING N N 18
D8M C4 C DOUB Y N 19
D8M C2 C1 DOUB Y N 20
D8M C C1 SING Y N 21
D8M O3 H1 SING N N 22
D8M C4 H2 SING N N 23
D8M C5 H3 SING N N 24
D8M C5 H4 SING N N 25
D8M N1 H5 SING N N 26
D8M C7 H6 SING N N 27
D8M C7 H7 SING N N 28
D8M C8 H8 SING N N 29
D8M N2 H9 SING N N 30
D8M N2 H10 SING N N 31
D8M C9 H12 SING N N 32
D8M C10 H13 SING N N 33
D8M C11 H14 SING N N 34
D8M C12 H15 SING N N 35
D8M C12 H16 SING N N 36
D8M C2 H17 SING N N 37
D8M C1 H18 SING N N 38
D8M C H19 SING N N 39
D8M O2 H20 SING N N 40
#
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
D8M SMILES ACDLabs 12.01 OC2C(CC(=O)NCc1ccccn1)OC(C2O)CN
D8M InChI InChI 1.03 InChI=1S/C13H19N3O4/c14-6-10-13(19)12(18)9(20-10)5-11(17)16-7-8-3-1-2-4-15-8/h1-4,9-10,12-13,18-19H,5-7,14H2,(H,16,17)/t9-,10+,12-,13+/m0/s1
D8M InChIKey InChI 1.03 BIGFPMOCLWRIMB-JULQROHOSA-N
D8M SMILES_CANONICAL CACTVS 3.385 NC[C@H]1O[C@@H](CC(=O)NCc2ccccn2)[C@H](O)[C@@H]1O
D8M SMILES CACTVS 3.385 NC[CH]1O[CH](CC(=O)NCc2ccccn2)[CH](O)[CH]1O
D8M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccnc(c1)CNC(=O)C[C@H]2[C@@H]([C@@H]([C@H](O2)CN)O)O
D8M SMILES "OpenEye OEToolkits" 2.0.6 c1ccnc(c1)CNC(=O)CC2C(C(C(O2)CN)O)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
D8M "SYSTEMATIC NAME" ACDLabs 12.01 "2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)"
D8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 2-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-~{N}-(pyridin-2-ylmethyl)ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D8M 'Create component' 2017-10-23 RCSB
D8M 'Initial release' 2020-04-22 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
D8M O3 O 5.730 3.196 1
D8M C4 C 13.908 3.369 2
D8M C5 C 12.608 1.119 3
D8M C6 C 10.011 1.119 4
D8M N1 N 11.309 1.869 5
D8M C7 C 8.711 1.869 6
D8M C8 C 7.412 1.119 7
D8M N2 N 6.060 -3.269 8
D8M C9 C 6.042 1.729 9
D8M C10 C 5.038 0.614 10
D8M C11 C 5.788 -0.685 11
D8M C12 C 5.178 -2.055 12
D8M O O 10.011 -0.382 13
D8M C3 C 13.908 1.869 14
D8M N N 15.207 1.119 15
D8M C2 C 16.506 1.869 16
D8M C1 C 16.506 3.369 17
D8M C C 15.207 4.119 18
D8M O1 O 7.256 -0.373 19
D8M O2 O 3.547 0.771 20
#
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
D8M N1 C5 SINGLE NONE 1
D8M N1 C6 SINGLE NONE 2
D8M C5 C3 SINGLE NONE 3
D8M C7 C6 SINGLE NONE 4
D8M C8 C7 SINGLE BEGINDASH 5
D8M C6 O DOUBLE NONE 6
D8M C9 O3 SINGLE BEGINWEDGE 7
D8M C9 C8 SINGLE NONE 8
D8M C9 C10 SINGLE NONE 9
D8M C8 O1 SINGLE NONE 10
D8M C3 N SINGLE NONE 11
D8M C3 C4 DOUBLE NONE 12
D8M C12 N2 SINGLE NONE 13
D8M C11 C12 SINGLE BEGINDASH 14
D8M N C2 DOUBLE NONE 15
D8M O1 C11 SINGLE NONE 16
D8M C10 C11 SINGLE NONE 17
D8M C10 O2 SINGLE BEGINWEDGE 18
D8M C4 C SINGLE NONE 19
D8M C2 C1 SINGLE NONE 20
D8M C C1 DOUBLE NONE 21
#
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
D8M MurckoScaffold S1 scaffold 'O=C(C[C@H]1CCCO1)NCc1ccccn1' InChI=1S/C12H16N2O2/c15-12(8-11-5-3-7-16-11)14-9-10-4-1-2-6-13-10/h1-2,4,6,11H,3,5,7-9H2,(H,14,15)/t11-/m1/s1 YPCYXVPTXXNCDN-LLVKDONJSA-N
D8M amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
D8M pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
D8M C4 S1 1
D8M C5 S1 1
D8M C6 S1 1
D8M N1 S1 1
D8M C7 S1 1
D8M C8 S1 1
D8M C9 S1 1
D8M C10 S1 1
D8M C11 S1 1
D8M O S1 1
D8M C3 S1 1
D8M N S1 1
D8M C2 S1 1
D8M C1 S1 1
D8M C S1 1
D8M O1 S1 1
D8M N1 F1 1
D8M C6 F1 1
D8M O F1 1
D8M C7 F1 1
D8M C3 F2 1
D8M C4 F2 1
D8M C F2 1
D8M C1 F2 1
D8M C2 F2 1
D8M N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id D8M
_pdbe_chem_comp_rdkit_properties.exactmw 281.138
_pdbe_chem_comp_rdkit_properties.amw 281.312
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.538
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 143.360
_pdbe_chem_comp_rdkit_properties.tpsa 117.700
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.519
_pdbe_chem_comp_rdkit_properties.CrippenMR 70.164
_pdbe_chem_comp_rdkit_properties.chi0v 9.475
_pdbe_chem_comp_rdkit_properties.chi1v 4.889
_pdbe_chem_comp_rdkit_properties.chi2v 1.875
_pdbe_chem_comp_rdkit_properties.chi3v 1.875
_pdbe_chem_comp_rdkit_properties.chi4v 1.069
_pdbe_chem_comp_rdkit_properties.chi0n 28.475
_pdbe_chem_comp_rdkit_properties.chi1n 14.047
_pdbe_chem_comp_rdkit_properties.chi2n 1.875
_pdbe_chem_comp_rdkit_properties.chi3n 1.875
_pdbe_chem_comp_rdkit_properties.chi4n 1.069
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.540
_pdbe_chem_comp_rdkit_properties.kappa1 3.805
_pdbe_chem_comp_rdkit_properties.kappa2 6.757
_pdbe_chem_comp_rdkit_properties.kappa3 3.514
_pdbe_chem_comp_rdkit_properties.Phi 1.285
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
D8M UniChem PDBe D8M
D8M UniChem ZINC ZINC000225394883
D8M UniChem PubChem 100614601
#
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
D8M O3 0.065 -1.585 0.254 ETKDGv3 1
D8M C4 3.121 -0.640 -1.652 ETKDGv3 2
D8M C5 3.013 1.776 -1.108 ETKDGv3 3
D8M C6 0.521 1.750 -1.548 ETKDGv3 4
D8M N1 1.650 2.173 -0.770 ETKDGv3 5
D8M C7 -0.850 1.720 -0.937 ETKDGv3 6
D8M C8 -1.269 0.285 -0.576 ETKDGv3 7
D8M N2 -5.165 0.050 1.223 ETKDGv3 8
D8M C9 -0.427 -0.304 0.577 ETKDGv3 9
D8M C10 -1.404 -0.332 1.730 ETKDGv3 10
D8M C11 -2.755 -0.398 1.023 ETKDGv3 11
D8M C12 -3.870 0.225 1.873 ETKDGv3 12
D8M O 0.680 1.357 -2.735 ETKDGv3 13
D8M C3 3.225 0.338 -0.735 ETKDGv3 14
D8M N 3.450 -0.003 0.646 ETKDGv3 15
D8M C2 3.571 -1.239 1.038 ETKDGv3 16
D8M C1 3.476 -2.337 0.058 ETKDGv3 17
D8M C 3.262 -2.047 -1.229 ETKDGv3 18
D8M O1 -2.634 0.293 -0.201 ETKDGv3 19
D8M O2 -1.181 -1.390 2.633 ETKDGv3 20
D8M H1 -0.697 -2.145 -0.048 ETKDGv3 21
D8M H2 2.924 -0.414 -2.692 ETKDGv3 22
D8M H3 3.729 2.402 -0.532 ETKDGv3 23
D8M H4 3.212 1.956 -2.187 ETKDGv3 24
D8M H5 1.487 2.647 0.147 ETKDGv3 25
D8M H6 -1.572 2.137 -1.673 ETKDGv3 26
D8M H7 -0.888 2.366 -0.033 ETKDGv3 27
D8M H8 -1.168 -0.346 -1.488 ETKDGv3 28
D8M H9 -5.204 0.684 0.392 ETKDGv3 29
D8M H10 -5.901 0.387 1.885 ETKDGv3 30
D8M H12 0.440 0.338 0.845 ETKDGv3 31
D8M H13 -1.316 0.630 2.284 ETKDGv3 32
D8M H14 -3.026 -1.455 0.799 ETKDGv3 33
D8M H15 -3.671 1.309 2.034 ETKDGv3 34
D8M H16 -3.893 -0.278 2.865 ETKDGv3 35
D8M H17 3.739 -1.459 2.083 ETKDGv3 36
D8M H18 3.576 -3.366 0.380 ETKDGv3 37
D8M H19 3.184 -2.841 -1.961 ETKDGv3 38
D8M H20 -1.437 -2.243 2.196 ETKDGv3 39
#