data_1N5
#
_chem_comp.id 1N5
_chem_comp.name "(2R,4S)-2,4,7-trihydroxyheptanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H14 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-05-01
_chem_comp.pdbx_modified_date 2011-06-04
_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 178.183
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 1N5
_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 3CXO
_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
1N5 C1 C1 C 0 1 N N N N N N 26.098 14.696 50.139 3.256 0.220 -0.191 C1 1N5 1
1N5 C2 C2 C 0 1 N N R N N N 25.738 16.168 50.434 1.974 -0.326 0.383 C2 1N5 2
1N5 C3 C3 C 0 1 N N N N N N 25.836 16.988 49.127 0.783 0.298 -0.347 C3 1N5 3
1N5 O4 O4 O 0 1 N N N N N N 26.351 19.256 49.799 -0.580 0.355 1.648 O4 1N5 4
1N5 C7 C7 C 0 1 N N N N N N 22.547 18.298 47.381 -4.200 0.325 -0.701 C7 1N5 5
1N5 C4 C4 C 0 1 N N S N N N 25.313 18.422 49.297 -0.518 -0.159 0.316 C4 1N5 6
1N5 C5 C5 C 0 1 N N N N N N 24.865 18.949 47.957 -1.711 0.363 -0.487 C5 1N5 7
1N5 C6 C6 C 0 1 N N N N N N 23.413 19.387 47.989 -3.007 -0.197 0.103 C6 1N5 8
1N5 O2 O2 O 0 1 N N N N N N 24.423 16.276 51.003 1.944 -1.745 0.218 O2 1N5 9
1N5 O7 O7 O 0 1 N N N N N N 21.185 18.692 47.413 -5.411 -0.198 -0.149 O7 1N5 10
1N5 O1A O1A O 0 1 N N N N N N 25.271 13.820 50.497 3.550 1.523 -0.059 O1A 1N5 11
1N5 O1B O1B O 0 1 N N N N N N 27.197 14.465 49.567 4.022 -0.517 -0.766 O1B 1N5 12
1N5 H2 H2 H 0 1 N N N N N N 26.450 16.568 51.171 1.918 -0.082 1.444 H2 1N5 13
1N5 H3 H3 H 0 1 N N N N N N 26.892 17.035 48.822 0.854 1.385 -0.297 H3 1N5 14
1N5 H3A H3A H 0 1 N N N N N N 25.215 16.490 48.368 0.789 -0.019 -1.390 H3A 1N5 15
1N5 HO4 HO4 H 0 1 N N N N N N 26.972 19.442 49.105 -0.558 1.320 1.699 HO4 1N5 16
1N5 H7 H7 H 0 1 N N N N N N 22.671 17.369 47.957 -4.221 1.414 -0.655 H7 1N5 17
1N5 H7A H7A H 0 1 N N N N N N 22.852 18.132 46.337 -4.107 0.006 -1.739 H7A 1N5 18
1N5 H4 H4 H 0 1 N N N N N N 24.469 18.420 50.003 -0.548 -1.248 0.345 H4 1N5 19
1N5 H5 H5 H 0 1 N N N N N N 25.490 19.813 47.689 -1.732 1.451 -0.442 H5 1N5 20
1N5 H5A H5A H 0 1 N N N N N N 24.967 18.142 47.216 -1.617 0.044 -1.525 H5A 1N5 21
1N5 H6 H6 H 0 1 N N N N N N 23.296 20.315 47.411 -3.101 0.122 1.141 H6 1N5 22
1N5 H6A H6A H 0 1 N N N N N N 23.105 19.565 49.030 -2.987 -1.286 0.058 H6A 1N5 23
1N5 HO2 HO2 H 0 1 N N N N N N 24.488 16.300 51.950 1.990 -2.035 -0.704 HO2 1N5 24
1N5 HO7 HO7 H 0 1 N N N N N N 20.901 18.780 48.315 -6.210 0.092 -0.610 HO7 1N5 25
1N5 HO1A HO1A H 0 0 N Y N N N N 25.603 12.959 50.270 4.383 1.826 -0.444 HO1A 1N5 26
#
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
1N5 O1B C1 DOUB N N 1
1N5 C1 C2 SING N N 2
1N5 C1 O1A SING N N 3
1N5 C3 C2 SING N N 4
1N5 C2 O2 SING N N 5
1N5 C2 H2 SING N N 6
1N5 C3 C4 SING N N 7
1N5 C3 H3 SING N N 8
1N5 C3 H3A SING N N 9
1N5 C4 O4 SING N N 10
1N5 O4 HO4 SING N N 11
1N5 C7 O7 SING N N 12
1N5 C7 C6 SING N N 13
1N5 C7 H7 SING N N 14
1N5 C7 H7A SING N N 15
1N5 C5 C4 SING N N 16
1N5 C4 H4 SING N N 17
1N5 C5 C6 SING N N 18
1N5 C5 H5 SING N N 19
1N5 C5 H5A SING N N 20
1N5 C6 H6 SING N N 21
1N5 C6 H6A SING N N 22
1N5 O2 HO2 SING N N 23
1N5 O7 HO7 SING N N 24
1N5 O1A HO1A SING N N 25
#
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
1N5 SMILES ACDLabs 10.04 O=C(O)C(O)CC(O)CCCO
1N5 SMILES_CANONICAL CACTVS 3.341 OCCC[C@H](O)C[C@@H](O)C(O)=O
1N5 SMILES CACTVS 3.341 OCCC[CH](O)C[CH](O)C(O)=O
1N5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C[C@@H](C[C@H](C(=O)O)O)O)CO
1N5 SMILES "OpenEye OEToolkits" 1.5.0 C(CC(CC(C(=O)O)O)O)CO
1N5 InChI InChI 1.03 InChI=1S/C7H14O5/c8-3-1-2-5(9)4-6(10)7(11)12/h5-6,8-10H,1-4H2,(H,11,12)/t5-,6+/m0/s1
1N5 InChIKey InChI 1.03 UZWBQTOHZVUOKI-NTSWFWBYSA-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
1N5 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,4S)-2,4,7-trihydroxyheptanoic acid"
1N5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S)-2,4,7-trihydroxyheptanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
1N5 'Create component' 2008-05-01 RCSB
1N5 'Modify descriptor' 2011-06-04 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
1N5 C1 C 5.104 0.608 1
1N5 C2 C 6.404 -0.142 2
1N5 C3 C 7.702 0.608 3
1N5 O4 O 9.002 -1.643 4
1N5 C7 C 12.899 0.608 5
1N5 C4 C 9.002 -0.142 6
1N5 C5 C 10.301 0.608 7
1N5 C6 C 11.600 -0.142 8
1N5 O2 O 6.404 -1.643 9
1N5 O7 O 14.198 -0.142 10
1N5 O1A O 5.104 2.107 11
1N5 O1B O 3.805 -0.142 12
#
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
1N5 O1B C1 DOUBLE NONE 1
1N5 C1 C2 SINGLE NONE 2
1N5 C1 O1A SINGLE NONE 3
1N5 C3 C2 SINGLE NONE 4
1N5 C2 O2 SINGLE BEGINWEDGE 5
1N5 C3 C4 SINGLE NONE 6
1N5 C4 O4 SINGLE BEGINDASH 7
1N5 C7 O7 SINGLE NONE 8
1N5 C7 C6 SINGLE NONE 9
1N5 C5 C4 SINGLE NONE 10
1N5 C5 C6 SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 1N5
_pdbe_chem_comp_rdkit_properties.exactmw 178.084
_pdbe_chem_comp_rdkit_properties.amw 178.184
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 90.284
_pdbe_chem_comp_rdkit_properties.tpsa 97.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.045
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.586
_pdbe_chem_comp_rdkit_properties.chi0v 5.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.521
_pdbe_chem_comp_rdkit_properties.chi2v 0.640
_pdbe_chem_comp_rdkit_properties.chi3v 0.640
_pdbe_chem_comp_rdkit_properties.chi4v 0.268
_pdbe_chem_comp_rdkit_properties.chi0n 19.541
_pdbe_chem_comp_rdkit_properties.chi1n 9.154
_pdbe_chem_comp_rdkit_properties.chi2n 0.640
_pdbe_chem_comp_rdkit_properties.chi3n 0.640
_pdbe_chem_comp_rdkit_properties.chi4n 0.268
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.650
_pdbe_chem_comp_rdkit_properties.kappa1 2.051
_pdbe_chem_comp_rdkit_properties.kappa2 5.932
_pdbe_chem_comp_rdkit_properties.kappa3 5.060
_pdbe_chem_comp_rdkit_properties.Phi 1.014
#
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
1N5 UniChem PDBe 1N5
1N5 UniChem ZINC ZINC000058631566
1N5 UniChem PubChem 24901728
#
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
1N5 C1 3.200 0.180 0.257 ETKDGv3 1
1N5 C2 2.403 -0.634 -0.726 ETKDGv3 2
1N5 C3 0.925 -0.191 -0.788 ETKDGv3 3
1N5 O4 0.556 0.264 1.596 ETKDGv3 4
1N5 C7 -3.420 0.985 -0.253 ETKDGv3 5
1N5 C4 0.140 -0.524 0.507 ETKDGv3 6
1N5 C5 -1.391 -0.438 0.320 ETKDGv3 7
1N5 C6 -1.907 0.975 -0.009 ETKDGv3 8
1N5 O2 2.994 -0.565 -2.000 ETKDGv3 9
1N5 O7 -4.116 0.695 0.930 ETKDGv3 10
1N5 O1A 3.726 -0.427 1.393 ETKDGv3 11
1N5 O1B 3.383 1.412 0.063 ETKDGv3 12
1N5 H2 2.438 -1.698 -0.407 ETKDGv3 13
1N5 H3 0.446 -0.724 -1.639 ETKDGv3 14
1N5 H3A 0.871 0.897 -1.009 ETKDGv3 15
1N5 HO4 0.551 1.213 1.308 ETKDGv3 16
1N5 H7 -3.689 0.272 -1.067 ETKDGv3 17
1N5 H7A -3.717 2.000 -0.592 ETKDGv3 18
1N5 H4 0.357 -1.583 0.766 ETKDGv3 19
1N5 H5 -1.694 -1.138 -0.490 ETKDGv3 20
1N5 H5A -1.872 -0.790 1.258 ETKDGv3 21
1N5 H6 -1.412 1.352 -0.928 ETKDGv3 22
1N5 H6A -1.677 1.672 0.824 ETKDGv3 23
1N5 HO2 2.906 0.369 -2.326 ETKDGv3 24
1N5 HO7 -4.259 -0.287 0.948 ETKDGv3 25
1N5 HO1A 4.258 0.107 2.069 ETKDGv3 26
#