data_UI5
#
_chem_comp.id UI5
_chem_comp.name "(1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H13 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-09-05
_chem_comp.pdbx_modified_date 2023-12-08
_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 147.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UI5
_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 8QF8
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
UI5 C6 C1 C 0 1 N N N N N N -13.696 -27.124 23.458 2.043 0.325 0.197 C6 UI5 1
UI5 C5 C2 C 0 1 N N S N N N -12.719 -28.093 22.813 0.719 0.172 -0.555 C5 UI5 2
UI5 C1 C3 C 0 1 N N R N N N -12.063 -27.623 21.496 -0.060 1.503 -0.551 C1 UI5 3
UI5 C2 C4 C 0 1 N N N N N N -11.562 -28.902 20.753 -1.548 1.141 -0.396 C2 UI5 4
UI5 C3 C5 C 0 1 N N S N N N -12.328 -30.047 21.453 -1.620 -0.398 -0.311 C3 UI5 5
UI5 O3 O1 O 0 1 N N N N N N -14.839 -26.912 22.643 2.780 -0.897 0.117 O3 UI5 6
UI5 C4 C6 C 0 1 N N S N N N -13.327 -29.454 22.451 -0.213 -0.820 0.184 C4 UI5 7
UI5 O2 O2 O 0 1 N N N N N N -13.416 -30.344 23.559 0.074 -2.168 -0.194 O2 UI5 8
UI5 N1 N1 N 0 1 N N N N N N -12.959 -26.780 20.646 0.375 2.338 0.577 N1 UI5 9
UI5 O1 O3 O 0 1 N N N N N N -13.075 -30.908 20.584 -2.622 -0.801 0.625 O1 UI5 10
UI5 H12 H1 H 0 1 N N N N N N -14.019 -27.535 24.426 2.625 1.130 -0.252 H12 UI5 11
UI5 H13 H2 H 0 1 N N N N N N -13.189 -26.161 23.619 1.842 0.561 1.242 H13 UI5 12
UI5 H11 H3 H 0 1 N N N N N N -11.909 -28.276 23.534 0.899 -0.162 -1.577 H11 UI5 13
UI5 H4 H4 H 0 1 N N N N N N -11.177 -27.026 21.759 0.099 2.032 -1.491 H4 UI5 14
UI5 H6 H5 H 0 1 N N N N N N -11.812 -28.858 19.683 -1.947 1.584 0.517 H6 UI5 15
UI5 H5 H6 H 0 1 N N N N N N -10.475 -29.026 20.871 -2.111 1.494 -1.260 H5 UI5 16
UI5 H7 H7 H 0 1 N N N N N N -11.598 -30.645 22.018 -1.823 -0.825 -1.293 H7 UI5 17
UI5 H14 H8 H 0 1 N N N N N N -15.427 -26.303 23.074 3.632 -0.873 0.573 H14 UI5 18
UI5 H9 H9 H 0 1 N N N N N N -14.304 -29.312 21.966 -0.130 -0.697 1.264 H9 UI5 19
UI5 H10 H10 H 0 1 N N N N N N -14.031 -29.998 24.195 -0.534 -2.819 0.181 H10 UI5 20
UI5 H1 H11 H 0 1 N N N N N N -13.252 -25.977 21.164 -0.143 3.204 0.606 H1 UI5 21
UI5 H2 H12 H 0 1 N N N N N N -12.463 -26.487 19.828 0.293 1.838 1.449 H2 UI5 22
UI5 H8 H14 H 0 1 N N N N N N -13.510 -31.578 21.098 -3.515 -0.513 0.393 H8 UI5 23
#
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
UI5 N1 C1 SING N N 1
UI5 C1 C2 SING N N 2
UI5 C1 C5 SING N N 3
UI5 C2 C3 SING N N 4
UI5 C3 O1 SING N N 5
UI5 C3 C4 SING N N 6
UI5 C4 O2 SING N N 7
UI5 C4 C5 SING N N 8
UI5 C5 C6 SING N N 9
UI5 C6 O3 SING N N 10
UI5 C6 H12 SING N N 11
UI5 C6 H13 SING N N 12
UI5 C5 H11 SING N N 13
UI5 C1 H4 SING N N 14
UI5 C2 H6 SING N N 15
UI5 C2 H5 SING N N 16
UI5 C3 H7 SING N N 17
UI5 O3 H14 SING N N 18
UI5 C4 H9 SING N N 19
UI5 O2 H10 SING N N 20
UI5 N1 H1 SING N N 21
UI5 N1 H2 SING N N 22
UI5 O1 H8 SING N N 23
#
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
UI5 InChI InChI 1.06 "InChI=1S/C6H13NO3/c7-4-1-5(9)6(10)3(4)2-8/h3-6,8-10H,1-2,7H2/t3-,4-,5+,6+/m1/s1"
UI5 InChIKey InChI 1.06 XJKPQBOZNVQXOP-ZXXMMSQZSA-N
UI5 SMILES_CANONICAL CACTVS 3.385 "N[C@@H]1C[C@H](O)[C@@H](O)[C@@H]1CO"
UI5 SMILES CACTVS 3.385 "N[CH]1C[CH](O)[CH](O)[CH]1CO"
UI5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@H]([C@H]([C@@H]([C@H]1O)O)CO)N"
UI5 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C1O)O)CO)N"
#
_pdbx_chem_comp_identifier.comp_id UI5
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-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
UI5 'Create component' 2023-09-05 PDBE
UI5 'Initial release' 2023-12-13 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
UI5 C6 C 6.331 2.096 1
UI5 C5 C 6.331 0.596 2
UI5 C1 C 5.118 -0.286 3
UI5 C2 C 5.581 -1.712 4
UI5 C3 C 7.081 -1.712 5
UI5 O3 O 7.630 2.846 6
UI5 C4 C 7.545 -0.286 7
UI5 O2 O 8.971 0.178 8
UI5 N1 N 3.691 0.178 9
UI5 O1 O 7.963 -2.926 10
#
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
UI5 C1 N1 SINGLE BEGINWEDGE 1
UI5 C1 C2 SINGLE NONE 2
UI5 C1 C5 SINGLE NONE 3
UI5 C2 C3 SINGLE NONE 4
UI5 C3 O1 SINGLE BEGINWEDGE 5
UI5 C3 C4 SINGLE NONE 6
UI5 C4 O2 SINGLE BEGINDASH 7
UI5 C4 C5 SINGLE NONE 8
UI5 C5 C6 SINGLE BEGINWEDGE 9
UI5 C6 O3 SINGLE NONE 10
#
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
UI5 MurckoScaffold S1 scaffold C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
UI5 cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-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
UI5 C5 S1 1
UI5 C1 S1 1
UI5 C2 S1 1
UI5 C3 S1 1
UI5 C4 S1 1
UI5 C5 F1 1
UI5 C1 F1 1
UI5 C2 F1 1
UI5 C3 F1 1
UI5 C4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UI5
_pdbe_chem_comp_rdkit_properties.exactmw 147.090
_pdbe_chem_comp_rdkit_properties.amw 147.174
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 77.921
_pdbe_chem_comp_rdkit_properties.tpsa 86.710
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.952
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.182
_pdbe_chem_comp_rdkit_properties.chi0v 4.672
_pdbe_chem_comp_rdkit_properties.chi1v 2.336
_pdbe_chem_comp_rdkit_properties.chi2v 1.004
_pdbe_chem_comp_rdkit_properties.chi3v 1.004
_pdbe_chem_comp_rdkit_properties.chi4v 0.543
_pdbe_chem_comp_rdkit_properties.chi0n 17.672
_pdbe_chem_comp_rdkit_properties.chi1n 8.455
_pdbe_chem_comp_rdkit_properties.chi2n 1.004
_pdbe_chem_comp_rdkit_properties.chi3n 1.004
_pdbe_chem_comp_rdkit_properties.chi4n 0.543
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.474
_pdbe_chem_comp_rdkit_properties.kappa2 2.837
_pdbe_chem_comp_rdkit_properties.kappa3 1.152
_pdbe_chem_comp_rdkit_properties.Phi 0.418
#
_pdbe_chem_comp_external_mappings.comp_id UI5
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id UI5
#
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
UI5 C6 2.155 0.294 -0.456 ETKDGv3 1
UI5 C5 0.672 -0.015 -0.746 ETKDGv3 2
UI5 C1 -0.260 1.195 -0.606 ETKDGv3 3
UI5 C2 -1.651 0.589 -0.380 ETKDGv3 4
UI5 C3 -1.436 -0.837 0.151 ETKDGv3 5
UI5 O3 2.953 -0.828 -0.720 ETKDGv3 6
UI5 C4 0.080 -1.073 0.183 ETKDGv3 7
UI5 O2 0.401 -2.361 -0.272 ETKDGv3 8
UI5 N1 0.128 2.060 0.515 ETKDGv3 9
UI5 O1 -1.971 -0.977 1.442 ETKDGv3 10
UI5 H12 2.490 1.155 -1.078 ETKDGv3 11
UI5 H13 2.292 0.577 0.610 ETKDGv3 12
UI5 H11 0.591 -0.377 -1.798 ETKDGv3 13
UI5 H4 -0.245 1.794 -1.545 ETKDGv3 14
UI5 H6 -2.262 1.206 0.316 ETKDGv3 15
UI5 H5 -2.191 0.541 -1.352 ETKDGv3 16
UI5 H7 -1.917 -1.567 -0.543 ETKDGv3 17
UI5 H14 3.031 -0.895 -1.708 ETKDGv3 18
UI5 H9 0.471 -0.922 1.218 ETKDGv3 19
UI5 H10 0.145 -2.988 0.454 ETKDGv3 20
UI5 H1 -0.022 1.557 1.421 ETKDGv3 21
UI5 H2 -0.496 2.899 0.518 ETKDGv3 22
UI5 H8 -2.957 -1.028 1.336 ETKDGv3 23
#