data_K71
#
_chem_comp.id K71
_chem_comp.name "3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H16 O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-11-05
_chem_comp.pdbx_modified_date 2022-04-15
_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 252.219
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K71
_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 6MZ4
_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
K71 CAQ C1 C 0 1 N N N N N N 19.976 -0.031 34.945 3.164 -2.907 -0.571 CAQ K71 1
K71 OAI O1 O 0 1 N N N N N N 18.947 0.508 35.787 2.053 -2.521 0.241 OAI K71 2
K71 CAC C2 C 0 1 N N R N N N 19.491 1.038 36.996 1.289 -1.439 -0.295 CAC K71 3
K71 CAB C3 C 0 1 N N R N N N 20.141 2.426 36.775 -0.169 -1.568 0.157 CAB K71 4
K71 OAJ O2 O 0 1 N N N N N N 19.214 3.332 36.125 -0.225 -1.603 1.584 OAJ K71 5
K71 CAD C4 C 0 1 N N N N N N 18.330 1.103 38.010 1.854 -0.110 0.214 CAD K71 6
K71 CAE C5 C 0 1 N N R N N N 18.759 1.808 39.304 0.982 1.038 -0.302 CAE K71 7
K71 CAG C6 C 0 1 N N N N N N 17.507 2.110 40.109 1.497 2.345 0.243 CAG K71 8
K71 OAM O3 O 0 1 N N N N N N 17.053 1.213 40.849 1.641 2.509 1.568 OAM K71 9
K71 OAL O4 O 0 1 N N N N N N 16.990 3.221 39.909 1.781 3.244 -0.511 OAL K71 10
K71 OAH O5 O 0 1 N N N N N N 19.648 0.976 40.071 1.028 1.066 -1.730 OAH K71 11
K71 OAF O6 O 0 1 N N N N N N 19.361 3.082 38.961 -0.366 0.840 0.128 OAF K71 12
K71 CAA C7 C 0 1 N N R N N N 20.540 2.989 38.147 -0.963 -0.364 -0.357 CAA K71 13
K71 CAK C8 C 0 1 N N R N N N 21.084 4.431 38.062 -2.407 -0.455 0.141 CAK K71 14
K71 OAN O7 O 0 1 N N N N N N 22.302 4.470 37.312 -3.003 -1.660 -0.343 OAN K71 15
K71 CAO C9 C 0 1 N N N N N N 21.261 4.993 39.473 -3.200 0.749 -0.373 CAO K71 16
K71 OAP O8 O 0 1 N N N N N N 22.198 4.108 40.114 -4.515 0.726 0.186 OAP K71 17
K71 H1 H1 H 0 1 N N N N N N 19.525 -0.430 34.024 3.841 -2.060 -0.685 H1 K71 18
K71 H2 H2 H 0 1 N N N N N N 20.693 0.763 34.688 3.692 -3.733 -0.094 H2 K71 19
K71 H3 H3 H 0 1 N N N N N N 20.499 -0.839 35.477 2.806 -3.221 -1.551 H3 K71 20
K71 H4 H4 H 0 1 N N N N N N 20.259 0.356 37.391 1.338 -1.463 -1.384 H4 K71 21
K71 H5 H5 H 0 1 N N N N N N 21.045 2.302 36.161 -0.596 -2.486 -0.248 H5 K71 22
K71 H6 H6 H 0 1 N N N N N N 19.631 4.176 35.999 0.262 -2.340 1.979 H6 K71 23
K71 H7 H7 H 0 1 N N N N N N 17.492 1.657 37.561 1.852 -0.107 1.304 H7 K71 24
K71 H8 H8 H 0 1 N N N N N N 18.006 0.080 38.250 2.874 0.015 -0.150 H8 K71 25
K71 H9 H9 H 0 1 N N N N N N 16.241 1.508 41.244 1.975 3.365 1.870 H9 K71 26
K71 H10 H10 H 0 1 N N N N N N 19.901 1.430 40.866 0.496 1.770 -2.126 H10 K71 27
K71 H11 H11 H 0 1 N N N N N N 21.294 2.336 38.612 -0.954 -0.361 -1.447 H11 K71 28
K71 H12 H12 H 0 1 N N N N N N 20.327 5.043 37.549 -2.416 -0.458 1.231 H12 K71 29
K71 H13 H13 H 0 1 N N N N N N 22.621 5.364 37.271 -3.029 -1.726 -1.308 H13 K71 30
K71 H14 H14 H 0 1 N N N N N N 21.662 6.017 39.434 -2.695 1.669 -0.078 H14 K71 31
K71 H15 H15 H 0 1 N N N N N N 20.302 4.995 40.011 -3.266 0.703 -1.459 H15 K71 32
K71 H16 H16 H 0 1 N N N N N N 22.355 4.402 41.004 -5.075 1.462 -0.096 H16 K71 33
#
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
K71 CAQ OAI SING N N 1
K71 OAI CAC SING N N 2
K71 OAJ CAB SING N N 3
K71 CAB CAC SING N N 4
K71 CAB CAA SING N N 5
K71 CAC CAD SING N N 6
K71 OAN CAK SING N N 7
K71 CAD CAE SING N N 8
K71 CAK CAA SING N N 9
K71 CAK CAO SING N N 10
K71 CAA OAF SING N N 11
K71 OAF CAE SING N N 12
K71 CAE OAH SING N N 13
K71 CAE CAG SING N N 14
K71 CAO OAP SING N N 15
K71 OAL CAG DOUB N N 16
K71 CAG OAM SING N N 17
K71 CAQ H1 SING N N 18
K71 CAQ H2 SING N N 19
K71 CAQ H3 SING N N 20
K71 CAC H4 SING N N 21
K71 CAB H5 SING N N 22
K71 OAJ H6 SING N N 23
K71 CAD H7 SING N N 24
K71 CAD H8 SING N N 25
K71 OAM H9 SING N N 26
K71 OAH H10 SING N N 27
K71 CAA H11 SING N N 28
K71 CAK H12 SING N N 29
K71 OAN H13 SING N N 30
K71 CAO H14 SING N N 31
K71 CAO H15 SING N N 32
K71 OAP H16 SING N N 33
#
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
K71 SMILES ACDLabs 12.01 COC1CC(O)(C(O)=O)OC(C1O)C(CO)O
K71 InChI InChI 1.03 InChI=1S/C9H16O8/c1-16-5-2-9(15,8(13)14)17-7(6(5)12)4(11)3-10/h4-7,10-12,15H,2-3H2,1H3,(H,13,14)/t4-,5-,6-,7-,9-/m1/s1
K71 InChIKey InChI 1.03 WLRWVSRKOWICBL-DMKSXPFUSA-N
K71 SMILES_CANONICAL CACTVS 3.385 CO[C@@H]1C[C@@](O)(O[C@H]([C@H](O)CO)[C@@H]1O)C(O)=O
K71 SMILES CACTVS 3.385 CO[CH]1C[C](O)(O[CH]([CH](O)CO)[CH]1O)C(O)=O
K71 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CO[C@@H]1C[C@@](O[C@@H]([C@@H]1O)[C@@H](CO)O)(C(=O)O)O
K71 SMILES "OpenEye OEToolkits" 2.0.6 COC1CC(OC(C1O)C(CO)O)(C(=O)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
K71 "SYSTEMATIC NAME" ACDLabs 12.01 "3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid"
K71 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-methoxy-2,5-bis(oxidanyl)oxane-2-carboxylic 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
K71 'Create component' 2018-11-05 RCSB
K71 'Initial release' 2022-04-20 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
K71 CAQ C 3.000 1.067 1
K71 OAI O 4.299 1.817 2
K71 CAC C 5.598 1.067 3
K71 CAB C 6.897 1.817 4
K71 OAJ O 6.897 3.317 5
K71 CAD C 5.598 -0.433 6
K71 CAE C 6.897 -1.183 7
K71 CAG C 6.147 -2.482 8
K71 OAM O 6.897 -3.781 9
K71 OAL O 4.647 -2.482 10
K71 OAH O 7.647 -2.482 11
K71 OAF O 8.196 -0.433 12
K71 CAA C 8.196 1.067 13
K71 CAK C 9.495 1.817 14
K71 OAN O 9.495 3.317 15
K71 CAO C 10.794 1.067 16
K71 OAP O 12.093 1.817 17
#
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
K71 CAQ OAI SINGLE NONE 1
K71 CAC OAI SINGLE BEGINWEDGE 2
K71 CAB OAJ SINGLE BEGINWEDGE 3
K71 CAB CAC SINGLE NONE 4
K71 CAB CAA SINGLE NONE 5
K71 CAC CAD SINGLE NONE 6
K71 CAK OAN SINGLE BEGINDASH 7
K71 CAD CAE SINGLE NONE 8
K71 CAK CAA SINGLE NONE 9
K71 CAK CAO SINGLE NONE 10
K71 CAA OAF SINGLE BEGINWEDGE 11
K71 OAF CAE SINGLE NONE 12
K71 CAE OAH SINGLE BEGINDASH 13
K71 CAE CAG SINGLE NONE 14
K71 CAO OAP SINGLE NONE 15
K71 OAL CAG DOUBLE NONE 16
K71 CAG OAM SINGLE NONE 17
#
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
K71 MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
K71 pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
K71 CAC S1 1
K71 CAB S1 1
K71 CAD S1 1
K71 CAE S1 1
K71 OAF S1 1
K71 CAA S1 1
K71 CAB F1 1
K71 CAA F1 1
K71 OAF F1 1
K71 CAE F1 1
K71 CAD F1 1
K71 CAC F1 1
K71 OAH F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K71
_pdbe_chem_comp_rdkit_properties.exactmw 252.085
_pdbe_chem_comp_rdkit_properties.amw 252.219
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.889
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 119.926
_pdbe_chem_comp_rdkit_properties.tpsa 136.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.722
_pdbe_chem_comp_rdkit_properties.CrippenMR 51.972
_pdbe_chem_comp_rdkit_properties.chi0v 7.766
_pdbe_chem_comp_rdkit_properties.chi1v 3.791
_pdbe_chem_comp_rdkit_properties.chi2v 1.606
_pdbe_chem_comp_rdkit_properties.chi3v 1.606
_pdbe_chem_comp_rdkit_properties.chi4v 0.885
_pdbe_chem_comp_rdkit_properties.chi0n 23.766
_pdbe_chem_comp_rdkit_properties.chi1n 11.332
_pdbe_chem_comp_rdkit_properties.chi2n 1.606
_pdbe_chem_comp_rdkit_properties.chi3n 1.606
_pdbe_chem_comp_rdkit_properties.chi4n 0.885
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.770
_pdbe_chem_comp_rdkit_properties.kappa1 3.624
_pdbe_chem_comp_rdkit_properties.kappa2 5.253
_pdbe_chem_comp_rdkit_properties.kappa3 2.733
_pdbe_chem_comp_rdkit_properties.Phi 1.120
#
_pdbe_chem_comp_external_mappings.comp_id K71
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id K71
#
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
K71 CAQ -2.029 2.133 1.550 ETKDGv3 1
K71 OAI -0.837 1.613 1.002 ETKDGv3 2
K71 CAC -1.118 0.807 -0.132 ETKDGv3 3
K71 CAB 0.076 0.853 -1.105 ETKDGv3 4
K71 OAJ 0.637 2.139 -1.162 ETKDGv3 5
K71 CAD -1.426 -0.641 0.304 ETKDGv3 6
K71 CAE -0.774 -1.700 -0.624 ETKDGv3 7
K71 CAG -1.080 -3.068 -0.067 ETKDGv3 8
K71 OAM -2.216 -3.758 -0.482 ETKDGv3 9
K71 OAL -0.338 -3.569 0.821 ETKDGv3 10
K71 OAH -1.283 -1.619 -1.937 ETKDGv3 11
K71 OAF 0.643 -1.565 -0.673 ETKDGv3 12
K71 CAA 1.153 -0.235 -0.794 ETKDGv3 13
K71 CAK 2.092 0.029 0.424 ETKDGv3 14
K71 OAN 1.368 0.060 1.626 ETKDGv3 15
K71 CAO 2.958 1.299 0.331 ETKDGv3 16
K71 OAP 3.579 1.409 -0.921 ETKDGv3 17
K71 H1 -1.780 2.678 2.483 ETKDGv3 18
K71 H2 -2.502 2.858 0.852 ETKDGv3 19
K71 H3 -2.745 1.323 1.814 ETKDGv3 20
K71 H4 -1.994 1.197 -0.707 ETKDGv3 21
K71 H5 -0.309 0.622 -2.126 ETKDGv3 22
K71 H6 -0.040 2.732 -1.583 ETKDGv3 23
K71 H7 -2.529 -0.786 0.330 ETKDGv3 24
K71 H8 -1.068 -0.804 1.344 ETKDGv3 25
K71 H9 -2.441 -4.668 -0.096 ETKDGv3 26
K71 H10 -2.275 -1.591 -1.887 ETKDGv3 27
K71 H11 1.813 -0.253 -1.688 ETKDGv3 28
K71 H12 2.816 -0.821 0.457 ETKDGv3 29
K71 H13 1.269 -0.879 1.932 ETKDGv3 30
K71 H14 3.731 1.274 1.133 ETKDGv3 31
K71 H15 2.351 2.206 0.523 ETKDGv3 32
K71 H16 4.298 0.725 -0.943 ETKDGv3 33
#