data_44S
#
_chem_comp.id 44S
_chem_comp.name 2-deoxy-6-O-phosphono-beta-D-lyxo-hexofuranose
_chem_comp.type 'D-saccharide, beta linking'
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C6 H13 O8 P'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;tagatose-6-phosphate, bound form; 2-deoxy-6-O-phosphono-beta-D-lyxo-hexose; 2-deoxy-6-O-phosphono-D-lyxo-hexose;
2-deoxy-6-O-phosphono-lyxo-hexose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-02-11
_chem_comp.pdbx_modified_date 2024-09-27
_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 244.136
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 44S
_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 4S2B
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 44S 'tagatose-6-phosphate, bound form' PDB ?
2 44S 2-deoxy-6-O-phosphono-beta-D-lyxo-hexose PDB ?
3 44S 2-deoxy-6-O-phosphono-D-lyxo-hexose PDB ?
4 44S 2-deoxy-6-O-phosphono-lyxo-hexose PDB ?
#
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
44S O1P O1P O 0 1 N N N N N N 29.055 -15.103 -24.366 -3.399 1.629 -0.357 O1P 44S 1
44S P P P 0 1 N N N N N N 30.461 -15.399 -23.950 -3.337 0.090 0.112 P 44S 2
44S O3P O3P O 0 1 N N N N N N 31.488 -15.368 -25.050 -3.551 0.010 1.574 O3P 44S 3
44S O2P O2P O 0 1 N N N N N N 30.479 -16.672 -23.099 -4.484 -0.748 -0.646 O2P 44S 4
44S O6 O6 O 0 1 N N N N N N 30.818 -14.300 -22.848 -1.894 -0.524 -0.254 O6 44S 5
44S C6 C6 C 0 1 N N N N N N 30.855 -12.900 -23.129 -0.679 -0.064 0.343 C6 44S 6
44S C5 C5 C 0 1 N N R N N N 30.561 -12.161 -21.831 0.500 -0.857 -0.225 C5 44S 7
44S O5 O5 O 0 1 N N N N N N 31.709 -12.150 -21.023 0.634 -0.576 -1.620 O5 44S 8
44S C4 C4 C 0 1 N N R N N N 30.121 -10.745 -22.104 1.784 -0.453 0.503 C4 44S 9
44S C3 C3 C 0 1 N N R N N N 29.889 -9.784 -20.945 2.996 -1.154 -0.147 C3 44S 10
44S O3 O3 O 0 1 N N N N N N 28.663 -9.998 -20.269 3.404 -2.285 0.625 O3 44S 11
44S C2 C2 C 0 1 N N N N N N 29.798 -8.530 -21.765 4.079 -0.041 -0.111 C2 44S 12
44S O4 O4 O 0 1 N N N N N N 31.058 -10.104 -22.950 1.986 0.960 0.384 O4 44S 13
44S C1 C1 C 0 1 N N R N N N 30.932 -8.696 -22.760 3.208 1.223 -0.323 C1 44S 14
44S O1 O1 O 0 1 N Y N N N N 30.650 -8.171 -24.041 3.859 2.372 0.223 O1 44S 15
44S H1A H1 H 0 1 N N N N N N 29.030 -14.934 -25.301 -3.267 1.757 -1.306 H1A 44S 16
44S H2A H2 H 0 1 N N N N N N 31.159 -17.255 -23.415 -5.381 -0.434 -0.472 H2A 44S 17
44S H61 H3 H 0 1 N N N N N N 31.850 -12.619 -23.503 -0.544 0.995 0.124 H61 44S 18
44S H62 H4 H 0 1 N N N N N N 30.095 -12.649 -23.884 -0.728 -0.209 1.423 H62 44S 19
44S H5 H5 H 0 1 N N N N N N 29.744 -12.685 -21.313 0.322 -1.923 -0.084 H5 44S 20
44S HO5 H6 H 0 1 N Y N N N N 31.523 -11.688 -20.214 0.794 0.356 -1.820 HO5 44S 21
44S H4 H7 H 0 1 N N N N N N 29.168 -10.811 -22.649 1.716 -0.731 1.554 H4 44S 22
44S H3 H8 H 0 1 N N N N N N 30.754 -9.762 -20.266 2.771 -1.447 -1.173 H3 44S 23
44S HO3 H9 H 0 1 N Y N N N N 28.578 -9.371 -19.561 4.163 -2.759 0.258 HO3 44S 24
44S H2 H10 H 0 1 N N N N N N 29.946 -7.637 -21.141 4.582 -0.013 0.856 H2 44S 25
44S H11 H11 H 0 1 N N N N N N 28.827 -8.462 -22.278 4.797 -0.164 -0.921 H11 44S 26
44S H1 H12 H 0 1 N N N N N N 31.857 -8.267 -22.346 3.007 1.370 -1.385 H1 44S 27
44S HO1 H13 H 0 1 N Y N N N N 30.554 -7.228 -23.983 3.341 3.186 0.157 HO1 44S 28
#
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
44S O3P P DOUB N N 1
44S O1P P SING N N 2
44S O1 C1 SING N N 3
44S P O2P SING N N 4
44S P O6 SING N N 5
44S C6 O6 SING N N 6
44S C6 C5 SING N N 7
44S O4 C1 SING N N 8
44S O4 C4 SING N N 9
44S C1 C2 SING N N 10
44S C4 C5 SING N N 11
44S C4 C3 SING N N 12
44S C5 O5 SING N N 13
44S C2 C3 SING N N 14
44S C3 O3 SING N N 15
44S O1P H1A SING N N 16
44S O2P H2A SING N N 17
44S C6 H61 SING N N 18
44S C6 H62 SING N N 19
44S C5 H5 SING N N 20
44S O5 HO5 SING N N 21
44S C4 H4 SING N N 22
44S C3 H3 SING N N 23
44S O3 HO3 SING N N 24
44S C2 H2 SING N N 25
44S C2 H11 SING N N 26
44S C1 H1 SING N N 27
44S O1 HO1 SING N N 28
#
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
44S SMILES ACDLabs 12.01 'O=P(O)(O)OCC(O)C1OC(O)CC1O'
44S InChI InChI 1.03 'InChI=1S/C6H13O8P/c7-3-1-5(9)14-6(3)4(8)2-13-15(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4-,5-,6-/m1/s1'
44S InChIKey InChI 1.03 YKPKUODDXPUHGL-KVTDHHQDSA-N
44S SMILES_CANONICAL CACTVS 3.385 'O[C@H]1C[C@@H](O)[C@@H](O1)[C@H](O)CO[P](O)(O)=O'
44S SMILES CACTVS 3.385 'O[CH]1C[CH](O)[CH](O1)[CH](O)CO[P](O)(O)=O'
44S SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'C1[C@H]([C@@H](O[C@H]1O)[C@@H](COP(=O)(O)O)O)O'
44S SMILES 'OpenEye OEToolkits' 1.7.6 'C1C(C(OC1O)C(COP(=O)(O)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
44S 'SYSTEMATIC NAME' ACDLabs 12.01 2-deoxy-6-O-phosphono-beta-D-lyxo-hexofuranose
44S 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '[(2R)-2-[(2R,3R,5R)-3,5-bis(oxidanyl)oxolan-2-yl]-2-oxidanyl-ethyl] dihydrogen phosphate'
#
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
44S 'CARBOHYDRATE ISOMER' D PDB ?
44S 'CARBOHYDRATE RING' furanose PDB ?
44S 'CARBOHYDRATE ANOMER' beta PDB ?
44S 'CARBOHYDRATE PRIMARY CARBONYL GROUP' aldose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
44S 'Create component' 2015-02-11 RCSB
44S 'Initial release' 2016-01-20 RCSB
44S 'Other modification' 2020-07-03 RCSB
44S 'Modify name' 2020-07-17 RCSB
44S 'Modify synonyms' 2020-07-17 RCSB
44S 'Modify internal type' 2020-07-17 RCSB
44S 'Modify linking type' 2020-07-17 RCSB
44S 'Modify atom id' 2020-07-17 RCSB
44S 'Modify component atom id' 2020-07-17 RCSB
44S 'Modify leaving atom flag' 2020-07-17 RCSB
44S 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 44S
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Carbohydrate
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C2
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 4S2B
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
44S 'tagatose-6-phosphate, bound form' wwPDB ?
44S 2-deoxy-6-O-phosphono-beta-D-lyxo-hexose wwPDB ?
44S 2-deoxy-6-O-phosphono-D-lyxo-hexose wwPDB ?
44S 2-deoxy-6-O-phosphono-lyxo-hexose wwPDB ?
#
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
44S O1P O 3.287 2.486 1
44S P P 4.755 2.798 2
44S O3P O 4.443 4.266 3
44S O2P O 6.222 3.110 4
44S O6 O 5.066 1.331 5
44S C6 C 6.493 0.868 6
44S C5 C 6.805 -0.600 7
44S O5 O 5.690 -1.603 8
44S C4 C 8.232 -1.063 9
44S C3 C 8.695 -2.490 10
44S O3 O 7.813 -3.703 11
44S C2 C 10.195 -2.490 12
44S O4 O 9.445 -0.181 13
44S C1 C 10.659 -1.063 14
44S O1 O 12.085 -0.600 15
#
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
44S O3P P DOUBLE NONE 1
44S O1P P SINGLE NONE 2
44S C1 O1 SINGLE BEGINWEDGE 3
44S P O2P SINGLE NONE 4
44S P O6 SINGLE NONE 5
44S C6 O6 SINGLE NONE 6
44S C6 C5 SINGLE NONE 7
44S O4 C1 SINGLE NONE 8
44S C4 O4 SINGLE BEGINDASH 9
44S C1 C2 SINGLE NONE 10
44S C4 C5 SINGLE NONE 11
44S C4 C3 SINGLE NONE 12
44S C5 O5 SINGLE BEGINDASH 13
44S C2 C3 SINGLE NONE 14
44S C3 O3 SINGLE BEGINWEDGE 15
#
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
44S MurckoScaffold S1 scaffold C1CCOC1 InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 WYURNTSHIVDZCO-UHFFFAOYSA-N
44S deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
44S furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
44S phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-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
44S C4 S1 1
44S C3 S1 1
44S C2 S1 1
44S O4 S1 1
44S C1 S1 1
44S C1 F1 1
44S C2 F1 1
44S C3 F1 1
44S O3 F1 1
44S C4 F1 1
44S O4 F1 1
44S C5 F1 1
44S O5 F1 1
44S C3 F2 1
44S C4 F2 1
44S O4 F2 1
44S C1 F2 1
44S C2 F2 1
44S O1 F2 1
44S O1P F3 1
44S P F3 1
44S O3P F3 1
44S O2P F3 1
44S O6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 44S
_pdbe_chem_comp_rdkit_properties.exactmw 244.035
_pdbe_chem_comp_rdkit_properties.amw 244.136
_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 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_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 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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 104.004
_pdbe_chem_comp_rdkit_properties.tpsa 136.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.075
_pdbe_chem_comp_rdkit_properties.CrippenMR 45.507
_pdbe_chem_comp_rdkit_properties.chi0v 7.608
_pdbe_chem_comp_rdkit_properties.chi1v 4.666
_pdbe_chem_comp_rdkit_properties.chi2v 1.388
_pdbe_chem_comp_rdkit_properties.chi3v 1.388
_pdbe_chem_comp_rdkit_properties.chi4v 0.802
_pdbe_chem_comp_rdkit_properties.chi0n 19.713
_pdbe_chem_comp_rdkit_properties.chi1n 9.246
_pdbe_chem_comp_rdkit_properties.chi2n 1.073
_pdbe_chem_comp_rdkit_properties.chi3n 1.073
_pdbe_chem_comp_rdkit_properties.chi4n 0.607
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.050
_pdbe_chem_comp_rdkit_properties.kappa1 3.724
_pdbe_chem_comp_rdkit_properties.kappa2 4.856
_pdbe_chem_comp_rdkit_properties.kappa3 4.135
_pdbe_chem_comp_rdkit_properties.Phi 1.206
#
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
44S UniChem PDBe 44S
44S UniChem ZINC ZINC000263621282
44S UniChem PubChem 137348206
#
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
44S O1P 2.133 -1.713 -1.701 ETKDGv3 1
44S P 2.948 -0.986 -0.408 ETKDGv3 2
44S O3P 3.609 -2.060 0.425 ETKDGv3 3
44S O2P 4.135 0.064 -1.005 ETKDGv3 4
44S O6 1.841 -0.132 0.567 ETKDGv3 5
44S C6 1.285 0.911 -0.200 ETKDGv3 6
44S C5 0.187 1.624 0.610 ETKDGv3 7
44S O5 -0.161 2.818 -0.043 ETKDGv3 8
44S C4 -1.077 0.756 0.846 ETKDGv3 9
44S C3 -1.951 0.572 -0.401 ETKDGv3 10
44S O3 -3.035 1.464 -0.388 ETKDGv3 11
44S C2 -2.414 -0.851 -0.275 ETKDGv3 12
44S O4 -0.728 -0.511 1.365 ETKDGv3 13
44S C1 -1.298 -1.490 0.525 ETKDGv3 14
44S O1 -1.802 -2.546 1.295 ETKDGv3 15
44S H1A 2.847 -2.112 -2.259 ETKDGv3 16
44S H2A 4.530 0.483 -0.199 ETKDGv3 17
44S H61 0.860 0.535 -1.156 ETKDGv3 18
44S H62 2.074 1.660 -0.436 ETKDGv3 19
44S H5 0.626 1.873 1.605 ETKDGv3 20
44S HO5 -0.646 3.377 0.619 ETKDGv3 21
44S H4 -1.686 1.266 1.627 ETKDGv3 22
44S H3 -1.363 0.693 -1.339 ETKDGv3 23
44S HO3 -3.471 1.392 -1.277 ETKDGv3 24
44S H2 -3.372 -0.899 0.292 ETKDGv3 25
44S H11 -2.538 -1.335 -1.268 ETKDGv3 26
44S H1 -0.516 -1.870 -0.173 ETKDGv3 27
44S HO1 -1.016 -2.983 1.716 ETKDGv3 28
#