data_PA5
#
_chem_comp.id PA5
_chem_comp.name "5-PHOSPHOARABINONIC ACID"
_chem_comp.type SACCHARIDE
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H11 O9 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-03-08
_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 246.109
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PA5
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1C7R
_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
PA5 O1A O1A O 0 1 N N N N N N 51.335 -12.388 21.123 -0.465 0.571 -4.861 O1A PA5 1
PA5 C1 C1 C 0 1 N N N N N N 51.824 -11.612 21.960 -0.249 -0.285 -4.038 C1 PA5 2
PA5 O1 O1 O 0 1 N N N N N N 52.537 -10.479 21.383 -0.788 -1.506 -4.182 O1 PA5 3
PA5 C2 C2 C 0 1 N N S N N N 52.725 -12.421 22.988 0.625 0.016 -2.848 C2 PA5 4
PA5 O2 O2 O 0 1 N N N N N N 54.023 -11.813 22.996 1.074 1.371 -2.918 O2 PA5 5
PA5 C3 C3 C 0 1 N N R N N N 51.995 -12.383 24.399 -0.176 -0.189 -1.561 C3 PA5 6
PA5 O3 O3 O 0 1 N N N N N N 52.582 -13.181 25.438 -1.304 0.687 -1.557 O3 PA5 7
PA5 C4 C4 C 0 1 N N R N N N 50.520 -12.666 23.999 0.712 0.117 -0.353 C4 PA5 8
PA5 O4 O4 O 0 1 N N N N N N 49.668 -12.972 25.178 1.840 -0.759 -0.357 O4 PA5 9
PA5 C5 C5 C 0 1 N N N N N N 50.421 -13.854 23.197 -0.089 -0.088 0.933 C5 PA5 10
PA5 O5 O5 O 0 1 N N N N N N 49.039 -14.160 22.780 0.740 0.198 2.061 O5 PA5 11
PA5 P P P 0 1 N N N N N N 48.956 -15.106 21.443 -0.162 -0.037 3.374 P PA5 12
PA5 O1P O1P O 0 1 N N N N N N 47.586 -15.755 21.258 -0.627 -1.441 3.407 O1P PA5 13
PA5 O2P O2P O 0 1 N N N N N N 49.297 -14.231 20.218 0.714 0.268 4.689 O2P PA5 14
PA5 O3P O3P O 0 1 N N N N N N 49.981 -16.262 21.477 -1.433 0.949 3.335 O3P PA5 15
PA5 HO1 HO1 H 0 1 N N N N N N 52.911 -9.885 22.023 -1.349 -1.700 -4.945 HO1 PA5 16
PA5 HC2 HC2 H 0 1 N N N N N N 52.860 -13.492 22.712 1.485 -0.652 -2.851 HC2 PA5 17
PA5 HO2 HO2 H 0 1 N N N N N N 54.561 -12.296 23.610 0.283 1.928 -2.913 HO2 PA5 18
PA5 HC3 HC3 H 0 1 N N N N N N 52.097 -11.411 24.936 -0.518 -1.222 -1.507 HC3 PA5 19
PA5 HO3 HO3 H 0 1 N N N N N N 52.145 -13.158 26.281 -0.958 1.589 -1.606 HO3 PA5 20
PA5 HC4 HC4 H 0 1 N N N N N N 50.187 -11.744 23.465 1.054 1.150 -0.407 HC4 PA5 21
PA5 HO4 HO4 H 0 1 N N N N N N 48.766 -13.145 24.933 1.494 -1.660 -0.308 HO4 PA5 22
PA5 H51 H51 H 0 1 N N N N N N 51.098 -13.793 22.313 -0.949 0.580 0.936 H51 PA5 23
PA5 H52 H52 H 0 1 N N N N N N 50.879 -14.725 23.720 -0.431 -1.121 0.987 H52 PA5 24
PA5 HOP2 2HOP H 0 0 N N N N N N 49.248 -14.779 19.443 0.138 0.116 5.451 HOP2 PA5 25
PA5 HOP3 3HOP H 0 0 N N N N N N 49.932 -16.810 20.702 -1.087 1.851 3.314 HOP3 PA5 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
PA5 O1A C1 DOUB N N 1
PA5 C1 O1 SING N N 2
PA5 C1 C2 SING N N 3
PA5 O1 HO1 SING N N 4
PA5 C2 O2 SING N N 5
PA5 C2 C3 SING N N 6
PA5 C2 HC2 SING N N 7
PA5 O2 HO2 SING N N 8
PA5 C3 O3 SING N N 9
PA5 C3 C4 SING N N 10
PA5 C3 HC3 SING N N 11
PA5 O3 HO3 SING N N 12
PA5 C4 O4 SING N N 13
PA5 C4 C5 SING N N 14
PA5 C4 HC4 SING N N 15
PA5 O4 HO4 SING N N 16
PA5 C5 O5 SING N N 17
PA5 C5 H51 SING N N 18
PA5 C5 H52 SING N N 19
PA5 O5 P SING N N 20
PA5 P O1P DOUB N N 21
PA5 P O2P SING N N 22
PA5 P O3P SING N N 23
PA5 O2P HOP2 SING N N 24
PA5 O3P HOP3 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
PA5 SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)C(=O)O
PA5 SMILES_CANONICAL CACTVS 3.341 O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)C(O)=O
PA5 SMILES CACTVS 3.341 O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)C(O)=O
PA5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H]([C@H]([C@@H](C(=O)O)O)O)O)OP(=O)(O)O
PA5 SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(C(=O)O)O)O)O)OP(=O)(O)O
PA5 InChI InChI 1.03 InChI=1S/C5H11O9P/c6-2(1-14-15(11,12)13)3(7)4(8)5(9)10/h2-4,6-8H,1H2,(H,9,10)(H2,11,12,13)/t2-,3-,4+/m1/s1
PA5 InChIKey InChI 1.03 HNECGPFIYSOYHF-JJYYJPOSSA-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
PA5 "SYSTEMATIC NAME" ACDLabs 10.04 "5-O-phosphono-D-arabinonic acid"
PA5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R,4R)-2,3,4-trihydroxy-5-phosphonooxy-pentanoic 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
PA5 'Create component' 2000-03-08 RCSB
PA5 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id PA5
_pdbe_chem_comp_drugbank_details.drugbank_id DB03042
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '5-Phosphoarabinonic Acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
PA5 DB03042 'Glucose-6-phosphate isomerase B' 'Geobacillus stearothermophilus' P13376 unknown 1
PA5 DB03042 'Glucose-6-phosphate isomerase' Humans P06744 unknown 2
#
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
PA5 O1A O 14.198 0.375 1
PA5 C1 C 12.899 -0.375 2
PA5 O1 O 12.899 -1.875 3
PA5 C2 C 11.600 0.375 4
PA5 O2 O 11.600 1.875 5
PA5 C3 C 10.301 -0.375 6
PA5 O3 O 10.301 -1.875 7
PA5 C4 C 9.002 0.375 8
PA5 O4 O 9.002 1.875 9
PA5 C5 C 7.702 -0.375 10
PA5 O5 O 6.404 0.375 11
PA5 P P 5.104 -0.375 12
PA5 O1P O 3.805 -1.125 13
PA5 O2P O 4.354 0.924 14
PA5 O3P O 5.854 -1.674 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
PA5 O1A C1 DOUBLE NONE 1
PA5 C1 O1 SINGLE NONE 2
PA5 C1 C2 SINGLE NONE 3
PA5 C2 O2 SINGLE BEGINDASH 4
PA5 C2 C3 SINGLE NONE 5
PA5 C3 O3 SINGLE BEGINDASH 6
PA5 C3 C4 SINGLE NONE 7
PA5 C4 O4 SINGLE BEGINWEDGE 8
PA5 C4 C5 SINGLE NONE 9
PA5 C5 O5 SINGLE NONE 10
PA5 O5 P SINGLE NONE 11
PA5 P O1P DOUBLE NONE 12
PA5 P O2P SINGLE NONE 13
PA5 P O3P SINGLE NONE 14
#
_pdbe_chem_comp_substructure.comp_id PA5
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys 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
PA5 O5 F1 1
PA5 P F1 1
PA5 O1P F1 1
PA5 O2P F1 1
PA5 O3P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PA5
_pdbe_chem_comp_rdkit_properties.exactmw 246.014
_pdbe_chem_comp_rdkit_properties.amw 246.108
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 99.764
_pdbe_chem_comp_rdkit_properties.tpsa 164.750
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.737
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.652
_pdbe_chem_comp_rdkit_properties.chi0v 7.516
_pdbe_chem_comp_rdkit_properties.chi1v 4.416
_pdbe_chem_comp_rdkit_properties.chi2v 1.163
_pdbe_chem_comp_rdkit_properties.chi3v 1.163
_pdbe_chem_comp_rdkit_properties.chi4v 0.534
_pdbe_chem_comp_rdkit_properties.chi0n 17.621
_pdbe_chem_comp_rdkit_properties.chi1n 7.905
_pdbe_chem_comp_rdkit_properties.chi2n 0.848
_pdbe_chem_comp_rdkit_properties.chi3n 0.848
_pdbe_chem_comp_rdkit_properties.chi4n 0.340
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.540
_pdbe_chem_comp_rdkit_properties.kappa1 4.379
_pdbe_chem_comp_rdkit_properties.kappa2 5.518
_pdbe_chem_comp_rdkit_properties.kappa3 5.799
_pdbe_chem_comp_rdkit_properties.Phi 1.611
#
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
PA5 UniChem DrugBank DB03042
PA5 UniChem PDBe PA5
PA5 UniChem SureChEMBL SCHEMBL4330442
PA5 UniChem PubChem 191445
PA5 UniChem ACTor 57287-61-3
PA5 UniChem BRENDA 66846
PA5 UniChem 'Probes And Drugs' PD059872
PA5 UniChem Nikkaji J1.223.929G
#
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
PA5 O1A -4.083 -0.779 -0.574 ETKDGv3 1
PA5 C1 -3.315 -0.907 0.418 ETKDGv3 2
PA5 O1 -3.843 -1.233 1.663 ETKDGv3 3
PA5 C2 -1.828 -0.715 0.261 ETKDGv3 4
PA5 O2 -1.284 -1.716 -0.566 ETKDGv3 5
PA5 C3 -1.488 0.715 -0.243 ETKDGv3 6
PA5 O3 -1.831 0.895 -1.597 ETKDGv3 7
PA5 C4 -0.031 1.174 0.059 ETKDGv3 8
PA5 O4 0.170 2.464 -0.460 ETKDGv3 9
PA5 C5 1.061 0.242 -0.491 ETKDGv3 10
PA5 O5 2.324 0.782 -0.176 ETKDGv3 11
PA5 P 3.528 -0.245 -0.815 ETKDGv3 12
PA5 O1P 3.449 -0.260 -2.325 ETKDGv3 13
PA5 O2P 5.048 0.332 -0.347 ETKDGv3 14
PA5 O3P 3.332 -1.820 -0.225 ETKDGv3 15
PA5 HO1 -4.839 -1.367 1.786 ETKDGv3 16
PA5 HC2 -1.375 -0.835 1.270 ETKDGv3 17
PA5 HO2 -1.800 -1.738 -1.413 ETKDGv3 18
PA5 HC3 -2.134 1.413 0.337 ETKDGv3 19
PA5 HO3 -1.209 0.359 -2.149 ETKDGv3 20
PA5 HC4 0.098 1.203 1.167 ETKDGv3 21
PA5 HO4 -0.308 3.095 0.139 ETKDGv3 22
PA5 H51 0.945 0.148 -1.593 ETKDGv3 23
PA5 H52 0.952 -0.755 -0.011 ETKDGv3 24
PA5 HOP2 5.063 1.275 -0.647 ETKDGv3 25
PA5 HOP3 3.400 -1.729 0.759 ETKDGv3 26
#