data_A5P
#
_chem_comp.id A5P
_chem_comp.name ARABINOSE-5-PHOSPHATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C5 H13 O8 P'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-10-06
_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 232.126
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A5P
_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 1FY6
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
A5P C1 C1 C 0 1 N N N N N N 35.633 51.745 18.964 0.469 -0.647 4.232 C1 A5P 1
A5P O1 O1 O 0 1 N N N N N N 35.601 51.172 17.889 -0.107 -0.273 5.485 O1 A5P 2
A5P C2 C2 C 0 1 N N R N N N 34.931 53.085 19.110 -0.329 -0.011 3.093 C2 A5P 3
A5P O2 O2 O 0 1 N N N N N N 34.038 53.017 20.223 -0.298 1.411 3.226 O2 A5P 4
A5P C3 C3 C 0 1 N N S N N N 36.077 54.092 18.982 0.288 -0.411 1.752 C3 A5P 5
A5P O3 O3 O 0 1 N N N N N N 35.949 55.048 20.035 1.642 0.043 1.696 O3 A5P 6
A5P C4 C4 C 0 1 N N R N N N 36.105 54.641 17.549 -0.510 0.225 0.612 C4 A5P 7
A5P O4 O4 O 0 1 N N N N N N 35.886 53.796 16.417 -1.863 -0.229 0.668 O4 A5P 8
A5P C5 C5 C 0 1 N N N N N N 37.544 55.148 17.439 0.107 -0.174 -0.728 C5 A5P 9
A5P O5 O5 O 0 1 N N N N N N 38.343 55.072 16.258 -0.638 0.419 -1.792 O5 A5P 10
A5P P P P 0 1 N N N N N N 39.530 55.854 15.526 0.062 -0.041 -3.166 P A5P 11
A5P O1P O1P O 0 1 N N N N N N 40.785 55.466 16.215 0.033 -1.517 -3.265 O1P A5P 12
A5P O2P O2P O 0 1 N N N N N N 39.464 55.398 14.117 -0.731 0.595 -4.414 O2P A5P 13
A5P O3P O3P O 0 1 N N N N N N 39.240 57.307 15.652 1.589 0.467 -3.186 O3P A5P 14
A5P H11 H11 H 0 1 N N N N N N 35.250 51.052 19.750 1.502 -0.300 4.190 H11 A5P 15
A5P H12 H12 H 0 1 N N N N N N 36.697 51.862 19.275 0.446 -1.732 4.131 H12 A5P 16
A5P HO1 HO1 H 0 1 N N N N N N 36.039 50.334 17.797 0.425 -0.694 6.174 HO1 A5P 17
A5P HC2 HC2 H 0 1 N N N N N N 34.189 53.428 18.351 -1.361 -0.358 3.135 HC2 A5P 18
A5P HO2 HO2 H 0 1 N N N N N N 33.599 53.854 20.314 0.630 1.676 3.184 HO2 A5P 19
A5P HC3 HC3 H 0 1 N N N N N N 37.085 53.637 19.120 0.265 -1.496 1.650 HC3 A5P 20
A5P HO3 HO3 H 0 1 N N N N N N 36.660 55.672 19.955 1.617 1.005 1.789 HO3 A5P 21
A5P HC4 HC4 H 0 1 N N N N N N 35.237 55.337 17.470 -0.487 1.310 0.714 HC4 A5P 22
A5P HO4 HO4 H 0 1 N N N N N N 35.903 54.135 15.530 -1.839 -1.192 0.575 HO4 A5P 23
A5P H51 H51 H 0 1 N N N N N N 37.535 56.217 17.755 1.139 0.172 -0.771 H51 A5P 24
A5P H52 H52 H 0 1 N N N N N N 38.123 54.654 18.253 0.084 -1.259 -0.830 H52 A5P 25
A5P HOP2 2HOP H 0 0 N N N N N N 40.169 55.862 13.682 -0.279 0.296 -5.215 HOP2 A5P 26
A5P HOP3 3HOP H 0 0 N N N N N N 39.945 57.771 15.217 1.564 1.432 -3.120 HOP3 A5P 27
#
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
A5P C1 O1 SING N N 1
A5P C1 C2 SING N N 2
A5P C1 H11 SING N N 3
A5P C1 H12 SING N N 4
A5P O1 HO1 SING N N 5
A5P C2 O2 SING N N 6
A5P C2 C3 SING N N 7
A5P C2 HC2 SING N N 8
A5P O2 HO2 SING N N 9
A5P C3 O3 SING N N 10
A5P C3 C4 SING N N 11
A5P C3 HC3 SING N N 12
A5P O3 HO3 SING N N 13
A5P C4 O4 SING N N 14
A5P C4 C5 SING N N 15
A5P C4 HC4 SING N N 16
A5P O4 HO4 SING N N 17
A5P C5 O5 SING N N 18
A5P C5 H51 SING N N 19
A5P C5 H52 SING N N 20
A5P O5 P SING N N 21
A5P P O1P DOUB N N 22
A5P P O2P SING N N 23
A5P P O3P SING N N 24
A5P O2P HOP2 SING N N 25
A5P O3P HOP3 SING N N 26
#
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
A5P SMILES ACDLabs 10.04 'O=P(O)(O)OCC(O)C(O)C(O)CO'
A5P SMILES_CANONICAL CACTVS 3.341 'OC[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O'
A5P SMILES CACTVS 3.341 'OC[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O'
A5P SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O'
A5P SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(C(COP(=O)(O)O)O)O)O)O'
A5P InChI InChI 1.03 'InChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1'
A5P InChIKey InChI 1.03 VJDOAZKNBQCAGE-WDCZJNDASA-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
A5P 'SYSTEMATIC NAME' ACDLabs 10.04 5-O-phosphono-D-arabinitol
A5P 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '[(2R,3S,4R)-2,3,4,5-tetrahydroxypentyl] dihydrogen phosphate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A5P 'Create component' 2000-10-06 RCSB
A5P 'Modify descriptor' 2011-06-04 RCSB
A5P 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id A5P
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_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 C1
_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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id A5P
_pdbe_chem_comp_drugbank_details.drugbank_id DB03745
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Arabinose-5-phosphate
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id A5P
_pdbe_chem_comp_synonyms.name Arabinose-5-phosphate
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id A5P
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03745
_pdbe_chem_comp_drugbank_classification.parent 'Monosaccharide phosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.'
#
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
A5P DB03745 '2-dehydro-3-deoxyphosphooctonate aldolase' 'Aquifex aeolicus (strain VF5)' O66496 unknown 1
A5P DB03745 'Ribose-5-phosphate isomerase A' 'Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)' Q5SIR5 unknown 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
A5P C1 C 5.104 -0.375 1
A5P O1 O 3.805 0.375 2
A5P C2 C 6.404 0.375 3
A5P O2 O 6.404 1.875 4
A5P C3 C 7.702 -0.375 5
A5P O3 O 7.702 -1.875 6
A5P C4 C 9.002 0.375 7
A5P O4 O 9.002 1.875 8
A5P C5 C 10.301 -0.375 9
A5P O5 O 11.600 0.375 10
A5P P P 12.899 -0.375 11
A5P O1P O 14.198 -1.125 12
A5P O2P O 13.649 0.924 13
A5P O3P O 12.149 -1.674 14
#
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
A5P C1 O1 SINGLE NONE 1
A5P C1 C2 SINGLE NONE 2
A5P C2 O2 SINGLE BEGINWEDGE 3
A5P C2 C3 SINGLE NONE 4
A5P C3 O3 SINGLE BEGINWEDGE 5
A5P C3 C4 SINGLE NONE 6
A5P C4 O4 SINGLE BEGINDASH 7
A5P C4 C5 SINGLE NONE 8
A5P C5 O5 SINGLE NONE 9
A5P O5 P SINGLE NONE 10
A5P P O1P DOUBLE NONE 11
A5P P O2P SINGLE NONE 12
A5P P O3P SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id A5P
_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
A5P O5 F1 1
A5P P F1 1
A5P O1P F1 1
A5P O2P F1 1
A5P O3P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id A5P
_pdbe_chem_comp_rdkit_properties.exactmw 232.035
_pdbe_chem_comp_rdkit_properties.amw 232.125
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_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 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 98.412
_pdbe_chem_comp_rdkit_properties.tpsa 147.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.829
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.102
_pdbe_chem_comp_rdkit_properties.chi0v 7.108
_pdbe_chem_comp_rdkit_properties.chi1v 4.212
_pdbe_chem_comp_rdkit_properties.chi2v 1.070
_pdbe_chem_comp_rdkit_properties.chi3v 1.070
_pdbe_chem_comp_rdkit_properties.chi4v 0.488
_pdbe_chem_comp_rdkit_properties.chi0n 19.213
_pdbe_chem_comp_rdkit_properties.chi1n 8.700
_pdbe_chem_comp_rdkit_properties.chi2n 0.755
_pdbe_chem_comp_rdkit_properties.chi3n 0.755
_pdbe_chem_comp_rdkit_properties.chi4n 0.293
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.050
_pdbe_chem_comp_rdkit_properties.kappa1 3.474
_pdbe_chem_comp_rdkit_properties.kappa2 5.740
_pdbe_chem_comp_rdkit_properties.kappa3 5.632
_pdbe_chem_comp_rdkit_properties.Phi 1.424
#
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
A5P UniChem BRENDA 51764
A5P UniChem BRENDA 17019
A5P UniChem BRENDA 137757
A5P UniChem SureChEMBL 2766970
A5P UniChem PubChem 5287584
A5P UniChem 'Probes And Drugs' PD040888
A5P UniChem DrugBank DB03745
#
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
A5P C1 -3.510 0.208 -0.283 ETKDGv3 1
A5P O1 -3.412 0.863 -1.518 ETKDGv3 2
A5P C2 -2.353 -0.784 -0.100 ETKDGv3 3
A5P O2 -2.341 -1.683 -1.181 ETKDGv3 4
A5P C3 -0.988 -0.060 0.021 ETKDGv3 5
A5P O3 -0.675 0.545 -1.210 ETKDGv3 6
A5P C4 0.148 -1.037 0.429 ETKDGv3 7
A5P O4 -0.182 -1.721 1.613 ETKDGv3 8
A5P C5 1.501 -0.323 0.605 ETKDGv3 9
A5P O5 2.006 0.061 -0.653 ETKDGv3 10
A5P P 3.415 0.991 -0.415 ETKDGv3 11
A5P O1P 3.057 2.312 0.230 ETKDGv3 12
A5P O2P 4.126 1.290 -1.921 ETKDGv3 13
A5P O3P 4.523 0.156 0.558 ETKDGv3 14
A5P H11 -4.472 -0.350 -0.237 ETKDGv3 15
A5P H12 -3.502 0.953 0.544 ETKDGv3 16
A5P HO1 -4.182 1.488 -1.560 ETKDGv3 17
A5P HC2 -2.561 -1.331 0.851 ETKDGv3 18
A5P HO2 -2.009 -2.552 -0.835 ETKDGv3 19
A5P HC3 -1.085 0.713 0.822 ETKDGv3 20
A5P HO3 -0.287 1.437 -1.012 ETKDGv3 21
A5P HC4 0.271 -1.798 -0.373 ETKDGv3 22
A5P HO4 -0.287 -1.042 2.331 ETKDGv3 23
A5P H51 2.206 -1.037 1.087 ETKDGv3 24
A5P H52 1.357 0.556 1.276 ETKDGv3 25
A5P HOP2 4.968 1.768 -1.712 ETKDGv3 26
A5P HOP3 4.267 0.374 1.490 ETKDGv3 27
#