data_RBL
#
_chem_comp.id RBL
_chem_comp.name D-ribulose
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C5 H10 O5'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-01-26
_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 150.130
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RBL
_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 2ZYD
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
_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
RBL C1 C2 C 0 1 N N N N N N -2.912 26.664 40.559 2.050 0.842 0.484 C2 RBL 1
RBL C2 C3 C 0 1 N N N N N N -2.044 27.561 39.692 1.307 -0.380 0.011 C3 RBL 2
RBL C3 C5 C 0 1 N N R N N N -1.065 26.940 38.723 -0.078 -0.669 0.532 C5 RBL 3
RBL O3 O13 O 0 1 N N N N N N 0.216 27.570 38.857 -0.384 -2.050 0.331 O13 RBL 4
RBL C4 C6 C 0 1 N N R N N N -1.535 27.087 37.267 -1.095 0.193 -0.218 C6 RBL 5
RBL O4 O14 O 0 1 N N N N N N -2.944 27.348 37.162 -0.789 1.575 -0.017 O14 RBL 6
RBL C5 C7 C 0 1 N N N N N N -1.185 25.815 36.506 -2.500 -0.100 0.310 C7 RBL 7
RBL O5 O8 O 0 1 N N N N N N -1.347 26.050 35.110 -3.461 0.618 -0.467 O8 RBL 8
RBL O2 O4 O 0 1 N N N N N N -2.121 28.772 39.786 1.821 -1.128 -0.786 O4 RBL 9
RBL O1 O1 O 0 1 N N N N N N -3.838 27.438 41.333 3.331 0.896 -0.148 O1 RBL 10
RBL H11 H2 H 0 1 N N N N N N -3.475 25.976 39.911 1.481 1.736 0.228 H2 RBL 11
RBL H12 H2A H 0 1 N N N N N N -2.261 26.104 41.247 2.181 0.793 1.565 H2A RBL 12
RBL H3 H5 H 0 1 N N N N N N -0.997 25.869 38.964 -0.121 -0.438 1.596 H5 RBL 13
RBL HO3 HO13 H 0 0 N N N N N N 0.592 27.709 37.996 -0.364 -2.326 -0.596 HO13 RBL 14
RBL H4 H6 H 0 1 N N N N N N -1.019 27.956 36.833 -1.052 -0.037 -1.283 H6 RBL 15
RBL HO4 HO14 H 0 0 N N N N N N -3.322 27.406 38.032 -0.808 1.851 0.909 HO14 RBL 16
RBL H51 H7 H 0 1 N N N N N N -0.142 25.535 36.715 -2.700 -1.169 0.238 H7 RBL 17
RBL H52 H7A H 0 1 N N N N N N -1.848 24.997 36.824 -2.569 0.214 1.352 H7A RBL 18
RBL HO5 HO8 H 0 1 N N N N N N -1.383 26.985 34.948 -4.376 0.479 -0.188 HO8 RBL 19
RBL HO1 HO1 H 0 1 N N N N N N -3.468 27.609 42.191 3.865 1.659 0.111 HO1 RBL 20
#
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
RBL C1 C2 SING N N 1
RBL C1 O1 SING N N 2
RBL C2 C3 SING N N 3
RBL C2 O2 DOUB N N 4
RBL C3 O3 SING N N 5
RBL C3 C4 SING N N 6
RBL C4 O4 SING N N 7
RBL C4 C5 SING N N 8
RBL C5 O5 SING N N 9
RBL C1 H11 SING N N 10
RBL C1 H12 SING N N 11
RBL C3 H3 SING N N 12
RBL O3 HO3 SING N N 13
RBL C4 H4 SING N N 14
RBL O4 HO4 SING N N 15
RBL C5 H51 SING N N 16
RBL C5 H52 SING N N 17
RBL O5 HO5 SING N N 18
RBL O1 HO1 SING N N 19
#
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
RBL SMILES ACDLabs 10.04 'O=C(CO)C(O)C(O)CO'
RBL SMILES_CANONICAL CACTVS 3.341 'OC[C@@H](O)[C@@H](O)C(=O)CO'
RBL SMILES CACTVS 3.341 'OC[CH](O)[CH](O)C(=O)CO'
RBL SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@H]([C@H](C(=O)CO)O)O)O'
RBL SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(C(=O)CO)O)O)O'
RBL InChI InChI 1.03 'InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1'
RBL InChIKey InChI 1.03 ZAQJHHRNXZUBTE-NQXXGFSBSA-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
RBL 'SYSTEMATIC NAME' ACDLabs 10.04 D-ribulose
RBL 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(3R,4R)-1,3,4,5-tetrahydroxypentan-2-one'
#
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
RBL 'CARBOHYDRATE ISOMER' D PDB ?
RBL 'CARBOHYDRATE PRIMARY CARBONYL GROUP' ketose 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
RBL 'Create component' 2009-01-26 PDBJ
RBL 'Modify descriptor' 2011-06-04 RCSB
RBL 'Initial release' 2013-11-27 RCSB
RBL 'Modify atom id' 2020-06-24 RCSB
RBL 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id RBL
_pdbx_chem_comp_pcm.modified_residue_id GLU
_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 C3
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
RBL C1 C 5.104 -0.375 1
RBL C2 C 6.404 0.375 2
RBL C3 C 7.702 -0.375 3
RBL O3 O 7.702 -1.875 4
RBL C4 C 9.002 0.375 5
RBL O4 O 9.002 1.875 6
RBL C5 C 10.301 -0.375 7
RBL O5 O 11.600 0.375 8
RBL O2 O 6.404 1.875 9
RBL O1 O 3.805 0.375 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
RBL C1 C2 SINGLE NONE 1
RBL C1 O1 SINGLE NONE 2
RBL C2 C3 SINGLE NONE 3
RBL C2 O2 DOUBLE NONE 4
RBL C3 O3 SINGLE BEGINWEDGE 5
RBL C3 C4 SINGLE NONE 6
RBL C4 O4 SINGLE BEGINDASH 7
RBL C4 C5 SINGLE NONE 8
RBL C5 O5 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id RBL
_pdbe_chem_comp_rdkit_properties.exactmw 150.053
_pdbe_chem_comp_rdkit_properties.amw 150.130
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 71.934
_pdbe_chem_comp_rdkit_properties.tpsa 97.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.738
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.192
_pdbe_chem_comp_rdkit_properties.chi0v 4.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.598
_pdbe_chem_comp_rdkit_properties.chi3v 0.598
_pdbe_chem_comp_rdkit_properties.chi4v 0.196
_pdbe_chem_comp_rdkit_properties.chi0n 14.541
_pdbe_chem_comp_rdkit_properties.chi1n 6.654
_pdbe_chem_comp_rdkit_properties.chi2n 0.598
_pdbe_chem_comp_rdkit_properties.chi3n 0.598
_pdbe_chem_comp_rdkit_properties.chi4n 0.196
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.490
_pdbe_chem_comp_rdkit_properties.kappa1 2.010
_pdbe_chem_comp_rdkit_properties.kappa2 4.345
_pdbe_chem_comp_rdkit_properties.kappa3 2.402
_pdbe_chem_comp_rdkit_properties.Phi 0.873
#
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
RBL UniChem ChEMBL CHEMBL195989
RBL UniChem ChEBI CHEBI:17173
RBL UniChem BRENDA 922
RBL UniChem BRENDA 44771
RBL UniChem BRENDA 182543
RBL UniChem BRENDA 182542
RBL UniChem BRENDA 182541
RBL UniChem BRENDA 182540
RBL UniChem BRENDA 182539
RBL UniChem BRENDA 182538
RBL UniChem BRENDA 182537
RBL UniChem BRENDA 182536
RBL UniChem MolPort Molport-004-780-313
RBL UniChem SureChEMBL 31338625
RBL UniChem SureChEMBL 44299
RBL UniChem 'EPA CompTox Dashboard' DTXSID30204115
RBL UniChem fdasrs Z7U4KG0138
RBL UniChem fdasrs DJM6K5T6YA
RBL UniChem PubChem 151261
RBL UniChem 'Probes And Drugs' PD017009
#
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
RBL C1 2.441 -0.953 -0.300 ETKDGv3 1
RBL C2 1.403 -0.329 0.592 ETKDGv3 2
RBL C3 0.266 0.489 0.021 ETKDGv3 3
RBL O3 0.280 1.768 0.602 ETKDGv3 4
RBL C4 -1.087 -0.196 0.299 ETKDGv3 5
RBL O4 -1.070 -1.492 -0.245 ETKDGv3 6
RBL C5 -2.246 0.601 -0.318 ETKDGv3 7
RBL O5 -3.465 -0.018 -0.011 ETKDGv3 8
RBL O2 1.487 -0.485 1.802 ETKDGv3 9
RBL O1 3.704 -0.413 -0.023 ETKDGv3 10
RBL H11 2.192 -0.812 -1.376 ETKDGv3 11
RBL H12 2.468 -2.046 -0.108 ETKDGv3 12
RBL H3 0.384 0.585 -1.084 ETKDGv3 13
RBL HO3 1.036 2.262 0.190 ETKDGv3 14
RBL H4 -1.238 -0.244 1.405 ETKDGv3 15
RBL HO4 -1.728 -2.031 0.267 ETKDGv3 16
RBL H51 -2.251 1.637 0.088 ETKDGv3 17
RBL H52 -2.120 0.649 -1.424 ETKDGv3 18
RBL HO5 -4.170 0.530 -0.444 ETKDGv3 19
RBL HO1 3.715 0.497 -0.419 ETKDGv3 20
#