data_3SY
#
_chem_comp.id 3SY
_chem_comp.name 2,2-bis(hydroxymethyl)propane-1,3-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H12 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-10-22
_chem_comp.pdbx_modified_date 2014-11-14
_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 136.146
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3SY
_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 4RMF
_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
3SY O7 O7 O 0 1 N N N N N N -39.601 -23.984 0.632 -2.416 0.000 0.058 O7 3SY 1
3SY C3 C3 C 0 1 N N N N N N -38.616 -23.646 -0.356 -1.249 0.000 0.883 C3 3SY 2
3SY C1 C1 C 0 1 N N N N N N -39.031 -22.392 -1.125 0.000 0.000 -0.000 C1 3SY 3
3SY C2 C2 C 0 1 N N N N N N -40.308 -22.686 -1.886 1.249 -0.000 0.883 C2 3SY 4
3SY O6 O6 O 0 1 N N N N N N -40.733 -21.460 -2.492 2.416 -0.000 0.058 O6 3SY 5
3SY C4 C4 C 0 1 N N N N N N -39.244 -21.185 -0.201 -0.000 -1.249 -0.883 C4 3SY 6
3SY O8 O8 O 0 1 N N N N N N -40.229 -21.404 0.824 -0.000 -2.416 -0.058 O8 3SY 7
3SY C5 C5 C 0 1 N N N N N N -37.949 -22.088 -2.153 0.000 1.249 -0.883 C5 3SY 8
3SY O9 O9 O 0 1 N N N N N N -36.996 -21.145 -1.655 0.000 2.416 -0.058 O9 3SY 9
3SY H1 H1 H 0 1 N N N N N N -39.327 -24.764 1.099 -3.247 0.000 0.553 H1 3SY 10
3SY H2 H2 H 0 1 N N N N N N -38.510 -24.483 -1.061 -1.249 0.890 1.513 H2 3SY 11
3SY H3 H3 H 0 1 N N N N N N -37.653 -23.462 0.142 -1.249 -0.890 1.513 H3 3SY 12
3SY H4 H4 H 0 1 N N N N N N -41.082 -23.053 -1.196 1.249 0.890 1.513 H4 3SY 13
3SY H5 H5 H 0 1 N N N N N N -40.119 -23.443 -2.661 1.249 -0.890 1.513 H5 3SY 14
3SY H6 H6 H 0 1 N N N N N N -41.535 -21.608 -2.979 3.247 -0.000 0.553 H6 3SY 15
3SY H7 H7 H 0 1 N N N N N N -38.286 -20.947 0.284 -0.890 -1.249 -1.513 H7 3SY 16
3SY H8 H8 H 0 1 N N N N N N -39.567 -20.331 -0.815 0.890 -1.249 -1.513 H8 3SY 17
3SY H9 H9 H 0 1 N N N N N N -40.311 -20.622 1.357 -0.000 -3.247 -0.553 H9 3SY 18
3SY H10 H10 H 0 1 N N N N N N -38.421 -21.674 -3.056 0.890 1.249 -1.513 H10 3SY 19
3SY H11 H11 H 0 1 N N N N N N -37.427 -23.022 -2.408 -0.890 1.249 -1.513 H11 3SY 20
3SY H12 H12 H 0 1 N N N N N N -36.338 -20.979 -2.319 0.000 3.247 -0.553 H12 3SY 21
#
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
3SY O6 C2 SING N N 1
3SY C5 O9 SING N N 2
3SY C5 C1 SING N N 3
3SY C2 C1 SING N N 4
3SY C1 C3 SING N N 5
3SY C1 C4 SING N N 6
3SY C3 O7 SING N N 7
3SY C4 O8 SING N N 8
3SY O7 H1 SING N N 9
3SY C3 H2 SING N N 10
3SY C3 H3 SING N N 11
3SY C2 H4 SING N N 12
3SY C2 H5 SING N N 13
3SY O6 H6 SING N N 14
3SY C4 H7 SING N N 15
3SY C4 H8 SING N N 16
3SY O8 H9 SING N N 17
3SY C5 H10 SING N N 18
3SY C5 H11 SING N N 19
3SY O9 H12 SING N N 20
#
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
3SY SMILES ACDLabs 12.01 OCC(CO)(CO)CO
3SY InChI InChI 1.03 InChI=1S/C5H12O4/c6-1-5(2-7,3-8)4-9/h6-9H,1-4H2
3SY InChIKey InChI 1.03 WXZMFSXDPGVJKK-UHFFFAOYSA-N
3SY SMILES_CANONICAL CACTVS 3.385 OCC(CO)(CO)CO
3SY SMILES CACTVS 3.385 OCC(CO)(CO)CO
3SY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C(C(CO)(CO)CO)O
3SY SMILES "OpenEye OEToolkits" 1.7.6 C(C(CO)(CO)CO)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
3SY "SYSTEMATIC NAME" ACDLabs 12.01 2,2-bis(hydroxymethyl)propane-1,3-diol
3SY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 2,2-bis(hydroxymethyl)propane-1,3-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3SY 'Create component' 2014-10-22 RCSB
3SY 'Initial release' 2014-11-19 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id 3SY
_pdbe_chem_comp_drugbank_details.drugbank_id DB13526
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Pentaerithrityl
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 115-77-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
3SY Pentaerithrityl DrugBank ?
3SY Pentaerythritol DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 3SY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB13526
_pdbe_chem_comp_drugbank_classification.parent 'Primary alcohols'
_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 primary alcohols. These are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).'
#
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
3SY O7 O 6.404 -2.598 1
3SY C3 C 7.154 -1.299 2
3SY C1 C 6.404 0.000 3
3SY C2 C 5.104 -0.750 4
3SY O6 O 3.805 0.000 5
3SY C4 C 5.654 1.299 6
3SY O8 O 6.404 2.598 7
3SY C5 C 7.702 0.750 8
3SY O9 O 9.002 0.000 9
#
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
3SY O6 C2 SINGLE NONE 1
3SY C5 O9 SINGLE NONE 2
3SY C5 C1 SINGLE NONE 3
3SY C2 C1 SINGLE NONE 4
3SY C1 C3 SINGLE NONE 5
3SY C1 C4 SINGLE NONE 6
3SY C3 O7 SINGLE NONE 7
3SY C4 O8 SINGLE NONE 8
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 3SY
_pdbe_chem_comp_rdkit_properties.exactmw 136.074
_pdbe_chem_comp_rdkit_properties.amw 136.147
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 70.582
_pdbe_chem_comp_rdkit_properties.tpsa 80.920
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.058
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.776
_pdbe_chem_comp_rdkit_properties.chi0v 4.133
_pdbe_chem_comp_rdkit_properties.chi1v 1.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.612
_pdbe_chem_comp_rdkit_properties.chi3v 0.612
_pdbe_chem_comp_rdkit_properties.chi4v 0.125
_pdbe_chem_comp_rdkit_properties.chi0n 16.133
_pdbe_chem_comp_rdkit_properties.chi1n 7.449
_pdbe_chem_comp_rdkit_properties.chi2n 0.612
_pdbe_chem_comp_rdkit_properties.chi3n 0.612
_pdbe_chem_comp_rdkit_properties.chi4n 0.125
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.380
_pdbe_chem_comp_rdkit_properties.kappa2 3.788
_pdbe_chem_comp_rdkit_properties.kappa3 1.907
_pdbe_chem_comp_rdkit_properties.Phi 0.581
#
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
3SY UniChem DrugBank DB13526
3SY UniChem ChEBI 134760
3SY UniChem ZINC ZINC000000391843
3SY UniChem eMolecules 490697
3SY UniChem fdasrs SU420W1S6N
3SY UniChem HMDB HMDB0062269
3SY UniChem 'PubChem TPHARMA' 14867291
3SY UniChem NMRShiftDB 10005615
3SY UniChem Nikkaji J5.273F
3SY UniChem 'EPA CompTox Dashboard' DTXSID2026943
3SY UniChem DrugCentral 2085
3SY UniChem ChemicalBook CB7852888
3SY UniChem rxnorm PENTAERYTHRITOL
3SY UniChem 'Probes And Drugs' PD073552
3SY UniChem CCDC PERYTO
3SY UniChem SureChEMBL SCHEMBL15049
3SY UniChem PubChem 8285
3SY UniChem Mcule MCULE-7635228253
3SY UniChem ACTor 115-77-5
#
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
3SY O7 1.911 0.591 1.239 ETKDGv3 1
3SY C3 1.111 -0.532 0.985 ETKDGv3 2
3SY C1 -0.036 -0.211 -0.015 ETKDGv3 3
3SY C2 -0.839 -1.524 -0.231 ETKDGv3 4
3SY O6 -1.887 -1.348 -1.151 ETKDGv3 5
3SY C4 0.542 0.246 -1.385 ETKDGv3 6
3SY O8 1.301 1.418 -1.260 ETKDGv3 7
3SY C5 -0.992 0.866 0.573 ETKDGv3 8
3SY O9 -0.314 2.061 0.852 ETKDGv3 9
3SY H1 2.607 0.296 1.881 ETKDGv3 10
3SY H2 0.678 -0.894 1.945 ETKDGv3 11
3SY H3 1.750 -1.346 0.571 ETKDGv3 12
3SY H4 -1.232 -1.906 0.741 ETKDGv3 13
3SY H5 -0.166 -2.314 -0.630 ETKDGv3 14
3SY H6 -2.704 -1.142 -0.626 ETKDGv3 15
3SY H7 -0.290 0.430 -2.102 ETKDGv3 16
3SY H8 1.183 -0.562 -1.806 ETKDGv3 17
3SY H9 1.634 1.630 -2.171 ETKDGv3 18
3SY H10 -1.454 0.481 1.511 ETKDGv3 19
3SY H11 -1.811 1.079 -0.150 ETKDGv3 20
3SY H12 -0.991 2.682 1.228 ETKDGv3 21
#