data_S3P
#
_chem_comp.id S3P
_chem_comp.name SHIKIMATE-3-PHOSPHATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H11 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-11-16
_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 254.131
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S3P
_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 1G6T
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
S3P C1 C1 C 0 1 N N N N N N 56.434 12.394 28.141 -0.284 0.031 2.050 C1 S3P 1
S3P C2 C2 C 0 1 N N N N N N 55.310 11.556 28.296 -0.683 -0.029 0.797 C2 S3P 2
S3P C3 C3 C 0 1 N N R N N N 55.351 10.296 29.102 0.251 -0.029 -0.376 C3 S3P 3
S3P C4 C4 C 0 1 N N S N N N 56.563 10.256 30.038 1.638 0.470 0.048 C4 S3P 4
S3P C5 C5 C 0 1 N N R N N N 57.844 10.617 29.272 2.062 -0.299 1.304 C5 S3P 5
S3P C6 C6 C 0 1 N N N N N N 57.688 12.080 28.779 1.156 0.117 2.464 C6 S3P 6
S3P C7 C7 C 0 1 N N N N N N 56.298 13.628 27.298 -1.307 0.014 3.104 C7 S3P 7
S3P O1 O1 O 0 1 N N N N N N 55.273 9.120 28.166 -0.266 0.829 -1.394 O1 S3P 8
S3P O2 O2 O 0 1 N N N N N N 56.620 8.972 30.618 1.577 1.868 0.335 O2 S3P 9
S3P O3 O3 O 0 1 N N N N N N 58.963 10.503 30.126 1.933 -1.703 1.074 O3 S3P 10
S3P O4 O4 O 0 1 N N N N N N 55.394 13.630 26.439 -0.941 0.074 4.400 O4 S3P 11
S3P O5 O5 O 0 1 N N N N N N 57.077 14.574 27.497 -2.484 -0.053 2.808 O5 S3P 12
S3P P1 P1 P 0 1 N N N N N N 53.891 8.107 27.871 -0.494 -0.082 -2.701 P1 S3P 13
S3P O6 O6 O 0 1 N N N N N N 52.883 8.963 27.253 -1.454 -1.163 -2.388 O6 S3P 14
S3P O7 O7 O 0 1 N N N N N N 53.519 7.654 29.241 -1.080 0.826 -3.894 O7 S3P 15
S3P O8 O8 O 0 1 N N N N N N 54.399 7.085 26.918 0.909 -0.726 -3.157 O8 S3P 16
S3P H2 H2 H 0 1 N N N N N N 54.391 11.888 27.783 -1.744 -0.082 0.603 H2 S3P 17
S3P H3 H3 H 0 1 N N N N N N 54.469 10.253 29.782 0.338 -1.042 -0.769 H3 S3P 18
S3P H4 H4 H 0 1 N N N N N N 56.465 11.012 30.851 2.353 0.291 -0.754 H4 S3P 19
S3P H5 H5 H 0 1 N N N N N N 58.000 9.928 28.409 3.098 -0.062 1.546 H5 S3P 20
S3P H61 1H6 H 0 1 N N N N N N 58.535 12.346 28.104 1.327 -0.544 3.313 H61 S3P 21
S3P H62 2H6 H 0 1 N N N N N N 57.874 12.787 29.620 1.388 1.142 2.754 H62 S3P 22
S3P HO2 HO2 H 0 1 N N N N N N 57.371 8.947 31.198 2.468 2.138 0.597 HO2 S3P 23
S3P HO3 HO3 H 0 1 N N N N N N 59.755 10.726 29.652 2.203 -2.147 1.890 HO3 S3P 24
S3P HO4 HO4 H 0 1 N N N N N N 55.307 14.411 25.905 -1.615 0.063 5.094 HO4 S3P 25
S3P HO7 HO7 H 0 1 N N N N N N 52.763 7.100 29.079 -1.201 0.243 -4.656 HO7 S3P 26
S3P HO8 HO8 H 0 1 N N N N N N 53.643 6.531 26.756 1.504 0.009 -3.352 HO8 S3P 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
S3P C1 C2 DOUB N N 1
S3P C1 C6 SING N N 2
S3P C1 C7 SING N N 3
S3P C2 C3 SING N N 4
S3P C2 H2 SING N N 5
S3P C3 C4 SING N N 6
S3P C3 O1 SING N N 7
S3P C3 H3 SING N N 8
S3P C4 C5 SING N N 9
S3P C4 O2 SING N N 10
S3P C4 H4 SING N N 11
S3P C5 C6 SING N N 12
S3P C5 O3 SING N N 13
S3P C5 H5 SING N N 14
S3P C6 H61 SING N N 15
S3P C6 H62 SING N N 16
S3P C7 O4 SING N N 17
S3P C7 O5 DOUB N N 18
S3P O1 P1 SING N N 19
S3P O2 HO2 SING N N 20
S3P O3 HO3 SING N N 21
S3P O4 HO4 SING N N 22
S3P P1 O6 DOUB N N 23
S3P P1 O7 SING N N 24
S3P P1 O8 SING N N 25
S3P O7 HO7 SING N N 26
S3P O8 HO8 SING N N 27
#
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
S3P SMILES ACDLabs 10.04 O=C(O)C1=CC(OP(=O)(O)O)C(O)C(O)C1
S3P SMILES_CANONICAL CACTVS 3.341 O[C@@H]1CC(=C[C@@H](O[P](O)(O)=O)[C@H]1O)C(O)=O
S3P SMILES CACTVS 3.341 O[CH]1CC(=C[CH](O[P](O)(O)=O)[CH]1O)C(O)=O
S3P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)OP(=O)(O)O)O)O
S3P SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(C(C=C1C(=O)O)OP(=O)(O)O)O)O
S3P InChI InChI 1.03 InChI=1S/C7H11O8P/c8-4-1-3(7(10)11)2-5(6(4)9)15-16(12,13)14/h2,4-6,8-9H,1H2,(H,10,11)(H2,12,13,14)/t4-,5-,6+/m1/s1
S3P InChIKey InChI 1.03 QYOJSKGCWNAKGW-PBXRRBTRSA-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
S3P "SYSTEMATIC NAME" ACDLabs 10.04 "(3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid"
S3P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(3R,4S,5R)-4,5-dihydroxy-3-phosphonooxy-cyclohexene-1-carboxylic 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
S3P 'Create component' 2000-11-16 PDBJ
S3P 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id S3P
_pdbe_chem_comp_drugbank_details.drugbank_id DB04328
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Shikimate-3-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 S3P
_pdbe_chem_comp_synonyms.name Shikimate-3-Phosphate
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id S3P
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04328
_pdbe_chem_comp_drugbank_classification.parent 'Monoalkyl phosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organic phosphoric acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.'
#
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
S3P DB04328 '3-phosphoshikimate 1-carboxyvinyltransferase' 'Escherichia coli (strain K12)' P0A6D3 unknown 1
S3P DB04328 '3-phosphoshikimate 1-carboxyvinyltransferase' 'Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)' Q9S400 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
S3P C1 C 7.702 -1.732 1
S3P C2 C 7.702 -0.233 2
S3P C3 C 6.404 0.517 3
S3P C4 C 5.104 -0.233 4
S3P C5 C 5.104 -1.732 5
S3P C6 C 6.404 -2.482 6
S3P C7 C 9.002 -2.482 7
S3P O1 O 6.404 2.018 8
S3P O2 O 3.805 0.517 9
S3P O3 O 3.805 -2.482 10
S3P O4 O 9.002 -3.982 11
S3P O5 O 10.301 -1.732 12
S3P P1 P 7.702 2.768 13
S3P O6 O 9.002 3.518 14
S3P O7 O 6.952 4.066 15
S3P O8 O 8.453 1.468 16
#
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
S3P C1 C2 DOUBLE NONE 1
S3P C1 C6 SINGLE NONE 2
S3P C1 C7 SINGLE NONE 3
S3P C2 C3 SINGLE NONE 4
S3P C3 C4 SINGLE NONE 5
S3P C3 O1 SINGLE BEGINDASH 6
S3P C4 C5 SINGLE NONE 7
S3P C4 O2 SINGLE BEGINDASH 8
S3P C5 C6 SINGLE NONE 9
S3P C5 O3 SINGLE BEGINWEDGE 10
S3P C7 O4 SINGLE NONE 11
S3P C7 O5 DOUBLE NONE 12
S3P O1 P1 SINGLE NONE 13
S3P P1 O6 DOUBLE NONE 14
S3P P1 O7 SINGLE NONE 15
S3P P1 O8 SINGLE NONE 16
#
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
S3P MurckoScaffold S1 scaffold C1=CCCCC1 InChI=1S/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2 HGCIXCUEYOPUTN-UHFFFAOYSA-N
S3P phosphate F1 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
S3P C1 S1 1
S3P C2 S1 1
S3P C3 S1 1
S3P C4 S1 1
S3P C5 S1 1
S3P C6 S1 1
S3P O1 F1 1
S3P P1 F1 1
S3P O6 F1 1
S3P O7 F1 1
S3P O8 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S3P
_pdbe_chem_comp_rdkit_properties.exactmw 254.019
_pdbe_chem_comp_rdkit_properties.amw 254.131
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_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 0.571
_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 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 105.917
_pdbe_chem_comp_rdkit_properties.tpsa 144.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.399
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.267
_pdbe_chem_comp_rdkit_properties.chi0v 8.108
_pdbe_chem_comp_rdkit_properties.chi1v 4.962
_pdbe_chem_comp_rdkit_properties.chi2v 1.703
_pdbe_chem_comp_rdkit_properties.chi3v 1.703
_pdbe_chem_comp_rdkit_properties.chi4v 1.105
_pdbe_chem_comp_rdkit_properties.chi0n 18.213
_pdbe_chem_comp_rdkit_properties.chi1n 8.542
_pdbe_chem_comp_rdkit_properties.chi2n 1.297
_pdbe_chem_comp_rdkit_properties.chi3n 1.297
_pdbe_chem_comp_rdkit_properties.chi4n 0.753
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.760
_pdbe_chem_comp_rdkit_properties.kappa1 4.488
_pdbe_chem_comp_rdkit_properties.kappa2 4.622
_pdbe_chem_comp_rdkit_properties.kappa3 3.376
_pdbe_chem_comp_rdkit_properties.Phi 1.296
#
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
S3P UniChem DrugBank DB04328
S3P UniChem 'KEGG LIGAND' C03175
S3P UniChem ChEBI 17052
S3P UniChem ZINC ZINC000003870237
S3P UniChem eMolecules 5750013
S3P UniChem HMDB HMDB0301781
S3P UniChem NMRShiftDB 60023381
S3P UniChem ACTor 63959-45-5
S3P UniChem BindingDb 100283
S3P UniChem MetaboLights MTBLC17052
S3P UniChem BRENDA 1318
S3P UniChem BRENDA 2096
S3P UniChem 'Probes And Drugs' PD059318
S3P UniChem Nikkaji J746.034A
S3P UniChem SureChEMBL SCHEMBL67425
S3P UniChem 'PubChem TPHARMA' 16120783
S3P UniChem PubChem 121947
#
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
S3P C1 -1.859 0.318 0.209 ETKDGv3 1
S3P C2 -0.657 0.920 0.306 ETKDGv3 2
S3P C3 0.648 0.255 -0.058 ETKDGv3 3
S3P C4 0.546 -1.289 -0.046 ETKDGv3 4
S3P C5 -0.732 -1.764 -0.756 ETKDGv3 5
S3P C6 -1.984 -1.162 -0.094 ETKDGv3 6
S3P C7 -3.091 1.080 0.524 ETKDGv3 7
S3P O1 1.633 0.676 0.869 ETKDGv3 8
S3P O2 0.626 -1.817 1.258 ETKDGv3 9
S3P O3 -0.679 -1.395 -2.111 ETKDGv3 10
S3P O4 -3.031 2.441 0.815 ETKDGv3 11
S3P O5 -4.210 0.498 0.532 ETKDGv3 12
S3P P1 3.086 1.063 0.057 ETKDGv3 13
S3P O6 2.887 2.308 -0.778 ETKDGv3 14
S3P O7 3.565 -0.218 -0.940 ETKDGv3 15
S3P O8 4.296 1.351 1.204 ETKDGv3 16
S3P H2 -0.604 1.974 0.552 ETKDGv3 17
S3P H3 0.855 0.581 -1.105 ETKDGv3 18
S3P H4 1.412 -1.694 -0.613 ETKDGv3 19
S3P H5 -0.783 -2.876 -0.678 ETKDGv3 20
S3P H61 -2.186 -1.698 0.858 ETKDGv3 21
S3P H62 -2.859 -1.337 -0.757 ETKDGv3 22
S3P HO2 -0.023 -1.333 1.831 ETKDGv3 23
S3P HO3 -1.338 -1.961 -2.591 ETKDGv3 24
S3P HO4 -3.870 2.965 1.031 ETKDGv3 25
S3P HO7 4.436 0.067 -1.316 ETKDGv3 26
S3P HO8 3.919 2.046 1.800 ETKDGv3 27
#