data_911
#
_chem_comp.id 911
_chem_comp.name "(1-hydroxyethane-1,1-diyl)bis(phosphonic acid)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C2 H8 O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Etidronic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-06-10
_chem_comp.pdbx_modified_date 2020-06-17
_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 206.028
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 911
_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 3SDV
_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
911 P1 P1 P 0 1 N N N N N N 105.801 28.759 47.649 -1.489 -0.227 -0.034 P1 911 1
911 O2 O2 O 0 1 N N N N N N 105.491 28.065 46.287 -1.456 -1.098 -1.230 O2 911 2
911 O3 O3 O 0 1 N N N N N N 105.447 27.755 48.787 -2.803 0.703 -0.083 O3 911 3
911 O5 O5 O 0 1 N N N N N N 107.233 29.203 47.744 -1.525 -1.138 1.293 O5 911 4
911 C7 C7 C 0 1 N N N N N N 104.659 30.167 47.855 -0.001 0.826 -0.008 C7 911 5
911 P8 P8 P 0 1 N N N N N N 105.121 31.094 49.357 1.487 -0.227 0.048 P8 911 6
911 O9 O9 O 0 1 N N N N N N 106.575 31.498 49.372 1.396 -1.149 1.202 O9 911 7
911 O10 O10 O 0 1 N N N N N N 104.179 32.330 49.437 1.592 -1.079 -1.314 O10 911 8
911 O12 O12 O 0 1 N N N N N N 104.774 30.136 50.540 2.794 0.700 0.203 O12 911 9
911 O14 O14 O 0 1 N N N N N N 103.393 29.669 48.058 0.031 1.634 -1.185 O14 911 10
911 C16 C16 C 0 1 N N N N N N 104.687 31.049 46.648 -0.034 1.726 1.229 C16 911 11
911 HO3 HO3 H 0 1 N N N N N N 105.123 26.947 48.407 -3.634 0.208 -0.098 HO3 911 12
911 HO5 HO5 H 0 1 N N N N N N 107.690 28.974 46.943 -1.548 -0.632 2.117 HO5 911 13
911 HO10 HO10 H 0 0 N N N N N N 104.700 33.123 49.481 1.655 -0.539 -2.113 HO10 911 14
911 HO12 HO12 H 0 0 N N N N N N 105.553 29.980 51.061 3.625 0.206 0.239 HO12 911 15
911 HO14 HO14 H 0 0 N N N N N N 102.783 30.389 48.168 0.054 1.129 -2.009 HO14 911 16
911 H16 H16 H 0 1 N N N N N N 103.993 31.890 46.792 -0.059 1.109 2.127 H16 911 17
911 H16A H16A H 0 0 N N N N N N 105.706 31.436 46.500 0.855 2.355 1.244 H16A 911 18
911 H16B H16B H 0 0 N N N N N N 104.383 30.470 45.764 -0.924 2.355 1.196 H16B 911 19
#
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
911 O2 P1 DOUB N N 1
911 P1 O5 SING N N 2
911 P1 C7 SING N N 3
911 P1 O3 SING N N 4
911 O3 HO3 SING N N 5
911 O5 HO5 SING N N 6
911 C16 C7 SING N N 7
911 C7 O14 SING N N 8
911 C7 P8 SING N N 9
911 P8 O9 DOUB N N 10
911 P8 O10 SING N N 11
911 P8 O12 SING N N 12
911 O10 HO10 SING N N 13
911 O12 HO12 SING N N 14
911 O14 HO14 SING N N 15
911 C16 H16 SING N N 16
911 C16 H16A SING N N 17
911 C16 H16B SING N N 18
#
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
911 SMILES ACDLabs 12.01 O=P(O)(O)C(O)(C)P(=O)(O)O
911 InChI InChI 1.03 InChI=1S/C2H8O7P2/c1-2(3,10(4,5)6)11(7,8)9/h3H,1H3,(H2,4,5,6)(H2,7,8,9)
911 InChIKey InChI 1.03 DBVJJBKOTRCVKF-UHFFFAOYSA-N
911 SMILES_CANONICAL CACTVS 3.370 CC(O)([P](O)(O)=O)[P](O)(O)=O
911 SMILES CACTVS 3.370 CC(O)([P](O)(O)=O)[P](O)(O)=O
911 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 CC(O)(P(=O)(O)O)P(=O)(O)O
911 SMILES "OpenEye OEToolkits" 1.7.2 CC(O)(P(=O)(O)O)P(=O)(O)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
911 "SYSTEMATIC NAME" ACDLabs 12.01 "(1-hydroxyethane-1,1-diyl)bis(phosphonic acid)"
911 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(1-oxidanyl-1-phosphono-ethyl)phosphonic 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
911 'Create component' 2011-06-10 RCSB
911 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 911
_pdbx_chem_comp_synonyms.name "Etidronic acid"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id 911
_pdbe_chem_comp_drugbank_details.drugbank_id DB01077
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Etidronic acid'
_pdbe_chem_comp_drugbank_details.description
'Etidronic acid is a first generation bisphosphonate similar to [clodronic acid] and [tiludronic acid].[A203111] These drugs were developed to mimic the action of pyrophosphate, a regulator of calcification and decalcification.[A1923] Etidronate’s use has decreased over the years in favor of the third generation, nitrogen containing bisphosphonate [zoledronic acid], [ibandronic acid], [minodronic acid], and [risedronic acid].[A203111]  Etidronic acid was granted FDA approval on 1 September 1977.[L13901]'
_pdbe_chem_comp_drugbank_details.cas_number 2809-21-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Bisphosphonates are taken into the bone where they bind to hydroxyapatite. Bone resorption by osteoclasts causes local acidification, releasing the bisphosphonate, which is taken into the osteoclast by fluid-phase endocytosis.[A959] Endocytic vesicles become acidified, releasing bisphosphonates into the cytosol of osteoclasts where they act.[A959]  Osteoclasts mediate resorption of bone.[A6366] When osteoclasts bind to bone they form podosomes, ring structures of F-actin.[A6366] Disruption of the podosomes causes osteoclasts to detach from bones, preventing bone resorption.[A6366]  First generation bisphosphonates closely mimic the structure of pyrophosphate, which can be incorporated into ATP anologues that cannot be hydrolyzed, disrupting all ATP mediated actions of osteoclasts.[A203360]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
911 'Etidronic acid' wwPDB ?
911 '(1-hydroxy-ethylidene)diphosphonic acid' DrugBank ?
911 '(1-Hydroxyethylene)diphosphonic acid' DrugBank ?
911 '(1-Hydroxyethylidene)bis(phosphonic acid)' DrugBank ?
911 '(1-Hydroxyethylidene)bisphosphonic acid' DrugBank ?
911 '(1-Hydroxyethylidene)diphosphonic acid' DrugBank ?
911 '(Hydroxyethylidene)diphosphonic acid' DrugBank ?
911 1-Hydroxy-1,1-diphosphonoethane DrugBank ?
911 '1-hydroxyethane 1,1-diphosphonic acid' DrugBank ?
911 '1-Hydroxyethane-1,1-bisphosphonic acid' DrugBank ?
911 1-Hydroxyethane-1,1-diphosphonate DrugBank ?
911 '1-Hydroxyethane-1,1-diphosphonic acid' DrugBank ?
911 '1-Hydroxyethanediphosphonic acid' DrugBank ?
911 1-Hydroxyethylidene-1,1-bisphosphonate DrugBank ?
911 '1-Hydroxyethylidene-1,1-diphosphonic acid' DrugBank ?
911 '1,1,1-Ethanetriol diphosphonate' DrugBank ?
911 'Acetodiphosphonic acid' DrugBank ?
911 'acidum etidronicum' DrugBank ?
911 EHDP DrugBank ?
911 'Ethane-1-hydroxy-1,1-bisphosphonic acid' DrugBank ?
911 Ethane-1-hydroxy-1,1-diphosphonate DrugBank ?
911 'Ethane-1-hydroxy-1,1-diphosphonic acid' DrugBank ?
911 Etidronate DrugBank ?
911 'Etidronic acid' DrugBank ?
911 HEDP DrugBank ?
911 'Hydroxyethanediphosphonic acid' DrugBank ?
911 'Oxyethylidenediphosphonic acid' DrugBank ?
911 Etidron DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id 911
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01077
_pdbe_chem_comp_drugbank_classification.parent Bisphosphonates
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organic phosphonic 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 bisphosphonates. These are organic compounds containing two phosphonate groups linked together through a carbon atoms.'
#
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
911 DB01077 'Receptor-type tyrosine-protein phosphatase S' Humans Q13332 yes 1
911 DB01077 'V-type proton ATPase catalytic subunit A' Humans P38606 unknown 2
911 DB01077 'ADP/ATP translocase 1' Humans P12235 unknown 3
911 DB01077 'ADP/ATP translocase 2' Humans P05141 unknown 4
911 DB01077 'ADP/ATP translocase 3' Humans P12236 unknown 5
#
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
911 P1 P 7.278 0.750 1
911 O2 O 8.577 1.500 2
911 O3 O 7.018 2.227 3
911 O5 O 8.028 -0.549 4
911 C7 C 5.979 0.000 5
911 P8 P 4.680 -0.750 6
911 O9 O 3.381 -1.500 7
911 O10 O 3.930 0.549 8
911 O12 O 5.430 -2.049 9
911 O14 O 6.729 -1.299 10
911 C16 C 5.229 1.299 11
#
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
911 O2 P1 DOUBLE NONE 1
911 P1 O5 SINGLE NONE 2
911 P1 C7 SINGLE NONE 3
911 P1 O3 SINGLE NONE 4
911 C16 C7 SINGLE NONE 5
911 C7 O14 SINGLE NONE 6
911 C7 P8 SINGLE NONE 7
911 P8 O9 DOUBLE NONE 8
911 P8 O10 SINGLE NONE 9
911 P8 O12 SINGLE NONE 10
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 911
_pdbe_chem_comp_rdkit_properties.exactmw 205.975
_pdbe_chem_comp_rdkit_properties.amw 206.027
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 73.674
_pdbe_chem_comp_rdkit_properties.tpsa 135.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.992
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.712
_pdbe_chem_comp_rdkit_properties.chi0v 6.541
_pdbe_chem_comp_rdkit_properties.chi1v 5.082
_pdbe_chem_comp_rdkit_properties.chi2v 3.697
_pdbe_chem_comp_rdkit_properties.chi3v 3.697
_pdbe_chem_comp_rdkit_properties.chi4v 1.350
_pdbe_chem_comp_rdkit_properties.chi0n 12.752
_pdbe_chem_comp_rdkit_properties.chi1n 5.538
_pdbe_chem_comp_rdkit_properties.chi2n 0.742
_pdbe_chem_comp_rdkit_properties.chi3n 0.742
_pdbe_chem_comp_rdkit_properties.chi4n 0.150
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.260
_pdbe_chem_comp_rdkit_properties.kappa1 3.555
_pdbe_chem_comp_rdkit_properties.kappa2 2.639
_pdbe_chem_comp_rdkit_properties.kappa3 2.099
_pdbe_chem_comp_rdkit_properties.Phi 0.853
#
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
911 UniChem DrugBank DB01077
911 UniChem 'Guide to Pharmacology' 7184
911 UniChem 'KEGG LIGAND' C07736
911 UniChem ChEBI 4907
911 UniChem ZINC ZINC000003830813
911 UniChem eMolecules 519300
911 UniChem fdasrs M2F465ROXU
911 UniChem SureChEMBL SCHEMBL18607
911 UniChem PharmGKB PA449548
911 UniChem HMDB HMDB0015210
911 UniChem Selleck etidronate-didronel
911 UniChem LINCS LSM-5508
911 UniChem ACTor 100511-44-2
911 UniChem ACTor 2809-21-4
911 UniChem BindingDb 50115102
911 UniChem 'EPA CompTox Dashboard' DTXSID6023028
911 UniChem DrugCentral 1098
911 UniChem BRENDA 5338
911 UniChem ChemicalBook CB4719658
911 UniChem ClinicalTrials DIDRONEL
911 UniChem ClinicalTrials 'ETIDRONATE DISODIUM'
911 UniChem ClinicalTrials 'ETIDRONIC ACID'
911 UniChem rxnorm ETIDRONATE
911 UniChem rxnorm 'ETIDRONATE DISODIUM'
911 UniChem rxnorm 'ETIDRONIC ACID'
911 UniChem MedChemExpress HY-B0302
911 UniChem 'Probes And Drugs' PD009821
911 UniChem CCDC ETHDPH
911 UniChem Nikkaji J7.915D
911 UniChem 'PubChem TPHARMA' 14797598
911 UniChem PubChem 3305
911 UniChem Mcule MCULE-3037955142
#
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
911 P1 -1.524 -0.119 0.016 ETKDGv3 1
911 O2 -1.750 -1.062 1.177 ETKDGv3 2
911 O3 -2.535 1.228 0.188 ETKDGv3 3
911 O5 -1.891 -0.911 -1.434 ETKDGv3 4
911 C7 0.223 0.434 -0.012 ETKDGv3 5
911 P8 1.317 -1.021 -0.183 ETKDGv3 6
911 O9 1.109 -1.966 0.979 ETKDGv3 7
911 O10 0.970 -1.827 -1.630 ETKDGv3 8
911 O12 2.932 -0.514 -0.201 ETKDGv3 9
911 O14 0.436 1.272 -1.119 ETKDGv3 10
911 C16 0.562 1.178 1.287 ETKDGv3 11
911 HO3 -3.454 0.859 0.184 ETKDGv3 12
911 HO5 -2.840 -1.180 -1.344 ETKDGv3 13
911 HO10 1.644 -2.550 -1.684 ETKDGv3 14
911 HO12 3.021 0.016 -1.033 ETKDGv3 15
911 HO14 -0.166 2.056 -1.026 ETKDGv3 16
911 H16 -0.101 2.059 1.415 ETKDGv3 17
911 H16A 1.613 1.536 1.261 ETKDGv3 18
911 H16B 0.435 0.512 2.167 ETKDGv3 19
#