data_RIS # _chem_comp.id RIS _chem_comp.name "1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H11 N O7 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Risedronate _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-12-17 _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 283.112 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RIS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1RQJ _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 RIS O12 O12 O 0 1 N N N N N N 57.820 74.304 11.572 -1.782 -2.872 -0.640 O12 RIS 1 RIS P9 P9 P 0 1 N N N N N N 58.623 73.691 10.433 -1.283 -2.401 0.824 P9 RIS 2 RIS O11 O11 O 0 1 N N N N N N 58.329 74.511 8.992 -2.061 -1.273 1.433 O11 RIS 3 RIS O10 O10 O 0 1 N N N N N N 58.206 72.094 10.263 -1.285 -3.772 1.679 O10 RIS 4 RIS C8 C8 C 0 1 N N N N N N 60.334 73.798 10.791 0.512 -2.044 0.553 C8 RIS 5 RIS O13 O13 O 0 1 N N N N N N 61.051 73.167 9.710 0.908 -1.644 1.865 O13 RIS 6 RIS P14 P14 P 0 1 N N N N N N 60.832 75.467 10.955 1.682 -3.382 0.138 P14 RIS 7 RIS O16 O16 O 0 1 N N N N N N 60.487 76.175 9.664 1.135 -3.926 -1.283 O16 RIS 8 RIS O15 O15 O 0 1 N N N N N N 60.014 76.127 12.259 1.286 -4.570 1.160 O15 RIS 9 RIS O17 O17 O 0 1 N N N N N N 62.473 75.654 11.235 3.132 -3.001 0.163 O17 RIS 10 RIS C7 C7 C 0 1 N N N N N N 60.517 73.036 12.110 0.597 -0.828 -0.405 C7 RIS 11 RIS C2 C2 C 0 1 Y N N N N N 61.916 72.843 12.658 1.950 -0.183 -0.567 C2 RIS 12 RIS C1 C1 C 0 1 Y N N N N N 62.030 72.693 14.038 2.334 0.848 0.266 C1 RIS 13 RIS C6 C6 C 0 1 Y N N N N N 63.284 72.496 14.614 3.588 1.424 0.092 C6 RIS 14 RIS C5 C5 C 0 1 Y N N N N N 64.396 72.454 13.790 4.395 0.928 -0.919 C5 RIS 15 RIS N4 N4 N 0 1 Y N N N N N 64.272 72.597 12.461 4.038 -0.081 -1.745 N4 RIS 16 RIS C3 C3 C 0 1 Y N N N N N 63.073 72.787 11.887 2.813 -0.615 -1.546 C3 RIS 17 RIS H12 H12 H 0 1 N N N N N N 57.986 73.841 12.385 -2.731 -3.086 -0.772 H12 RIS 18 RIS H13 H13 H 0 1 N N N N N N 61.979 73.225 9.904 1.870 -1.501 1.860 H13 RIS 19 RIS H16 H16 H 0 1 N N N N N N 60.757 77.081 9.753 1.629 -4.641 -1.739 H16 RIS 20 RIS H15 H15 H 0 1 N N N N N N 60.284 77.033 12.348 1.806 -5.401 1.146 H15 RIS 21 RIS HC71 1HC7 H 0 0 N N N N N N 60.026 72.039 12.020 0.235 -1.139 -1.393 HC71 RIS 22 RIS HC72 2HC7 H 0 0 N N N N N N 59.888 73.519 12.894 -0.100 -0.048 -0.070 HC72 RIS 23 RIS HC1 HC1 H 0 1 N N N N N N 61.129 72.730 14.673 1.679 1.216 1.051 HC1 RIS 24 RIS HC6 HC6 H 0 1 N N N N N N 63.395 72.375 15.705 3.923 2.236 0.728 HC6 RIS 25 RIS HC5 HC5 H 0 1 N N N N N N 65.407 72.303 14.203 5.381 1.343 -1.096 HC5 RIS 26 RIS HC3 HC3 H 0 1 N N N N N N 63.039 72.896 10.790 2.553 -1.422 -2.225 HC3 RIS 27 RIS HO1 HO1 H 0 1 N N N N N N 58.126 71.884 9.340 -2.142 -4.148 1.971 HO1 RIS 28 # 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 RIS O12 P9 SING N N 1 RIS O12 H12 SING N N 2 RIS P9 O11 DOUB N N 3 RIS P9 O10 SING N N 4 RIS P9 C8 SING N N 5 RIS C8 O13 SING N N 6 RIS C8 P14 SING N N 7 RIS C8 C7 SING N N 8 RIS O13 H13 SING N N 9 RIS P14 O16 SING N N 10 RIS P14 O15 SING N N 11 RIS P14 O17 DOUB N N 12 RIS O16 H16 SING N N 13 RIS O15 H15 SING N N 14 RIS C7 C2 SING N N 15 RIS C7 HC71 SING N N 16 RIS C7 HC72 SING N N 17 RIS C2 C1 DOUB Y N 18 RIS C2 C3 SING Y N 19 RIS C1 C6 SING Y N 20 RIS C1 HC1 SING N N 21 RIS C6 C5 DOUB Y N 22 RIS C6 HC6 SING N N 23 RIS C5 N4 SING Y N 24 RIS C5 HC5 SING N N 25 RIS N4 C3 DOUB Y N 26 RIS C3 HC3 SING N N 27 RIS HO1 O10 SING N N 28 # 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 RIS SMILES ACDLabs 10.04 O=P(O)(O)C(O)(P(=O)(O)O)Cc1cccnc1 RIS SMILES_CANONICAL CACTVS 3.341 OC(Cc1cccnc1)([P](O)(O)=O)[P](O)(O)=O RIS SMILES CACTVS 3.341 OC(Cc1cccnc1)([P](O)(O)=O)[P](O)(O)=O RIS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(cnc1)CC(O)(P(=O)(O)O)P(=O)(O)O RIS SMILES "OpenEye OEToolkits" 1.5.0 c1cc(cnc1)CC(O)(P(=O)(O)O)P(=O)(O)O RIS InChI InChI 1.03 InChI=1S/C7H11NO7P2/c9-7(16(10,11)12,17(13,14)15)4-6-2-1-3-8-5-6/h1-3,5,9H,4H2,(H2,10,11,12)(H2,13,14,15) RIS InChIKey InChI 1.03 IIDJRNMFWXDHID-UHFFFAOYSA-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 RIS "SYSTEMATIC NAME" ACDLabs 10.04 "(1-hydroxy-2-pyridin-3-ylethane-1,1-diyl)bis(phosphonic acid)" RIS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1-hydroxy-1-phosphono-2-pyridin-3-yl-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 RIS 'Create component' 2003-12-17 RCSB RIS 'Modify descriptor' 2011-06-04 RCSB RIS 'Modify synonyms' 2017-09-22 RCSB RIS 'Modify synonyms' 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RIS _pdbx_chem_comp_synonyms.name Risedronate _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbe_chem_comp_drugbank_details.comp_id RIS _pdbe_chem_comp_drugbank_details.drugbank_id DB00884 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name 'Risedronic acid' _pdbe_chem_comp_drugbank_details.description "Risedronic acid is a third generation bisphosphonate that is used for the treatment of some forms of osteoperosis and Paget's disease[FDA Label][A959,A203111]. It functions by preventing resorption of bone[FDA Label][A959]." _pdbe_chem_comp_drugbank_details.cas_number 105462-24-6 _pdbe_chem_comp_drugbank_details.mechanism_of_action 'Risedronatic acid binds to bone hydroxyapatite[FDA Label]. Bone resorption causes local acidification, releasing risedronic acid which is that taken into osteoclasts by fluid-phase endocytosis[A959]. Endocytic vesicles are acidified, releasing risedronic acid to the cytosol of osteoclasts where they induce apoptosis through inhbition of farnesyl pyrophosphate synthase[A959]. Inhibition of osteoclasts results in decreased bone resorption[A959].' # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type RIS Risedronate wwPDB ? RIS 'Acidum risedronicum' DrugBank ? RIS Risedronate DrugBank ? RIS 'Risedronic acid' DrugBank ? RIS Benet DrugBank 'International brand' RIS Ridron DrugBank 'International brand' # _pdbe_chem_comp_drugbank_classification.comp_id RIS _pdbe_chem_comp_drugbank_classification.drugbank_id DB00884 _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.' # _pdbe_chem_comp_drugbank_targets.comp_id RIS _pdbe_chem_comp_drugbank_targets.drugbank_id DB00884 _pdbe_chem_comp_drugbank_targets.name 'Farnesyl pyrophosphate synthase' _pdbe_chem_comp_drugbank_targets.organism Humans _pdbe_chem_comp_drugbank_targets.uniprot_id P14324 _pdbe_chem_comp_drugbank_targets.pharmacologically_active yes _pdbe_chem_comp_drugbank_targets.ordinal 1 # 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 RIS O12 O 8.453 2.771 1 RIS P9 P 7.154 2.021 2 RIS O11 O 7.904 0.722 3 RIS O10 O 7.414 3.498 4 RIS C8 C 5.854 1.271 5 RIS O13 O 6.604 -0.028 6 RIS P14 P 5.104 2.570 7 RIS O16 O 4.354 3.869 8 RIS O15 O 3.805 1.820 9 RIS O17 O 5.617 3.979 10 RIS C7 C 4.555 0.521 11 RIS C2 C 4.555 -0.979 12 RIS C1 C 3.256 -1.729 13 RIS C6 C 3.256 -3.229 14 RIS C5 C 4.555 -3.979 15 RIS N4 N 5.854 -3.229 16 RIS C3 C 5.854 -1.729 17 # 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 RIS O12 P9 SINGLE NONE 1 RIS P9 O11 DOUBLE NONE 2 RIS P9 O10 SINGLE NONE 3 RIS P9 C8 SINGLE NONE 4 RIS C8 O13 SINGLE NONE 5 RIS C8 P14 SINGLE NONE 6 RIS C8 C7 SINGLE NONE 7 RIS P14 O16 SINGLE NONE 8 RIS P14 O15 SINGLE NONE 9 RIS P14 O17 DOUBLE NONE 10 RIS C7 C2 SINGLE NONE 11 RIS C2 C1 DOUBLE NONE 12 RIS C2 C3 SINGLE NONE 13 RIS C1 C6 SINGLE NONE 14 RIS C6 C5 DOUBLE NONE 15 RIS C5 N4 SINGLE NONE 16 RIS N4 C3 DOUBLE NONE 17 # 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 RIS MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N RIS pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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 RIS C2 S1 1 RIS C1 S1 1 RIS C6 S1 1 RIS C5 S1 1 RIS N4 S1 1 RIS C3 S1 1 RIS C5 F1 1 RIS C6 F1 1 RIS C1 F1 1 RIS C2 F1 1 RIS C3 F1 1 RIS N4 F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id RIS _pdbe_chem_comp_rdkit_properties.exactmw 283.001 _pdbe_chem_comp_rdkit_properties.amw 283.113 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 8 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 8 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17 _pdbe_chem_comp_rdkit_properties.NumAtoms 28 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.286 _pdbe_chem_comp_rdkit_properties.NumRings 1 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1 _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 112.166 _pdbe_chem_comp_rdkit_properties.tpsa 148.180 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.429 _pdbe_chem_comp_rdkit_properties.CrippenMR 56.713 _pdbe_chem_comp_rdkit_properties.chi0v 9.488 _pdbe_chem_comp_rdkit_properties.chi1v 6.779 _pdbe_chem_comp_rdkit_properties.chi2v 4.675 _pdbe_chem_comp_rdkit_properties.chi3v 4.675 _pdbe_chem_comp_rdkit_properties.chi4v 2.437 _pdbe_chem_comp_rdkit_properties.chi0n 18.699 _pdbe_chem_comp_rdkit_properties.chi1n 8.735 _pdbe_chem_comp_rdkit_properties.chi2n 1.497 _pdbe_chem_comp_rdkit_properties.chi3n 1.497 _pdbe_chem_comp_rdkit_properties.chi4n 0.739 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.590 _pdbe_chem_comp_rdkit_properties.kappa1 5.187 _pdbe_chem_comp_rdkit_properties.kappa2 4.588 _pdbe_chem_comp_rdkit_properties.kappa3 2.997 _pdbe_chem_comp_rdkit_properties.Phi 1.400 # 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 RIS UniChem DrugBank DB00884 RIS UniChem 'Guide to Pharmacology' 3176 RIS UniChem 'KEGG LIGAND' C08233 RIS UniChem ChEBI 8869 RIS UniChem ZINC ZINC000001531009 RIS UniChem eMolecules 902400 RIS UniChem atlas risedronate RIS UniChem fdasrs KM2Z91756Z RIS UniChem SureChEMBL SCHEMBL18378 RIS UniChem PharmGKB PA451255 RIS UniChem HMDB HMDB0015022 RIS UniChem Selleck risedronic-acid-actonel RIS UniChem ACTor 105462-24-6 RIS UniChem 'EPA CompTox Dashboard' DTXSID2023563 RIS UniChem DrugCentral 2387 RIS UniChem BRENDA 125151 RIS UniChem BRENDA 212816 RIS UniChem BRENDA 252914 RIS UniChem BRENDA 3722 RIS UniChem BRENDA 42323 RIS UniChem BRENDA 88566 RIS UniChem ChemicalBook CB1118762 RIS UniChem DailyMed 'RISEDRONIC ACID' RIS UniChem ClinicalTrials 'RISEDRONATE SODIUM' RIS UniChem ClinicalTrials 'RISEDRONIC ACID' RIS UniChem rxnorm ACTONEL RIS UniChem rxnorm RISEDRONATE RIS UniChem rxnorm 'RISEDRONATE SODIUM' RIS UniChem rxnorm 'RISEDRONIC ACID' RIS UniChem MedChemExpress HY-B0148 RIS UniChem 'Probes And Drugs' PD009664 RIS UniChem CCDC MOFVOS RIS UniChem 'PubChem TPHARMA' 14799749 RIS UniChem PubChem 44400168 RIS UniChem PubChem 5245 RIS UniChem Nikkaji J476.065D RIS UniChem BindingDb 12576 # 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 RIS O12 -2.994 -1.823 0.187 ETKDGv3 1 RIS P9 -1.402 -1.510 -0.297 ETKDGv3 2 RIS O11 -0.466 -2.036 0.767 ETKDGv3 3 RIS O10 -1.091 -2.318 -1.753 ETKDGv3 4 RIS C8 -1.164 0.302 -0.526 ETKDGv3 5 RIS O13 -2.149 0.779 -1.410 ETKDGv3 6 RIS P14 -1.357 1.160 1.090 ETKDGv3 7 RIS O16 -1.037 2.811 0.891 ETKDGv3 8 RIS O15 -2.941 0.964 1.656 ETKDGv3 9 RIS O17 -0.405 0.585 2.114 ETKDGv3 10 RIS C7 0.207 0.620 -1.180 ETKDGv3 11 RIS C2 1.434 0.216 -0.391 ETKDGv3 12 RIS C1 2.006 -0.989 -0.562 ETKDGv3 13 RIS C6 3.215 -1.350 0.202 ETKDGv3 14 RIS C5 3.749 -0.460 1.044 ETKDGv3 15 RIS N4 3.152 0.839 1.193 ETKDGv3 16 RIS C3 2.080 1.178 0.536 ETKDGv3 17 RIS H12 -3.524 -1.812 -0.650 ETKDGv3 18 RIS H13 -3.039 0.589 -1.015 ETKDGv3 19 RIS H16 -1.184 3.207 1.787 ETKDGv3 20 RIS H15 -3.467 1.660 1.188 ETKDGv3 21 RIS HC71 0.246 0.140 -2.183 ETKDGv3 22 RIS HC72 0.261 1.713 -1.376 ETKDGv3 23 RIS HC1 1.590 -1.707 -1.257 ETKDGv3 24 RIS HC6 3.664 -2.327 0.080 ETKDGv3 25 RIS HC5 4.637 -0.711 1.610 ETKDGv3 26 RIS HC3 1.667 2.168 0.670 ETKDGv3 27 RIS HO1 -1.688 -1.887 -2.416 ETKDGv3 28 #