data_VK3 # _chem_comp.id VK3 _chem_comp.name MENADIONE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H8 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "VITAMIN K3; 2-METHYL-1,4-NAPHTHALENEDIONE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 172.180 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VK3 _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 2QR2 _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 VK3 C1K C1K C 0 1 N N N N N N 34.006 14.994 33.258 1.677 -0.000 0.275 C1K VK3 1 VK3 O1K O1K O 0 1 N N N N N N 33.215 14.480 34.059 2.854 -0.002 -0.025 O1K VK3 2 VK3 C2K C2K C 0 1 N N N N N N 33.423 15.860 32.227 1.275 0.000 1.694 C2K VK3 3 VK3 C3K C3K C 0 1 N N N N N N 34.233 16.448 31.282 -0.017 0.002 2.044 C3K VK3 4 VK3 C4K C4K C 0 1 N N N N N N 35.699 16.281 31.319 -1.079 -0.002 1.020 C4K VK3 5 VK3 O4K O4K O 0 1 N N N N N N 36.312 16.870 30.414 -2.247 -0.005 1.353 O4K VK3 6 VK3 C5K C5K C 0 1 Y N N N N N 36.261 15.514 32.408 -0.716 0.002 -0.413 C5K VK3 7 VK3 C6K C6K C 0 1 Y N N N N N 37.620 15.439 32.522 -1.697 0.002 -1.397 C6K VK3 8 VK3 C7K C7K C 0 1 Y N N N N N 38.159 14.745 33.569 -1.331 0.001 -2.734 C7K VK3 9 VK3 C8K C8K C 0 1 Y N N N N N 37.373 14.145 34.510 0.002 -0.000 -3.095 C8K VK3 10 VK3 C9K C9K C 0 1 Y N N N N N 36.015 14.221 34.421 0.992 -0.000 -2.125 C9K VK3 11 VK3 C10 C10 C 0 1 Y N N N N N 35.444 14.908 33.377 0.641 0.000 -0.780 C10 VK3 12 VK3 C11 C11 C 0 1 N N N N N N 33.589 17.300 30.166 -0.392 0.003 3.503 C11 VK3 13 VK3 H2K1 1H2K H 0 0 N N N N N N 32.343 16.075 32.160 2.035 -0.000 2.462 H2K1 VK3 14 VK3 H6K1 1H6K H 0 0 N N N N N N 38.271 15.931 31.780 -2.741 0.004 -1.121 H6K1 VK3 15 VK3 H7K1 1H7K H 0 0 N N N N N N 39.255 14.667 33.656 -2.093 0.002 -3.499 H7K1 VK3 16 VK3 H8K1 1H8K H 0 0 N N N N N N 37.837 13.596 35.346 0.275 -0.000 -4.140 H8K1 VK3 17 VK3 H9K1 1H9K H 0 0 N N N N N N 35.386 13.732 35.184 2.033 -0.001 -2.412 H9K1 VK3 18 VK3 H111 1H11 H 0 0 N N N N N N 34.245 17.776 29.400 0.512 0.002 4.111 H111 VK3 19 VK3 H112 2H11 H 0 0 N N N N N N 32.818 16.685 29.645 -0.979 0.894 3.727 H112 VK3 20 VK3 H113 3H11 H 0 0 N N N N N N 32.956 18.088 30.636 -0.982 -0.885 3.728 H113 VK3 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 VK3 C1K O1K DOUB N N 1 VK3 C1K C2K SING N N 2 VK3 C1K C10 SING N N 3 VK3 C2K C3K DOUB N N 4 VK3 C2K H2K1 SING N N 5 VK3 C3K C4K SING N N 6 VK3 C3K C11 SING N N 7 VK3 C4K O4K DOUB N N 8 VK3 C4K C5K SING N N 9 VK3 C5K C6K DOUB Y N 10 VK3 C5K C10 SING Y N 11 VK3 C6K C7K SING Y N 12 VK3 C6K H6K1 SING N N 13 VK3 C7K C8K DOUB Y N 14 VK3 C7K H7K1 SING N N 15 VK3 C8K C9K SING Y N 16 VK3 C8K H8K1 SING N N 17 VK3 C9K C10 DOUB Y N 18 VK3 C9K H9K1 SING N N 19 VK3 C11 H111 SING N N 20 VK3 C11 H112 SING N N 21 VK3 C11 H113 SING N N 22 # 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 VK3 SMILES ACDLabs 10.04 O=C2c1c(cccc1)C(=O)C(=C2)C VK3 SMILES_CANONICAL CACTVS 3.341 CC1=CC(=O)c2ccccc2C1=O VK3 SMILES CACTVS 3.341 CC1=CC(=O)c2ccccc2C1=O VK3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CC(=O)c2ccccc2C1=O VK3 SMILES "OpenEye OEToolkits" 1.5.0 CC1=CC(=O)c2ccccc2C1=O VK3 InChI InChI 1.03 InChI=1S/C11H8O2/c1-7-6-10(12)8-4-2-3-5-9(8)11(7)13/h2-6H,1H3 VK3 InChIKey InChI 1.03 MJVAVZPDRWSRRC-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 VK3 "SYSTEMATIC NAME" ACDLabs 10.04 2-methylnaphthalene-1,4-dione VK3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-methylnaphthalene-1,4-dione # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VK3 'Create component' 1999-07-08 RCSB VK3 'Modify descriptor' 2011-06-04 RCSB VK3 'Modify synonyms' 2020-06-05 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 VK3 "VITAMIN K3" ? ? 2 VK3 2-METHYL-1,4-NAPHTHALENEDIONE ? ? # _pdbe_chem_comp_drugbank_details.comp_id VK3 _pdbe_chem_comp_drugbank_details.drugbank_id DB00170 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name Menadione _pdbe_chem_comp_drugbank_details.description 'A synthetic naphthoquinone without the isoprenoid side chain and biological activity, but can be converted to active vitamin K2, menaquinone, after alkylation in vivo.' _pdbe_chem_comp_drugbank_details.cas_number 58-27-5 _pdbe_chem_comp_drugbank_details.mechanism_of_action 'Menadione (vitamin K3) is involved as a cofactor in the posttranslational gamma-carboxylation of glutamic acid residues of certain proteins in the body. These proteins include the vitamin K-dependent coagulation factors II (prothrombin), VII (proconvertin), IX (Christmas factor), X (Stuart factor), protein C, protein S, protein Zv and a growth-arrest-specific factor (Gas6). In contrast to the other vitamin K-dependent proteins in the blood coagulation cascade, protein C and protein S serve anticoagulant roles. The two vitamin K-dependent proteins found in bone are osteocalcin, also known as bone G1a (gamma-carboxyglutamate) protein or BGP, and the matrix G1a protein or MGP. Gamma-carboxylation is catalyzed by the vitamin K-dependent gamma-carboxylases. The reduced form of vitamin K, vitamin K hydroquinone, is the actual cofactor for the gamma-carboxylases. Proteins containing gamma-carboxyglutamate are called G1a proteins.' # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type VK3 Kappaxin ChEMBL Tradename VK3 Menadione ChEMBL Tradename VK3 Menadione ChEMBL 'United States Accepted Names' VK3 'Vitamin K 3' ChEMBL Tradename VK3 'VITAMIN K3' wwPDB ? VK3 2-METHYL-1,4-NAPHTHALENEDIONE wwPDB ? VK3 2-Methyl-1,4-Naphthalenedione DrugBank ? VK3 2-Methyl-1,4-naphthochinon DrugBank ? VK3 2-Methyl-1,4-naphthoquinone DrugBank ? VK3 Menadione DrugBank ? VK3 'Vitamin K 3' DrugBank ? VK3 'Vitamin K3' DrugBank ? VK3 Synkavite DrugBank 'International brand' # _pdbe_chem_comp_drugbank_classification.comp_id VK3 _pdbe_chem_comp_drugbank_classification.drugbank_id DB00170 _pdbe_chem_comp_drugbank_classification.parent Naphthoquinones _pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds' _pdbe_chem_comp_drugbank_classification.class Naphthalenes _pdbe_chem_comp_drugbank_classification.superclass Benzenoids _pdbe_chem_comp_drugbank_classification.description 'This compound belongs to the class of organic compounds known as naphthoquinones. These are compounds containing a naphthohydroquinone moiety, which consists of a benzene ring linearly fused to a bezene-1,4-dione (quinone).' # 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 VK3 DB00170 'Vitamin K-dependent gamma-carboxylase' Humans P38435 yes 1 VK3 DB00170 'Vitamin K epoxide reductase complex subunit 1' Humans Q9BQB6 yes 2 VK3 DB00170 'Vitamin K epoxide reductase complex subunit 1-like protein 1' Humans Q8N0U8 yes 3 VK3 DB00170 Prothrombin Humans P00734 unknown 4 VK3 DB00170 'Coagulation factor IX' Humans P00740 unknown 5 VK3 DB00170 'Vitamin K-dependent protein C' Humans P04070 unknown 6 VK3 DB00170 'Vitamin K-dependent protein S' Humans P07225 unknown 7 VK3 DB00170 'Ribosyldihydronicotinamide dehydrogenase [quinone]' Humans P16083 unknown 8 VK3 DB00170 'NAD(P)H dehydrogenase [quinone] 1' Humans P15559 unknown 9 VK3 DB00170 Osteocalcin Humans P02818 unknown 10 # loop_ _software.name _software.version _software.description rdkit 2023.09.6 'Core functionality.' pdbeccdutils 0.8.6 '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 VK3 C1K C 5.598 1.500 1 VK3 O1K O 5.598 3.000 2 VK3 C2K C 4.299 0.750 3 VK3 C3K C 4.299 -0.750 4 VK3 C4K C 5.598 -1.500 5 VK3 O4K O 5.598 -3.000 6 VK3 C5K C 6.897 -0.750 7 VK3 C6K C 8.238 -1.552 8 VK3 C7K C 9.597 -0.781 9 VK3 C8K C 9.597 0.781 10 VK3 C9K C 8.238 1.552 11 VK3 C10 C 6.897 0.750 12 VK3 C11 C 3.000 -1.500 13 # 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 VK3 C1K O1K DOUBLE NONE 1 VK3 C1K C2K SINGLE NONE 2 VK3 C1K C10 SINGLE NONE 3 VK3 C2K C3K DOUBLE NONE 4 VK3 C3K C4K SINGLE NONE 5 VK3 C3K C11 SINGLE NONE 6 VK3 C4K O4K DOUBLE NONE 7 VK3 C4K C5K SINGLE NONE 8 VK3 C5K C6K SINGLE NONE 9 VK3 C5K C10 DOUBLE NONE 10 VK3 C6K C7K DOUBLE NONE 11 VK3 C7K C8K SINGLE NONE 12 VK3 C8K C9K DOUBLE NONE 13 VK3 C9K C10 SINGLE NONE 14 # 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 VK3 MurckoScaffold S1 scaffold O=C1C=CC(=O)c2ccccc21 InChI=1S/C10H6O2/c11-9-5-6-10(12)8-4-2-1-3-7(8)9/h1-6H FRASJONUBLZVQX-UHFFFAOYSA-N VK3 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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 VK3 C1K S1 1 VK3 O1K S1 1 VK3 C2K S1 1 VK3 C3K S1 1 VK3 C4K S1 1 VK3 O4K S1 1 VK3 C5K S1 1 VK3 C6K S1 1 VK3 C7K S1 1 VK3 C8K S1 1 VK3 C9K S1 1 VK3 C10 S1 1 VK3 C5K F1 1 VK3 C6K F1 1 VK3 C7K F1 1 VK3 C8K F1 1 VK3 C9K F1 1 VK3 C10 F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id VK3 _pdbe_chem_comp_rdkit_properties.exactmw 172.052 _pdbe_chem_comp_rdkit_properties.amw 172.183 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 2 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 0 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1 _pdbe_chem_comp_rdkit_properties.NumHBD 0 _pdbe_chem_comp_rdkit_properties.NumHBA 2 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13 _pdbe_chem_comp_rdkit_properties.NumAtoms 21 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.091 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _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 0 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 87.123 _pdbe_chem_comp_rdkit_properties.tpsa 34.140 _pdbe_chem_comp_rdkit_properties.CrippenClogP 1.902 _pdbe_chem_comp_rdkit_properties.CrippenMR 48.328 _pdbe_chem_comp_rdkit_properties.chi0v 6.316 _pdbe_chem_comp_rdkit_properties.chi1v 3.408 _pdbe_chem_comp_rdkit_properties.chi2v 1.607 _pdbe_chem_comp_rdkit_properties.chi3v 1.607 _pdbe_chem_comp_rdkit_properties.chi4v 1.011 _pdbe_chem_comp_rdkit_properties.chi0n 14.316 _pdbe_chem_comp_rdkit_properties.chi1n 7.408 _pdbe_chem_comp_rdkit_properties.chi2n 1.607 _pdbe_chem_comp_rdkit_properties.chi3n 1.607 _pdbe_chem_comp_rdkit_properties.chi4n 1.011 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.700 _pdbe_chem_comp_rdkit_properties.kappa1 2.909 _pdbe_chem_comp_rdkit_properties.kappa2 2.660 _pdbe_chem_comp_rdkit_properties.kappa3 1.109 _pdbe_chem_comp_rdkit_properties.Phi 0.595 # 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 VK3 UniChem ChEMBL CHEMBL590 VK3 UniChem DrugBank DB00170 VK3 UniChem 'KEGG LIGAND' C05377 VK3 UniChem ChEBI 28869 VK3 UniChem ZINC ZINC000000001677 VK3 UniChem fdasrs 723JX6CXY5 VK3 UniChem PharmGKB PA450358 VK3 UniChem HMDB HMDB0001892 VK3 UniChem Selleck Menadione VK3 UniChem 'PubChem TPHARMA' 14772598 VK3 UniChem NMRShiftDB 20097597 VK3 UniChem LINCS LSM-3755 VK3 UniChem ACTor 34524-96-4 VK3 UniChem ACTor 72060-21-0 VK3 UniChem BindingDb 24778 VK3 UniChem 'EPA CompTox Dashboard' DTXSID4021715 VK3 UniChem DrugCentral 1683 VK3 UniChem MetaboLights MTBLC28869 VK3 UniChem BRENDA 108128 VK3 UniChem BRENDA 16686 VK3 UniChem BRENDA 1950 VK3 UniChem BRENDA 240 VK3 UniChem BRENDA 4340 VK3 UniChem BRENDA 49730 VK3 UniChem BRENDA 83128 VK3 UniChem Rhea 28869 VK3 UniChem ChemicalBook CB4494726 VK3 UniChem DailyMed MENADIONE VK3 UniChem ClinicalTrials MENADIONE VK3 UniChem rxnorm 'VITAMIN K3' VK3 UniChem MedChemExpress HY-B0332 VK3 UniChem 'Probes And Drugs' PD001331 VK3 UniChem CCDC IVEJUO VK3 UniChem Nikkaji J4.591H VK3 UniChem eMolecules 513358 VK3 UniChem SureChEMBL SCHEMBL25970 VK3 UniChem PubChem 4055 VK3 UniChem Mcule MCULE-2487773379 VK3 UniChem ACTor 58-27-5 # 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 VK3 C1K -0.322 1.744 0.055 ETKDGv3 1 VK3 O1K -0.101 2.985 0.060 ETKDGv3 2 VK3 C2K -1.709 1.253 0.129 ETKDGv3 3 VK3 C3K -1.973 -0.062 0.137 ETKDGv3 4 VK3 C4K -0.857 -1.034 0.031 ETKDGv3 5 VK3 O4K -1.099 -2.271 -0.002 ETKDGv3 6 VK3 C5K 0.543 -0.549 -0.038 ETKDGv3 7 VK3 C6K 1.672 -1.511 -0.122 ETKDGv3 8 VK3 C7K 2.933 -1.068 -0.185 ETKDGv3 9 VK3 C8K 3.211 0.381 -0.171 ETKDGv3 10 VK3 C9K 2.203 1.257 -0.095 ETKDGv3 11 VK3 C10 0.799 0.779 -0.025 ETKDGv3 12 VK3 C11 -3.396 -0.548 0.177 ETKDGv3 13 VK3 H2K1 -2.516 1.975 0.176 ETKDGv3 14 VK3 H6K1 1.483 -2.577 -0.134 ETKDGv3 15 VK3 H7K1 3.753 -1.772 -0.246 ETKDGv3 16 VK3 H8K1 4.234 0.732 -0.222 ETKDGv3 17 VK3 H9K1 2.422 2.318 -0.086 ETKDGv3 18 VK3 H111 -3.474 -1.453 0.816 ETKDGv3 19 VK3 H112 -3.728 -0.801 -0.852 ETKDGv3 20 VK3 H113 -4.077 0.223 0.597 ETKDGv3 21 #