Structure

Physi-Chem Properties

Molecular Weight:  194.06
Volume:  189.018
LogP:  1.257
LogD:  0.999
LogS:  -2.357
# Rotatable Bonds:  0
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.604
Synthetic Accessibility Score:  3.273
Fsp3:  0.3
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.786
MDCK Permeability:  1.3194582606956828e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.275

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.966
Plasma Protein Binding (PPB):  70.27154541015625%
Volume Distribution (VD):  0.833
Pgp-substrate:  30.98193359375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.69
CYP1A2-substrate:  0.801
CYP2C19-inhibitor:  0.088
CYP2C19-substrate:  0.367
CYP2C9-inhibitor:  0.039
CYP2C9-substrate:  0.777
CYP2D6-inhibitor:  0.417
CYP2D6-substrate:  0.534
CYP3A4-inhibitor:  0.076
CYP3A4-substrate:  0.193

ADMET: Excretion

Clearance (CL):  9.18
Half-life (T1/2):  0.742

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.084
Drug-inuced Liver Injury (DILI):  0.672
AMES Toxicity:  0.069
Rat Oral Acute Toxicity:  0.062
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.11
Carcinogencity:  0.22
Eye Corrosion:  0.005
Eye Irritation:  0.543
Respiratory Toxicity:  0.177

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Structure MOL file  
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  Natural Product: NPC172259

Natural Product ID:  NPC172259
Common Name*:   STSOHAOGZMLWFR-MLUIRONXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  STSOHAOGZMLWFR-MLUIRONXSA-N
Standard InCHI:  InChI=1S/C10H10O4/c1-5-9(12)6-3-2-4-7(11)8(6)10(13)14-5/h2-5,9,11-12H,1H3/t5-,9-/m1/s1
SMILES:  C[C@@H]1[C@H](c2cccc(c2C(=O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10262028
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003411] 2-benzopyrans

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[10869191]
NPO27746 Taxus mairei Species Taxaceae Eukaryota stem bark n.a. n.a. PMID[11473432]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[12027766]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota Fruits n.a. n.a. PMID[12713411]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[16124776]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO10872 Aglaia ponapensis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[17055270]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[17907781]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[18804027]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[19646881]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota nut shell n.a. n.a. PMID[23044367]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. PMID[24460410]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[2553871]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[32058711]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[32243151]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[8557595]
NPO27746 Taxus mairei Species Taxaceae Eukaryota Roots n.a. n.a. PMID[8991951]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9644081]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[9917295]
NPO40084 Coniothyrium sp. Species Coniothyriaceae Eukaryota n.a. n.a. n.a. PMID[9917295]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10872 Aglaia ponapensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10872 Aglaia ponapensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14189 Osmundaria spiralis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23994 Ormosia macrophylla Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20264 Moonia heterophylla n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25441 Desmodium pulchellu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22618 Psolus eximius Species Psolidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22727 Avena fatua Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15482 Vanderbylia fraxinea Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16885 Phonus arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10872 Aglaia ponapensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24461 Clusia sandiensis Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24566 Marasmiellus ramealis Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24607 Goniothalamus dolichocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10510 Aconitum naviculare Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22152 Tecoma undulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3721 Achyranthes obtusifolia Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25466 Lecanora sulphurella Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24882 Erythrophleum chlorostachys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28460 Achyrocline tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25389 Allium angulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16798 Piper sylvaticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24730 Lactarius deliciosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25492 Botryllus leachi Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27390 Vernonia brevifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21569 Helichrysum fulvum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24802 Diploprion bifasciatum Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18706 Anemone thalictroides Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25277 Seiridium cupressi Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23894 Pulicaria insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC172259 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC172259 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data