Structure

Physi-Chem Properties

Molecular Weight:  366.17
Volume:  368.417
LogP:  2.144
LogD:  1.749
LogS:  -3.183
# Rotatable Bonds:  5
TPSA:  110.13
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.437
Synthetic Accessibility Score:  4.59
Fsp3:  0.632
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.471
MDCK Permeability:  0.00015134061686694622
Pgp-inhibitor:  0.218
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.022
30% Bioavailability (F30%):  0.683

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.741
Plasma Protein Binding (PPB):  67.25074005126953%
Volume Distribution (VD):  1.687
Pgp-substrate:  29.61942481994629%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.568
CYP2C19-inhibitor:  0.085
CYP2C19-substrate:  0.808
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.022
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.02
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.93

ADMET: Excretion

Clearance (CL):  2.915
Half-life (T1/2):  0.092

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.938
Drug-inuced Liver Injury (DILI):  0.933
AMES Toxicity:  0.852
Rat Oral Acute Toxicity:  0.161
Maximum Recommended Daily Dose:  0.199
Skin Sensitization:  0.456
Carcinogencity:  0.605
Eye Corrosion:  0.826
Eye Irritation:  0.318
Respiratory Toxicity:  0.979

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC259150

Natural Product ID:  NPC259150
Common Name*:   MMPBHSBVPREJQC-WSWLIKMPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MMPBHSBVPREJQC-WSWLIKMPSA-N
Standard InCHI:  InChI=1S/C15H16O9/c16-5-8-10(19)11(20)12(21)15(22-8)24-14-7(17)3-1-6-2-4-9(18)23-13(6)14/h1-4,8,10-12,15-17,19-21H,5H2/t8-,10-,11-,12-,15+/m1/s1
SMILES:  c1cc(c(c2c1ccc(=O)o2)O[C@H]1[C@@H]([C@@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   22524175
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0001743] Coumarin glycosides

*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
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[10092191]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[10724012]
NPO28843 Astragalus zahlbruckneri Species Fabaceae Eukaryota Roots n.a. n.a. PMID[11575952]
NPO24786 Eunicea pinta Species Plexauridae Eukaryota n.a. n.a. n.a. PMID[12350138]
NPO1145 Coussarea paniculata Species Rubiaceae Eukaryota twigs n.a. n.a. PMID[12662105]
NPO22193 Ophioglossum petiolatum Species Ophioglossaceae Eukaryota n.a. whole plant n.a. PMID[15787440]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[15787462]
NPO28797 Hypoxylon carneum Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[16933875]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota stem bark Kunming, Yunnan Province, China n.a. PMID[18986199]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[32997496]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9066761]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9249977]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9510911]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24554 Hymenocallis speciosa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24984 Hydrocotyle leucocephala Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24637 Oyedaea verbesinoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24203 Sphoeroides vermicularis Species Tetraodontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1145 Coussarea paniculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28843 Astragalus zahlbruckneri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13482 Nierembergia hippomanica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22193 Ophioglossum petiolatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25289 Lonchocarpus salvadorensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7329 Ligularia pleurocaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25563 Axinella cannabina Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23383 Nigritella suaveolens n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24786 Eunicea pinta Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28797 Hypoxylon carneum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25233 Crocodylus niloticus Species Crocodylidae 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 NPC259150 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 NPC259150 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