Structure

Physi-Chem Properties

Molecular Weight:  286.12
Volume:  296.261
LogP:  2.626
LogD:  2.468
LogS:  -3.801
# Rotatable Bonds:  2
TPSA:  69.92
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.794
Synthetic Accessibility Score:  2.896
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.756
MDCK Permeability:  7.72454950492829e-06
Pgp-inhibitor:  0.007
Pgp-substrate:  0.902
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.975
30% Bioavailability (F30%):  0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.116
Plasma Protein Binding (PPB):  95.82820892333984%
Volume Distribution (VD):  0.765
Pgp-substrate:  3.693575143814087%

ADMET: Metabolism

CYP1A2-inhibitor:  0.945
CYP1A2-substrate:  0.944
CYP2C19-inhibitor:  0.176
CYP2C19-substrate:  0.106
CYP2C9-inhibitor:  0.211
CYP2C9-substrate:  0.868
CYP2D6-inhibitor:  0.764
CYP2D6-substrate:  0.926
CYP3A4-inhibitor:  0.662
CYP3A4-substrate:  0.395

ADMET: Excretion

Clearance (CL):  11.92
Half-life (T1/2):  0.794

ADMET: Toxicity

hERG Blockers:  0.11
Human Hepatotoxicity (H-HT):  0.156
Drug-inuced Liver Injury (DILI):  0.128
AMES Toxicity:  0.649
Rat Oral Acute Toxicity:  0.387
Maximum Recommended Daily Dose:  0.954
Skin Sensitization:  0.923
Carcinogencity:  0.134
Eye Corrosion:  0.004
Eye Irritation:  0.758
Respiratory Toxicity:  0.45

Download Data

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

  Natural Product: NPC107070

Natural Product ID:  NPC107070
Common Name*:   OPBSKOXPQSRNGB-NSHDSACASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OPBSKOXPQSRNGB-NSHDSACASA-N
Standard InCHI:  InChI=1S/C17H18O4/c1-21-17-8-14-11(9-18)3-2-10-6-12(19)4-5-13(10)15(14)7-16(17)20/h4-8,11,18-20H,2-3,9H2,1H3/t11-/m0/s1
SMILES:  COc1cc2[C@@H](CCc3cc(ccc3-c2cc1O)O)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   71620318
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002341] Phenol ethers
        • [CHEMONTID:0000138] Anisoles

*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
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. PMID[10924179]
NPO8035 Tylophora tanakae Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12350151]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stems Wulai Hsiang, Taipei County, Taiwan 2005-MAY PMID[17253858]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19581087]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[20299229]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota bark n.a. n.a. PMID[20363129]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21214253]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota Leaves n.a. n.a. PMID[23025417]
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. PMID[23131412]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stem bark Laifeng, Hubei Province, China 2012-JUL PMID[26087384]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota Fruit juice n.a. n.a. PMID[3404148]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12669 Cassine papillosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6253 Conus pulicarius Species Conidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5384 Ligustrum obtusifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20291 Phyllanthus oligospermus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11256 Pseudowintera colorata Species Winteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12544 Dioscorea olfersiana Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10737 Asteriscus aquaticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5823 Helichrysum auriceps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9922 Myelobia smerintha Species Crambidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11553 Phebalium dentatum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7709 Spiracantha cornifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3736 Scrophularia koelzii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9672 Lotus ucrainicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12188 Datisca glomerata Species Datiscaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7045 Viviparus japonicus Species Viviparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2608 Solanum andigena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8035 Tylophora tanakae Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10393 Ophidiaster ophidianus Species Ophidiasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9509 Charpentiera obovata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4493 Polygonum flaccidum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5008 Hubertia tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15252 Clathria prolifera Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11811 Capparis ovata Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8477 Myristica cagayanensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3378 Alstonia undulifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12888 Echinus microtuberculatus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1182 Croton montevidensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO761 Fagus fusca Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12308 Metridium senile Species Metridiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12436 Quercus imbricaria Species Fagaceae 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 NPC107070 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 NPC107070 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