Structure

Physi-Chem Properties

Molecular Weight:  208.02
Volume:  174.745
LogP:  -1.409
LogD:  -0.754
LogS:  -0.76
# Rotatable Bonds:  5
TPSA:  152.36
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.239
Synthetic Accessibility Score:  3.564
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.348
MDCK Permeability:  0.0049306778237223625
Pgp-inhibitor:  0.0
Pgp-substrate:  0.533
Human Intestinal Absorption (HIA):  0.282
20% Bioavailability (F20%):  0.084
30% Bioavailability (F30%):  0.45

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.321
Plasma Protein Binding (PPB):  17.665760040283203%
Volume Distribution (VD):  0.25
Pgp-substrate:  72.37809753417969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.039
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.531
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.083
CYP3A4-inhibitor:  0.016
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.51
Half-life (T1/2):  0.842

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.069
Drug-inuced Liver Injury (DILI):  0.828
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.207
Carcinogencity:  0.01
Eye Corrosion:  0.883
Eye Irritation:  0.98
Respiratory Toxicity:  0.028

Download Data

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

  Natural Product: NPC105881

Natural Product ID:  NPC105881
Common Name*:   ZMJBYMUCKBYSCP-BBIVZNJYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZMJBYMUCKBYSCP-BBIVZNJYSA-N
Standard InCHI:  InChI=1S/C6H8O8/c7-2(8)1-6(14,5(12)13)3(9)4(10)11/h3,9,14H,1H2,(H,7,8)(H,10,11)(H,12,13)/t3-,6+/m0/s1
SMILES:  C(C(=O)O)[C@@]([C@H](C(=O)O)O)(C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13037289
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001986] Tricarboxylic acids and derivatives

*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
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(74)80113-5]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. whole plant n.a. PMID[10361686]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[16724839]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17287127]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19113969]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota leaves Bobai, Guangxi Province, China 2005-Dec PMID[24679044]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota Barks n.a. n.a. PMID[24754786]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1154 Neomeris annulata Species Dasycladaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6948 Davidsoniella virescens Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2382 Nicotiana excelsior Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15242 Setosphaeria holmii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO769 Eria elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24463 Linum corymbulosum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9298 Piper wightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26341 Trifolium resupinatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2812 Lecanora kukunorensis Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12849 Lagerstroemia subcostata Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10228 Ascochyta viciae Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1330 Stachybotrys alternans Species Stachybotryaceae 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 NPC105881 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 NPC105881 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