Structure

Physi-Chem Properties

Molecular Weight:  112.05
Volume:  122.003
LogP:  1.517
LogD:  1.278
LogS:  -0.442
# Rotatable Bonds:  2
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.43
Synthetic Accessibility Score:  2.78
Fsp3:  0.167
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:  -4.725
MDCK Permeability:  1.971961864910554e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.902
Plasma Protein Binding (PPB):  58.376434326171875%
Volume Distribution (VD):  0.352
Pgp-substrate:  44.458648681640625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.067
CYP2C9-substrate:  0.486
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.248
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.084

ADMET: Excretion

Clearance (CL):  2.484
Half-life (T1/2):  0.85

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.86
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.274
Rat Oral Acute Toxicity:  0.919
Maximum Recommended Daily Dose:  0.752
Skin Sensitization:  0.964
Carcinogencity:  0.571
Eye Corrosion:  0.965
Eye Irritation:  0.994
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC63598

Natural Product ID:  NPC63598
Common Name*:   Sorbic Acid
IUPAC Name:   (2E,4E)-hexa-2,4-dienoic acid
Synonyms:   E200; Sorbic Acid
Standard InCHIKey:  WSWCOQWTEOXDQX-MQQKCMAXSA-N
Standard InCHI:  InChI=1S/C6H8O2/c1-2-3-4-5-6(7)8/h2-5H,1H3,(H,7,8)/b3-2+,5-4+
SMILES:  C/C=C/C=C/C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL250212
PubChem CID:   643460
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty acids

*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
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae 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
NPT3 Individual Protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 39810.7 nM PMID[555721]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 35481.3 nM PMID[555722]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 89125.1 nM PMID[555721]
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 22.4 nM PMID[555722]
NPT249 Individual Protein Glucocorticoid receptor Homo sapiens Potency n.a. 50118.7 nM PMID[555722]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 183.6 nM PMID[555721]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 24336.5 nM PubChem BioAssay data set
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 194.9 nM PubChem BioAssay data set
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 33491.5 nM PubChem BioAssay data set
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 112201845.43 nM PMID[555719]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 141253754.46 nM PMID[555719]
NPT19 Organism Escherichia coli Escherichia coli MIC = 177827941.0 nM PMID[555719]
NPT20 Organism Candida albicans Candida albicans MIC = 112201845.43 nM PMID[555719]
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 125892541.18 nM PMID[555719]
NPT35 Others n.a. LogP = 1.47 n.a. PMID[555719]
NPT664 Protein Family Histone deacetylase Homo sapiens Activity = 91.0 % PMID[555720]
NPT2 Others Unspecified Potency n.a. 29092.9 nM PMID[555721]
NPT32 Organism Mus musculus Mus musculus IC50 = 210.0 nM PMID[555723]
NPT774 Organism Zygosaccharomyces bailii Zygosaccharomyces bailii MIC = 1600.0 ug.mL-1 PMID[555724]
NPT774 Organism Zygosaccharomyces bailii Zygosaccharomyces bailii MFC = 800.0 ug ml-1 PMID[555724]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MFC = 3200.0 ug ml-1 PMID[555725]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MFC = 1600.0 ug ml-1 PMID[555725]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC > 1600.0 ug.mL-1 PMID[555725]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 800.0 ug.mL-1 PMID[555725]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 400.0 ug.mL-1 PMID[555725]
NPT35 Others n.a. pKa n.a. 4.5 n.a. PMID[555726]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 512.0 ug.mL-1 PMID[555727]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC > 512.0 ug.mL-1 PMID[555727]
NPT3721 Organism Enterococcus hirae Enterococcus hirae MIC = 512.0 ug.mL-1 PMID[555727]
NPT19 Organism Escherichia coli Escherichia coli MIC = 512.0 ug.mL-1 PMID[555727]
NPT19 Organism Escherichia coli Escherichia coli MIC > 512.0 ug.mL-1 PMID[555727]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 512.0 ug.mL-1 PMID[555727]
NPT2 Others Unspecified Potency n.a. 21872.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27056.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27306 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48966.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30357.7 nM PubChem BioAssay data set

☑ 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 NPC63598 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
0.9167 High Similarity NPC107877
0.9143 High Similarity NPC60675
0.9143 High Similarity NPC297363
0.8974 High Similarity NPC102879
0.8462 Intermediate Similarity NPC8270
0.8378 Intermediate Similarity NPC308418
0.8333 Intermediate Similarity NPC224651
0.8333 Intermediate Similarity NPC98098
0.825 Intermediate Similarity NPC221250
0.775 Intermediate Similarity NPC298413
0.7619 Intermediate Similarity NPC41409
0.7609 Intermediate Similarity NPC221467
0.7556 Intermediate Similarity NPC128520
0.7447 Intermediate Similarity NPC43053
0.7429 Intermediate Similarity NPC20903
0.7222 Intermediate Similarity NPC323552
0.7143 Intermediate Similarity NPC297608
0.7021 Intermediate Similarity NPC126184
0.6923 Remote Similarity NPC217161
0.6889 Remote Similarity NPC6963
0.6889 Remote Similarity NPC304079
0.6809 Remote Similarity NPC90490
0.6744 Remote Similarity NPC250954
0.6744 Remote Similarity NPC281043
0.6731 Remote Similarity NPC324224
0.6731 Remote Similarity NPC472808
0.6667 Remote Similarity NPC82446
0.6667 Remote Similarity NPC144407
0.6596 Remote Similarity NPC87137
0.6596 Remote Similarity NPC308331
0.6512 Remote Similarity NPC147824
0.65 Remote Similarity NPC146507
0.65 Remote Similarity NPC310810
0.6481 Remote Similarity NPC189700
0.6346 Remote Similarity NPC474127
0.6346 Remote Similarity NPC218486
0.6341 Remote Similarity NPC122676
0.625 Remote Similarity NPC130953
0.619 Remote Similarity NPC65353
0.6111 Remote Similarity NPC51846
0.6098 Remote Similarity NPC63354
0.6047 Remote Similarity NPC8416
0.6038 Remote Similarity NPC322461
0.6034 Remote Similarity NPC77891
0.6034 Remote Similarity NPC473737
0.6 Remote Similarity NPC137419
0.6 Remote Similarity NPC234084
0.6 Remote Similarity NPC203382
0.6 Remote Similarity NPC129150
0.6 Remote Similarity NPC313553
0.6 Remote Similarity NPC122212
0.6 Remote Similarity NPC294938
0.5965 Remote Similarity NPC98519
0.5962 Remote Similarity NPC191643
0.5897 Remote Similarity NPC8466
0.5897 Remote Similarity NPC280312
0.5893 Remote Similarity NPC474084
0.5893 Remote Similarity NPC254095
0.5893 Remote Similarity NPC223679
0.5882 Remote Similarity NPC275316
0.5882 Remote Similarity NPC15789
0.5862 Remote Similarity NPC326645
0.5862 Remote Similarity NPC317177
0.5862 Remote Similarity NPC317025
0.5862 Remote Similarity NPC329416
0.5818 Remote Similarity NPC325977
0.5818 Remote Similarity NPC150717
0.5818 Remote Similarity NPC86948
0.5789 Remote Similarity NPC97570
0.5789 Remote Similarity NPC302564
0.5789 Remote Similarity NPC82465
0.5763 Remote Similarity NPC2328
0.575 Remote Similarity NPC242117
0.5745 Remote Similarity NPC57923
0.5741 Remote Similarity NPC478120
0.5738 Remote Similarity NPC255781
0.5738 Remote Similarity NPC146811
0.5714 Remote Similarity NPC135863
0.5714 Remote Similarity NPC249850
0.5714 Remote Similarity NPC472445
0.5714 Remote Similarity NPC245650
0.5714 Remote Similarity NPC283502
0.5714 Remote Similarity NPC44542
0.5714 Remote Similarity NPC293437
0.5714 Remote Similarity NPC270706
0.5714 Remote Similarity NPC250734
0.5652 Remote Similarity NPC323278
0.5645 Remote Similarity NPC254886
0.5636 Remote Similarity NPC478117
0.5636 Remote Similarity NPC173157
0.5625 Remote Similarity NPC270796
0.5614 Remote Similarity NPC471619
0.5614 Remote Similarity NPC21946
0.5614 Remote Similarity NPC34416
0.561 Remote Similarity NPC273054
0.56 Remote Similarity NPC128280

  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 NPC63598 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
0.8333 Intermediate Similarity NPD8573 Approved
0.7429 Intermediate Similarity NPD8187 Phase 3
0.7391 Intermediate Similarity NPD4220 Pre-registration
0.725 Intermediate Similarity NPD9115 Approved
0.6154 Remote Similarity NPD9114 Clinical (unspecified phase)
0.5957 Remote Similarity NPD9411 Phase 1
0.5862 Remote Similarity NPD4191 Approved
0.5862 Remote Similarity NPD4194 Approved
0.5862 Remote Similarity NPD4192 Approved
0.5862 Remote Similarity NPD4193 Approved
0.5625 Remote Similarity NPD5326 Phase 3

  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