Structure

Physi-Chem Properties

Molecular Weight:  420.25
Volume:  457.946
LogP:  3.8
LogD:  3.629
LogS:  -4.625
# Rotatable Bonds:  16
TPSA:  85.22
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.183
Synthetic Accessibility Score:  4.6
Fsp3:  0.625
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.283
MDCK Permeability:  3.083772389800288e-05
Pgp-inhibitor:  0.073
Pgp-substrate:  0.016
Human Intestinal Absorption (HIA):  0.812
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.213
Plasma Protein Binding (PPB):  99.79856872558594%
Volume Distribution (VD):  1.164
Pgp-substrate:  1.8120458126068115%

ADMET: Metabolism

CYP1A2-inhibitor:  0.069
CYP1A2-substrate:  0.581
CYP2C19-inhibitor:  0.8
CYP2C19-substrate:  0.706
CYP2C9-inhibitor:  0.89
CYP2C9-substrate:  0.884
CYP2D6-inhibitor:  0.255
CYP2D6-substrate:  0.174
CYP3A4-inhibitor:  0.948
CYP3A4-substrate:  0.286

ADMET: Excretion

Clearance (CL):  8.391
Half-life (T1/2):  0.31

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.784
Drug-inuced Liver Injury (DILI):  0.97
AMES Toxicity:  0.501
Rat Oral Acute Toxicity:  0.96
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.936
Carcinogencity:  0.35
Eye Corrosion:  0.501
Eye Irritation:  0.236
Respiratory Toxicity:  0.983

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  Natural Product: NPC120625

Natural Product ID:  NPC120625
Common Name*:   LCCGCXCFZHBCJT-TUAHSIHMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LCCGCXCFZHBCJT-TUAHSIHMSA-N
Standard InCHI:  InChI=1S/C24H36O6/c1-5-7-10-16-21(26)24(30-19-14-13-18-23(27)29-4)22(28-3)17-12-9-8-11-15-20(25)6-2/h6,12,17,20-22,24-26H,2,5,7,10,13-14,16,18-19H2,1,3-4H3/b17-12+/t20-,21-,22-,24-/m0/s1
SMILES:  CCCCC[C@@H]([C@@H]([C@H](/C=C/C#CC#C[C@H](C=C)O)OC)OCCCCC(=O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/BF02675902]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11816-015-0350-y]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1055/s-2008-1074888]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1248/cpb.30.4088]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[10353265]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[10553679]
NPO22175 Perovskia abrotanoides Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11720520]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[12055308]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[15070765]
NPO28035 Streptomyces fumanus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[15730262]
NPO28391 Euonymus nanoides Species Celastraceae Eukaryota n.a. seed n.a. PMID[16462067]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. aerial part n.a. PMID[17520525]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota roots Gabon 1987 PMID[18327911]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[18327911]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[19276083]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[20448045]
NPO10946 Pseudallescheria boydii Species Microascaceae Eukaryota n.a. n.a. n.a. PMID[20509707]
NPO28217 Septoria pistaciarum Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. PMID[20550123]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[20843794]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[22194604]
NPO28217 Septoria pistaciarum Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. PMID[22530813]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[22966846]
NPO10946 Pseudallescheria boydii Species Microascaceae Eukaryota n.a. n.a. n.a. PMID[23964677]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[24516143]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[25028392]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[26466957]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[26774486]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[26938998]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[26996316]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[27242221]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[27807341]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[5583807]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[8917504]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[97292]
NPO28576 Berberis julianae Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28334 Pyrola decorata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO28576 Berberis julianae Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28334 Pyrola decorata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28334 Pyrola decorata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28576 Berberis julianae Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29115 Rhinella arenarum Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28576 Berberis julianae Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27959 Codonocarpus australis Species Gyrostemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20395 Athanasia crithmifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28614 Zieria smithii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28035 Streptomyces fumanus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28053 Quercus serrata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28596 Streptomyces lavendofoliae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28633 Bystropogon origanifolius Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29353 Benzoin praecox n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11144 Centella asiatica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6331 Jacobaea subalpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28334 Pyrola decorata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28670 Mortierella elongata Species Mortierellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28391 Euonymus nanoides Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25704 Tetraneuris acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28269 Rubus rosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28374 Pleogyne cunninghami Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20081 Mycobacterium tuberculosis Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28073 Crateva nurvala Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28200 Unonopsis glaucopetala Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28509 Achillea clypeolata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28656 Lactobacillus casei Species Lactobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28217 Septoria pistaciarum Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28161 Stephania sutchuenensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28303 Pleogyne cunninghamii Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16669 Diospyros verrucosa Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28691 Streptomyces odorifer Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28704 Agaricus hortensis Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27867 Turbo argyrostoma Species Turbinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27990 Schizonepeta multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28131 Polygala amara Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22175 Perovskia abrotanoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28481 Cerbera dilatata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27943 Cardamine pinnata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10946 Pseudallescheria boydii Species Microascaceae 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 NPC120625 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 NPC120625 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