Structure

Physi-Chem Properties

Molecular Weight:  422.19
Volume:  408.698
LogP:  1.735
LogD:  1.363
LogS:  -4.053
# Rotatable Bonds:  1
TPSA:  111.52
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.601
Synthetic Accessibility Score:  5.544
Fsp3:  0.818
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:  -5.218
MDCK Permeability:  4.06138387916144e-05
Pgp-inhibitor:  0.996
Pgp-substrate:  0.089
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.696
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.831
Plasma Protein Binding (PPB):  33.503021240234375%
Volume Distribution (VD):  0.801
Pgp-substrate:  48.60599136352539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.95
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.654
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.016
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.741
CYP3A4-substrate:  0.518

ADMET: Excretion

Clearance (CL):  4.016
Half-life (T1/2):  0.336

ADMET: Toxicity

hERG Blockers:  0.097
Human Hepatotoxicity (H-HT):  0.711
Drug-inuced Liver Injury (DILI):  0.197
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.612
Maximum Recommended Daily Dose:  0.766
Skin Sensitization:  0.575
Carcinogencity:  0.87
Eye Corrosion:  0.012
Eye Irritation:  0.023
Respiratory Toxicity:  0.982

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

  Natural Product: NPC202219

Natural Product ID:  NPC202219
Common Name*:   YNNJQADRYQOWDM-LPWIECGZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YNNJQADRYQOWDM-LPWIECGZSA-N
Standard InCHI:  InChI=1S/C20H26O4/c1-13-3-7-20-12-24-15(9-16(20)18(21)22)10-17(20)19(13,2)6-4-14-5-8-23-11-14/h5,8-9,11,13,15,17H,3-4,6-7,10,12H2,1-2H3,(H,21,22)/t13-,15+,17-,19+,20-/m0/s1
SMILES:  C[C@H]1CC[C@]23CO[C@H](C=C2C(=O)O)C[C@H]3[C@]1(C)CCc1ccoc1
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:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001757] Colensane and clerodane diterpenoids

*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
NPO16484 Muraltia heisteria Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[11858755]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. PMID[15974602]
NPO17462 Pouteria sapota Species Sapotaceae Eukaryota n.a. ripe fruit n.a. PMID[21214217]
NPO2286 Fischerella muscicola Species Hapalosiphonaceae Bacteria n.a. n.a. n.a. PMID[22863526]
NPO17620 Rhodopirellula baltica Species Planctomycetaceae Bacteria n.a. n.a. n.a. PMID[23826385]
NPO17462 Pouteria sapota Species Sapotaceae Eukaryota n.a. n.a. n.a. PMID[26057604]
NPO17462 Pouteria sapota Species Sapotaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14039 Leucaena leucocephala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15771 Polygonatum prattii Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15031 Senecio microglossus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15771 Polygonatum prattii Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17155 Selaginella apoda Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16484 Muraltia heisteria Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO669 Crepis pygmaea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16065 Micromeria japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16352 Peperomia villipetiola Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2286 Fischerella muscicola Species Hapalosiphonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17620 Rhodopirellula baltica Species Planctomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14039 Leucaena leucocephala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17462 Pouteria sapota Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9405 Siphocampylus foliosus Species Campanulaceae 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 NPC202219 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 NPC202219 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