Structure

Physi-Chem Properties

Molecular Weight:  262.19
Volume:  289.226
LogP:  4.51
LogD:  3.749
LogS:  -4.318
# Rotatable Bonds:  3
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.556
Synthetic Accessibility Score:  5.669
Fsp3:  0.824
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.607
MDCK Permeability:  2.351626790186856e-05
Pgp-inhibitor:  0.084
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.762
30% Bioavailability (F30%):  0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.282
Plasma Protein Binding (PPB):  84.4578628540039%
Volume Distribution (VD):  1.333
Pgp-substrate:  16.35176658630371%

ADMET: Metabolism

CYP1A2-inhibitor:  0.84
CYP1A2-substrate:  0.156
CYP2C19-inhibitor:  0.355
CYP2C19-substrate:  0.782
CYP2C9-inhibitor:  0.142
CYP2C9-substrate:  0.091
CYP2D6-inhibitor:  0.094
CYP2D6-substrate:  0.166
CYP3A4-inhibitor:  0.871
CYP3A4-substrate:  0.326

ADMET: Excretion

Clearance (CL):  9.519
Half-life (T1/2):  0.166

ADMET: Toxicity

hERG Blockers:  0.063
Human Hepatotoxicity (H-HT):  0.331
Drug-inuced Liver Injury (DILI):  0.767
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.467
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.912
Carcinogencity:  0.566
Eye Corrosion:  0.731
Eye Irritation:  0.911
Respiratory Toxicity:  0.94

Download Data

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

  Natural Product: NPC64001

Natural Product ID:  NPC64001
Common Name*:   KXXPDJVJYDZZOJ-SOKJMZBUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KXXPDJVJYDZZOJ-SOKJMZBUSA-N
Standard InCHI:  InChI=1S/C17H26O2/c1-11-7-8-17-9-14(11)16(4,10-19-13(3)18)15(17)6-5-12(17)2/h7,12,14-15H,5-6,8-10H2,1-4H3/t12-,14+,15-,16+,17+/m1/s1
SMILES:  CC1=CC[C@]23C[C@@H]1[C@](C)(COC(=O)C)[C@H]3CC[C@H]2C
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:0001550] Sesquiterpenoids
          • [CHEMONTID:0003752] Cedrane and isocedrane sesquiterpenoids

*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
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[20209910]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10742 Galium verum Species Rubiaceae 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 NPC64001 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 NPC64001 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