Structure

Physi-Chem Properties

Molecular Weight:  236.16
Volume:  258.199
LogP:  4.336
LogD:  4.852
LogS:  -5.049
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.508
Synthetic Accessibility Score:  4.603
Fsp3:  0.867
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:  -4.478
MDCK Permeability:  1.868778417701833e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.677

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.193
Plasma Protein Binding (PPB):  97.99402618408203%
Volume Distribution (VD):  1.589
Pgp-substrate:  2.700305700302124%

ADMET: Metabolism

CYP1A2-inhibitor:  0.91
CYP1A2-substrate:  0.524
CYP2C19-inhibitor:  0.295
CYP2C19-substrate:  0.886
CYP2C9-inhibitor:  0.288
CYP2C9-substrate:  0.323
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.793
CYP3A4-inhibitor:  0.368
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  13.443
Half-life (T1/2):  0.461

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.115
Drug-inuced Liver Injury (DILI):  0.484
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.227
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.812
Carcinogencity:  0.049
Eye Corrosion:  0.985
Eye Irritation:  0.985
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC471681

Natural Product ID:  NPC471681
Common Name*:   MOLPJMOYBINZPO-JJLDBEOISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MOLPJMOYBINZPO-JJLDBEOISA-N
Standard InCHI:  InChI=1S/C15H24S/c1-9-4-5-11-13(9)14(10(2)8-16)12-6-7-15(11,12)3/h9,11-13,16H,4-8H2,1-3H3/b14-10+/t9-,11+,12+,13-,15-/m1/s1
SMILES:  CC1CCC2C1C(=C(C)CS)C3C2(CC3)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3104455
PubChem CID:   73213093
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001565] Iridoids 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
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. formosan soft coral n.a. PMID[17845002]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[24370010]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[9722490]
NPO13916 Nephthea erecta Species Nephtheidae 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
NPT139 Cell Line HT-29 Homo sapiens ED50 = 1.8 ug ml-1 PMID[488993]
NPT168 Cell Line P388 Mus musculus ED50 = 1.3 ug ml-1 PMID[488993]

☑ 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 NPC471681 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
0.7755 Intermediate Similarity NPC474118
0.7755 Intermediate Similarity NPC51762
0.7347 Intermediate Similarity NPC473614
0.7222 Intermediate Similarity NPC200129
0.717 Intermediate Similarity NPC178644
0.7115 Intermediate Similarity NPC49088
0.7059 Intermediate Similarity NPC166362
0.7059 Intermediate Similarity NPC141777
0.7059 Intermediate Similarity NPC227670
0.6981 Remote Similarity NPC323445
0.6792 Remote Similarity NPC229403
0.6731 Remote Similarity NPC60556
0.6731 Remote Similarity NPC109813
0.6538 Remote Similarity NPC473912
0.6471 Remote Similarity NPC246165
0.6415 Remote Similarity NPC90803
0.6415 Remote Similarity NPC23145
0.6415 Remote Similarity NPC90506
0.6182 Remote Similarity NPC114239
0.6182 Remote Similarity NPC13991
0.6182 Remote Similarity NPC241784
0.6154 Remote Similarity NPC78551
0.6154 Remote Similarity NPC62086
0.6154 Remote Similarity NPC227632
0.6111 Remote Similarity NPC192529
0.6111 Remote Similarity NPC86538
0.6094 Remote Similarity NPC47840
0.6094 Remote Similarity NPC234264
0.6066 Remote Similarity NPC123194
0.6 Remote Similarity NPC248411
0.5909 Remote Similarity NPC124112
0.5893 Remote Similarity NPC86683
0.5893 Remote Similarity NPC296337
0.5873 Remote Similarity NPC49575
0.5873 Remote Similarity NPC55004
0.5873 Remote Similarity NPC267626
0.5846 Remote Similarity NPC162109
0.5833 Remote Similarity NPC473728
0.5821 Remote Similarity NPC475704
0.5806 Remote Similarity NPC470893
0.5781 Remote Similarity NPC469769
0.5781 Remote Similarity NPC472830
0.5758 Remote Similarity NPC15152
0.5692 Remote Similarity NPC5698
0.5692 Remote Similarity NPC309825
0.569 Remote Similarity NPC124851
0.5672 Remote Similarity NPC472306
0.5652 Remote Similarity NPC135650
0.5652 Remote Similarity NPC176171
0.5652 Remote Similarity NPC162309
0.5636 Remote Similarity NPC177470
0.5625 Remote Similarity NPC230823
0.5606 Remote Similarity NPC252809
0.5606 Remote Similarity NPC323153
0.5606 Remote Similarity NPC25853

  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 NPC471681 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
NPD

  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