Structure

Physi-Chem Properties

Molecular Weight:  263.17
Volume:  289.776
LogP:  5.314
LogD:  4.337
LogS:  -5.109
# Rotatable Bonds:  2
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.386
Synthetic Accessibility Score:  4.759
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.751
MDCK Permeability:  2.5654551791376434e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.896
Plasma Protein Binding (PPB):  62.513336181640625%
Volume Distribution (VD):  1.559
Pgp-substrate:  24.228282928466797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.134
CYP1A2-substrate:  0.469
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.917
CYP2C9-inhibitor:  0.044
CYP2C9-substrate:  0.176
CYP2D6-inhibitor:  0.048
CYP2D6-substrate:  0.556
CYP3A4-inhibitor:  0.718
CYP3A4-substrate:  0.327

ADMET: Excretion

Clearance (CL):  3.758
Half-life (T1/2):  0.273

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.09
Drug-inuced Liver Injury (DILI):  0.391
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.915
Skin Sensitization:  0.872
Carcinogencity:  0.13
Eye Corrosion:  0.994
Eye Irritation:  0.966
Respiratory Toxicity:  0.873

Download Data

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

  Natural Product: NPC152211

Natural Product ID:  NPC152211
Common Name*:   (1R,4Ar,7R,8Ar)-1-Isothiocyanato-1,4A-Dimethyl-7-(Prop-1-En-2-Yl)Decahydronaphthalene
IUPAC Name:   (3R,4aR,5R,8aR)-5-isothiocyanato-5,8a-dimethyl-3-prop-1-en-2-yl-1,2,3,4,4a,6,7,8-octahydronaphthalene
Synonyms:  
Standard InCHIKey:  HTWIRGRTEPTBCC-KLHDSHLOSA-N
Standard InCHI:  InChI=1S/C16H25NS/c1-12(2)13-6-9-15(3)7-5-8-16(4,17-11-18)14(15)10-13/h13-14H,1,5-10H2,2-4H3/t13-,14-,15-,16-/m1/s1
SMILES:  S=C=N[C@]1(C)CCC[C@]2([C@H]1C[C@@H](CC2)C(=C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL454852
PubChem CID:   23427224
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane 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
NPO4958 Acanthella klethra Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[1294700]
NPO4958 Acanthella klethra Species Melastomataceae 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
NPT91 Cell Line KB Homo sapiens IC50 > 20.0 ug.mL-1 PMID[482795]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10.0 ug.mL-1 PMID[482795]

☑ 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 NPC152211 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
1.0 High Similarity NPC28755
0.8594 High Similarity NPC184919
0.8525 High Similarity NPC145715
0.85 High Similarity NPC311809
0.8413 Intermediate Similarity NPC474456
0.8387 Intermediate Similarity NPC473959
0.8136 Intermediate Similarity NPC318036
0.8125 Intermediate Similarity NPC37792
0.8095 Intermediate Similarity NPC476682
0.8 Intermediate Similarity NPC173815
0.7869 Intermediate Similarity NPC324944
0.7761 Intermediate Similarity NPC138409
0.7639 Intermediate Similarity NPC79704
0.7619 Intermediate Similarity NPC317778
0.7463 Intermediate Similarity NPC476135
0.7419 Intermediate Similarity NPC470370
0.7419 Intermediate Similarity NPC470369
0.7231 Intermediate Similarity NPC219621
0.7123 Intermediate Similarity NPC476308
0.7121 Intermediate Similarity NPC475755
0.7119 Intermediate Similarity NPC476681
0.7119 Intermediate Similarity NPC472829
0.7091 Intermediate Similarity NPC193180
0.7049 Intermediate Similarity NPC475272
0.7049 Intermediate Similarity NPC474416
0.7042 Intermediate Similarity NPC476329
0.6935 Remote Similarity NPC476683
0.6923 Remote Similarity NPC472827
0.6909 Remote Similarity NPC103290
0.6753 Remote Similarity NPC250632
0.6667 Remote Similarity NPC22765
0.6615 Remote Similarity NPC475696
0.6615 Remote Similarity NPC474415
0.6615 Remote Similarity NPC474528
0.6615 Remote Similarity NPC474457
0.6528 Remote Similarity NPC472831
0.6491 Remote Similarity NPC190232
0.6491 Remote Similarity NPC105246
0.6463 Remote Similarity NPC474458
0.6456 Remote Similarity NPC475724
0.6418 Remote Similarity NPC474420
0.6418 Remote Similarity NPC474455
0.6418 Remote Similarity NPC475716
0.6418 Remote Similarity NPC474454
0.64 Remote Similarity NPC476904
0.6393 Remote Similarity NPC17518
0.6377 Remote Similarity NPC474027
0.6377 Remote Similarity NPC474435
0.6377 Remote Similarity NPC474596
0.6351 Remote Similarity NPC265789
0.6351 Remote Similarity NPC21773
0.6349 Remote Similarity NPC212905
0.6316 Remote Similarity NPC125828
0.6265 Remote Similarity NPC56107
0.625 Remote Similarity NPC127944
0.623 Remote Similarity NPC124851
0.6197 Remote Similarity NPC475812
0.6167 Remote Similarity NPC86683
0.6143 Remote Similarity NPC477740
0.6143 Remote Similarity NPC474086
0.614 Remote Similarity NPC62086
0.614 Remote Similarity NPC227632
0.614 Remote Similarity NPC78551
0.6102 Remote Similarity NPC192529
0.6061 Remote Similarity NPC469770
0.6026 Remote Similarity NPC7214
0.6 Remote Similarity NPC472828
0.6 Remote Similarity NPC211322
0.6 Remote Similarity NPC477739
0.5976 Remote Similarity NPC283277
0.5946 Remote Similarity NPC476288
0.5915 Remote Similarity NPC89921
0.5854 Remote Similarity NPC329782
0.5846 Remote Similarity NPC473728
0.5821 Remote Similarity NPC123194
0.5797 Remote Similarity NPC472830
0.5783 Remote Similarity NPC472312
0.5765 Remote Similarity NPC152684
0.5765 Remote Similarity NPC24733
0.5758 Remote Similarity NPC476679
0.5738 Remote Similarity NPC202189
0.5735 Remote Similarity NPC264779
0.5732 Remote Similarity NPC12035
0.5714 Remote Similarity NPC21781
0.5714 Remote Similarity NPC171639
0.5698 Remote Similarity NPC166458
0.5663 Remote Similarity NPC152039
0.5663 Remote Similarity NPC118329
0.5663 Remote Similarity NPC257962
0.5645 Remote Similarity NPC114239
0.5645 Remote Similarity NPC13991
0.5645 Remote Similarity NPC241784
0.5645 Remote Similarity NPC296337
0.5625 Remote Similarity NPC106990

  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 NPC152211 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
0.6491 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6 Remote Similarity NPD873 Approved
0.6 Remote Similarity NPD6939 Phase 2
0.6 Remote Similarity NPD871 Approved
0.6 Remote Similarity NPD6938 Clinical (unspecified phase)

  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