Structure

Physi-Chem Properties

Molecular Weight:  231.2
Volume:  271.267
LogP:  4.273
LogD:  3.572
LogS:  -4.443
# Rotatable Bonds:  1
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.6
Synthetic Accessibility Score:  4.342
Fsp3:  0.812
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:  -4.612
MDCK Permeability:  2.5489460313110612e-05
Pgp-inhibitor:  0.438
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.515
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.9
Plasma Protein Binding (PPB):  62.84965515136719%
Volume Distribution (VD):  1.367
Pgp-substrate:  36.695701599121094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.358
CYP1A2-substrate:  0.84
CYP2C19-inhibitor:  0.224
CYP2C19-substrate:  0.838
CYP2C9-inhibitor:  0.215
CYP2C9-substrate:  0.279
CYP2D6-inhibitor:  0.044
CYP2D6-substrate:  0.103
CYP3A4-inhibitor:  0.897
CYP3A4-substrate:  0.4

ADMET: Excretion

Clearance (CL):  12.353
Half-life (T1/2):  0.227

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.557
Drug-inuced Liver Injury (DILI):  0.846
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.925
Maximum Recommended Daily Dose:  0.225
Skin Sensitization:  0.659
Carcinogencity:  0.685
Eye Corrosion:  0.973
Eye Irritation:  0.949
Respiratory Toxicity:  0.971

Download Data

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

  Natural Product: NPC476681

Natural Product ID:  NPC476681
Common Name*:   (1R,4aS,8S,8aS)-1,4a-dimethyl-8-prop-1-en-2-yl-2,3,4,5,6,7,8,8a-octahydronaphthalene-1-carbonitrile
IUPAC Name:   (1R,4aS,8S,8aS)-1,4a-dimethyl-8-prop-1-en-2-yl-2,3,4,5,6,7,8,8a-octahydronaphthalene-1-carbonitrile
Synonyms:  
Standard InCHIKey:  UZOKDTCVQZBQPP-UGUYLWEFSA-N
Standard InCHI:  InChI=1S/C16H25N/c1-12(2)13-7-5-8-15(3)9-6-10-16(4,11-17)14(13)15/h13-14H,1,5-10H2,2-4H3/t13-,14+,15+,16+/m1/s1
SMILES:  CC(=C)[C@H]1CCC[C@@]2([C@H]1[C@](CCC2)(C)C#N)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44575477
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO33521 Axinyssa terpnis Species Halichondriidae Eukaryota n.a. Chuuk Atoll, Federated States of Micronesia n.a. PMID[9548881]

☑ 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
NPT168 Cell Line P388 Mus musculus IC50 = 8.3 ug/ml PMID[9548881]
NPT140 Organism Artemia Artemia LC50 = 50 ug/ml PMID[9548881]

☑ 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 NPC476681 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
0.9388 High Similarity NPC474416
0.8679 High Similarity NPC474457
0.8679 High Similarity NPC474415
0.8679 High Similarity NPC474528
0.8679 High Similarity NPC475696
0.8364 Intermediate Similarity NPC475716
0.8364 Intermediate Similarity NPC474420
0.8364 Intermediate Similarity NPC474455
0.8364 Intermediate Similarity NPC474454
0.8261 Intermediate Similarity NPC103290
0.8085 Intermediate Similarity NPC193180
0.7931 Intermediate Similarity NPC474086
0.7778 Intermediate Similarity NPC476683
0.7593 Intermediate Similarity NPC476679
0.7541 Intermediate Similarity NPC474456
0.75 Intermediate Similarity NPC22765
0.7347 Intermediate Similarity NPC190232
0.7347 Intermediate Similarity NPC105246
0.7292 Intermediate Similarity NPC227632
0.7292 Intermediate Similarity NPC78551
0.7292 Intermediate Similarity NPC62086
0.7255 Intermediate Similarity NPC86683
0.7193 Intermediate Similarity NPC318036
0.717 Intermediate Similarity NPC17518
0.7119 Intermediate Similarity NPC28755
0.7119 Intermediate Similarity NPC152211
0.7069 Intermediate Similarity NPC173815
0.6981 Remote Similarity NPC124851
0.6964 Remote Similarity NPC127944
0.6949 Remote Similarity NPC324944
0.6863 Remote Similarity NPC192529
0.6833 Remote Similarity NPC472827
0.6724 Remote Similarity NPC469770
0.6721 Remote Similarity NPC317778
0.6721 Remote Similarity NPC311809
0.6667 Remote Similarity NPC476682
0.6613 Remote Similarity NPC219621
0.6538 Remote Similarity NPC141777
0.6538 Remote Similarity NPC227670
0.6538 Remote Similarity NPC166362
0.6441 Remote Similarity NPC123194
0.6415 Remote Similarity NPC202189
0.6393 Remote Similarity NPC60772
0.6333 Remote Similarity NPC264779
0.6308 Remote Similarity NPC475812
0.6296 Remote Similarity NPC114239
0.6296 Remote Similarity NPC229403
0.6296 Remote Similarity NPC13991
0.6296 Remote Similarity NPC296337
0.6296 Remote Similarity NPC241784
0.6275 Remote Similarity NPC246165
0.623 Remote Similarity NPC470369
0.623 Remote Similarity NPC470370
0.6176 Remote Similarity NPC138409
0.6176 Remote Similarity NPC184919
0.6129 Remote Similarity NPC189290
0.6129 Remote Similarity NPC474769
0.6129 Remote Similarity NPC469769
0.6111 Remote Similarity NPC248411
0.6094 Remote Similarity NPC41160
0.6034 Remote Similarity NPC236623
0.6 Remote Similarity NPC49088
0.6 Remote Similarity NPC21773
0.6 Remote Similarity NPC474596
0.6 Remote Similarity NPC202118
0.6 Remote Similarity NPC197238
0.6 Remote Similarity NPC145715
0.6 Remote Similarity NPC265789
0.597 Remote Similarity NPC37792
0.5968 Remote Similarity NPC11130
0.5965 Remote Similarity NPC17810
0.5932 Remote Similarity NPC473728
0.5926 Remote Similarity NPC474118
0.5926 Remote Similarity NPC90506
0.5926 Remote Similarity NPC90803
0.5926 Remote Similarity NPC51762
0.5926 Remote Similarity NPC60556
0.5926 Remote Similarity NPC23145
0.5926 Remote Similarity NPC86538
0.5926 Remote Similarity NPC109813
0.5909 Remote Similarity NPC469662
0.5909 Remote Similarity NPC473959
0.5909 Remote Similarity NPC169275
0.5909 Remote Similarity NPC52449
0.5902 Remote Similarity NPC470893
0.5902 Remote Similarity NPC200258
0.5897 Remote Similarity NPC477289
0.5893 Remote Similarity NPC323445
0.5882 Remote Similarity NPC476135
0.5873 Remote Similarity NPC472830
0.5862 Remote Similarity NPC200129
0.5846 Remote Similarity NPC469728
0.5833 Remote Similarity NPC472828
0.5833 Remote Similarity NPC476904
0.5821 Remote Similarity NPC474768
0.5821 Remote Similarity NPC107258
0.5821 Remote Similarity NPC27243
0.5821 Remote Similarity NPC476737
0.5821 Remote Similarity NPC268039
0.5821 Remote Similarity NPC64123
0.5806 Remote Similarity NPC39068
0.5758 Remote Similarity NPC475755
0.5758 Remote Similarity NPC474435
0.5758 Remote Similarity NPC474027
0.5741 Remote Similarity NPC177470
0.5735 Remote Similarity NPC43300
0.5735 Remote Similarity NPC476406
0.5735 Remote Similarity NPC96812
0.5735 Remote Similarity NPC107704
0.5735 Remote Similarity NPC185587
0.5735 Remote Similarity NPC168824
0.5735 Remote Similarity NPC476039
0.5735 Remote Similarity NPC39462
0.5735 Remote Similarity NPC149680
0.5735 Remote Similarity NPC222366
0.5735 Remote Similarity NPC92327
0.5735 Remote Similarity NPC286669
0.5735 Remote Similarity NPC189917
0.5714 Remote Similarity NPC472831
0.5692 Remote Similarity NPC127582
0.5692 Remote Similarity NPC176621
0.5676 Remote Similarity NPC476308
0.5676 Remote Similarity NPC7214
0.5672 Remote Similarity NPC144650
0.5672 Remote Similarity NPC68656
0.5672 Remote Similarity NPC101128
0.5652 Remote Similarity NPC176107
0.5652 Remote Similarity NPC197805
0.5652 Remote Similarity NPC68703
0.5652 Remote Similarity NPC69649
0.5606 Remote Similarity NPC60565

  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 NPC476681 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
0.7347 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6087 Remote Similarity NPD6939 Phase 2
0.6087 Remote Similarity NPD6938 Clinical (unspecified phase)
0.5965 Remote Similarity NPD8262 Approved
0.5921 Remote Similarity NPD8028 Phase 2

  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