Structure

Physi-Chem Properties

Molecular Weight:  249.21
Volume:  282.693
LogP:  4.166
LogD:  3.646
LogS:  -3.7
# Rotatable Bonds:  3
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.6
Synthetic Accessibility Score:  4.492
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:  -4.483
MDCK Permeability:  1.4585004464606754e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.795
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.896
Plasma Protein Binding (PPB):  31.16571807861328%
Volume Distribution (VD):  1.635
Pgp-substrate:  56.90271759033203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.158
CYP1A2-substrate:  0.802
CYP2C19-inhibitor:  0.552
CYP2C19-substrate:  0.911
CYP2C9-inhibitor:  0.149
CYP2C9-substrate:  0.462
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.656
CYP3A4-inhibitor:  0.842
CYP3A4-substrate:  0.316

ADMET: Excretion

Clearance (CL):  8.85
Half-life (T1/2):  0.204

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.255
Drug-inuced Liver Injury (DILI):  0.226
AMES Toxicity:  0.066
Rat Oral Acute Toxicity:  0.185
Maximum Recommended Daily Dose:  0.085
Skin Sensitization:  0.537
Carcinogencity:  0.243
Eye Corrosion:  0.013
Eye Irritation:  0.135
Respiratory Toxicity:  0.843

Download Data

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

  Natural Product: NPC476682

Natural Product ID:  NPC476682
Common Name*:   N-[(1R,4aS,8S,8aS)-1,4a-dimethyl-8-prop-1-en-2-yl-2,3,4,5,6,7,8,8a-octahydronaphthalen-1-yl]formamide
IUPAC Name:   N-[(1R,4aS,8S,8aS)-1,4a-dimethyl-8-prop-1-en-2-yl-2,3,4,5,6,7,8,8a-octahydronaphthalen-1-yl]formamide
Synonyms:  
Standard InCHIKey:  JBJCEWWBNURZRA-FXUDXRNXSA-N
Standard InCHI:  InChI=1S/C16H27NO/c1-12(2)13-7-5-8-15(3)9-6-10-16(4,14(13)15)17-11-18/h11,13-14H,1,5-10H2,2-4H3,(H,17,18)/t13-,14+,15+,16-/m1/s1
SMILES:  CC(=C)[C@H]1CCC[C@@]2([C@H]1[C@](CCC2)(C)NC=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44575483
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 = 1.2 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 NPC476682 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
0.8906 High Similarity NPC476135
0.8429 Intermediate Similarity NPC476308
0.8382 Intermediate Similarity NPC476329
0.8095 Intermediate Similarity NPC28755
0.8095 Intermediate Similarity NPC152211
0.7826 Intermediate Similarity NPC472831
0.7571 Intermediate Similarity NPC138409
0.7463 Intermediate Similarity NPC477740
0.7344 Intermediate Similarity NPC318036
0.7313 Intermediate Similarity NPC477739
0.7231 Intermediate Similarity NPC173815
0.7206 Intermediate Similarity NPC89921
0.7183 Intermediate Similarity NPC476288
0.7164 Intermediate Similarity NPC311809
0.7121 Intermediate Similarity NPC324944
0.7083 Intermediate Similarity NPC184919
0.7013 Intermediate Similarity NPC79704
0.6957 Remote Similarity NPC145715
0.6912 Remote Similarity NPC317778
0.6901 Remote Similarity NPC474456
0.6901 Remote Similarity NPC37792
0.6857 Remote Similarity NPC473959
0.6812 Remote Similarity NPC219621
0.6747 Remote Similarity NPC56107
0.6667 Remote Similarity NPC476681
0.6622 Remote Similarity NPC124384
0.6471 Remote Similarity NPC470369
0.6471 Remote Similarity NPC470370
0.6441 Remote Similarity NPC103290
0.6364 Remote Similarity NPC474416
0.6333 Remote Similarity NPC193180
0.6286 Remote Similarity NPC472827
0.625 Remote Similarity NPC474596
0.625 Remote Similarity NPC474435
0.625 Remote Similarity NPC474027
0.6235 Remote Similarity NPC152684
0.6232 Remote Similarity NPC11130
0.6163 Remote Similarity NPC166458
0.6163 Remote Similarity NPC474458
0.6145 Remote Similarity NPC257962
0.6145 Remote Similarity NPC475724
0.6087 Remote Similarity NPC264779
0.6081 Remote Similarity NPC475812
0.6081 Remote Similarity NPC476737
0.6081 Remote Similarity NPC27243
0.6076 Remote Similarity NPC476904
0.6071 Remote Similarity NPC224072
0.6044 Remote Similarity NPC280710
0.6044 Remote Similarity NPC243985
0.6029 Remote Similarity NPC476683
0.6026 Remote Similarity NPC21773
0.6026 Remote Similarity NPC265789
0.6024 Remote Similarity NPC250632
0.6 Remote Similarity NPC125828
0.6 Remote Similarity NPC476039
0.6 Remote Similarity NPC476406
0.6 Remote Similarity NPC149680
0.6 Remote Similarity NPC474457
0.6 Remote Similarity NPC222366
0.6 Remote Similarity NPC475696
0.6 Remote Similarity NPC22765
0.6 Remote Similarity NPC474528
0.6 Remote Similarity NPC286669
0.6 Remote Similarity NPC474415
0.5974 Remote Similarity NPC245223
0.5946 Remote Similarity NPC144650
0.5946 Remote Similarity NPC68656
0.5946 Remote Similarity NPC101128
0.5921 Remote Similarity NPC69649
0.5921 Remote Similarity NPC68703
0.5921 Remote Similarity NPC197805
0.5915 Remote Similarity NPC474769
0.5915 Remote Similarity NPC189290
0.5909 Remote Similarity NPC472829
0.589 Remote Similarity NPC41160
0.5882 Remote Similarity NPC283277
0.5882 Remote Similarity NPC39966
0.5867 Remote Similarity NPC282619
0.5867 Remote Similarity NPC172613
0.5867 Remote Similarity NPC60837
0.5867 Remote Similarity NPC2728
0.5867 Remote Similarity NPC258595
0.5867 Remote Similarity NPC11555
0.5867 Remote Similarity NPC208198
0.5851 Remote Similarity NPC240650
0.5844 Remote Similarity NPC160209
0.5843 Remote Similarity NPC34754
0.5833 Remote Similarity NPC474420
0.5833 Remote Similarity NPC474454
0.5833 Remote Similarity NPC475716
0.5833 Remote Similarity NPC309825
0.5833 Remote Similarity NPC474455
0.5811 Remote Similarity NPC475755
0.5806 Remote Similarity NPC105246
0.5806 Remote Similarity NPC311164
0.5806 Remote Similarity NPC272732
0.5806 Remote Similarity NPC190232
0.5789 Remote Similarity NPC475897
0.5789 Remote Similarity NPC473929
0.5781 Remote Similarity NPC86683
0.5769 Remote Similarity NPC9942
0.5758 Remote Similarity NPC17518
0.5745 Remote Similarity NPC476903
0.5738 Remote Similarity NPC62086
0.5738 Remote Similarity NPC227632
0.5738 Remote Similarity NPC78551
0.5735 Remote Similarity NPC212905
0.5732 Remote Similarity NPC7214
0.5714 Remote Similarity NPC139207
0.5714 Remote Similarity NPC211322
0.5714 Remote Similarity NPC253303
0.5714 Remote Similarity NPC185874
0.5714 Remote Similarity NPC269077
0.5714 Remote Similarity NPC474583
0.5699 Remote Similarity NPC477290
0.5698 Remote Similarity NPC215474
0.5696 Remote Similarity NPC145498
0.5696 Remote Similarity NPC45296
0.5696 Remote Similarity NPC91369
0.5696 Remote Similarity NPC189745
0.5694 Remote Similarity NPC60772
0.5694 Remote Similarity NPC472830
0.5684 Remote Similarity NPC167419
0.5684 Remote Similarity NPC184033
0.5682 Remote Similarity NPC24733
0.5682 Remote Similarity NPC75810
0.5676 Remote Similarity NPC469728
0.5676 Remote Similarity NPC147524
0.5658 Remote Similarity NPC163678
0.5658 Remote Similarity NPC64123
0.5658 Remote Similarity NPC107258
0.5652 Remote Similarity NPC475272
0.5652 Remote Similarity NPC472828
0.5652 Remote Similarity NPC127944
0.5641 Remote Similarity NPC244790
0.5641 Remote Similarity NPC208999
0.5641 Remote Similarity NPC276616
0.5641 Remote Similarity NPC245795
0.5641 Remote Similarity NPC216460
0.5641 Remote Similarity NPC32055
0.5634 Remote Similarity NPC39068
0.5632 Remote Similarity NPC246956
0.5625 Remote Similarity NPC242001
0.5625 Remote Similarity NPC164045
0.5625 Remote Similarity NPC111234
0.5625 Remote Similarity NPC167706
0.5625 Remote Similarity NPC301226
0.5618 Remote Similarity NPC157479
0.5612 Remote Similarity NPC247060
0.5612 Remote Similarity NPC471083
0.5612 Remote Similarity NPC50815
0.5606 Remote Similarity NPC124851
0.5604 Remote Similarity NPC249312
0.56 Remote Similarity NPC474086
0.56 Remote Similarity NPC55462

  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 NPC476682 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
0.5897 Remote Similarity NPD6939 Phase 2
0.5897 Remote Similarity NPD6938 Clinical (unspecified phase)
0.587 Remote Similarity NPD5771 Approved
0.5806 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5699 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5625 Remote Similarity NPD873 Approved
0.5625 Remote Similarity NPD871 Approved

  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