Structure

Physi-Chem Properties

Molecular Weight:  149.12
Volume:  181.967
LogP:  3.629
LogD:  2.838
LogS:  -3.909
# Rotatable Bonds:  3
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.446
Synthetic Accessibility Score:  3.014
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.25
MDCK Permeability:  2.8029147870256566e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.445
30% Bioavailability (F30%):  0.055

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.945
Plasma Protein Binding (PPB):  96.78057098388672%
Volume Distribution (VD):  2.267
Pgp-substrate:  3.058823823928833%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.618
CYP2C19-inhibitor:  0.951
CYP2C19-substrate:  0.77
CYP2C9-inhibitor:  0.503
CYP2C9-substrate:  0.253
CYP2D6-inhibitor:  0.265
CYP2D6-substrate:  0.111
CYP3A4-inhibitor:  0.368
CYP3A4-substrate:  0.281

ADMET: Excretion

Clearance (CL):  9.876
Half-life (T1/2):  0.71

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.968
Drug-inuced Liver Injury (DILI):  0.114
AMES Toxicity:  0.474
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.124
Skin Sensitization:  0.428
Carcinogencity:  0.732
Eye Corrosion:  0.896
Eye Irritation:  0.988
Respiratory Toxicity:  0.85

Download Data

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

  Natural Product: NPC13217

Natural Product ID:  NPC13217
Common Name*:   (2Z)-3,7-Dimethylocta-2,6-Dienenitrile
IUPAC Name:   (2Z)-3,7-dimethylocta-2,6-dienenitrile
Synonyms:  
Standard InCHIKey:  HLCSDJLATUNSSI-YFHOEESVSA-N
Standard InCHI:  InChI=1S/C10H15N/c1-9(2)5-4-6-10(3)7-8-11/h5,7H,4,6H2,1-3H3/b10-7-
SMILES:  CC(=CCC/C(=CC#N)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3188973
PubChem CID:   1551245
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota stems n.a. n.a. PMID[20387902]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29334 Oplopanax elatus Species Araliaceae 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
NPT2 Others Unspecified Potency n.a. 2169 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76958.8 nM PubChem BioAssay data set

☑ 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 NPC13217 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
0.7742 Intermediate Similarity NPC19070
0.7742 Intermediate Similarity NPC51067
0.7742 Intermediate Similarity NPC225191
0.7273 Intermediate Similarity NPC115959
0.7273 Intermediate Similarity NPC138113
0.7273 Intermediate Similarity NPC123965
0.7188 Intermediate Similarity NPC179860
0.7059 Intermediate Similarity NPC60288
0.6857 Remote Similarity NPC206088
0.6857 Remote Similarity NPC3649
0.6857 Remote Similarity NPC100879
0.6857 Remote Similarity NPC66577
0.6857 Remote Similarity NPC471327
0.6667 Remote Similarity NPC213749
0.6486 Remote Similarity NPC99088
0.6486 Remote Similarity NPC305759
0.6486 Remote Similarity NPC173592
0.6471 Remote Similarity NPC262789
0.6471 Remote Similarity NPC64176
0.6471 Remote Similarity NPC288991
0.6471 Remote Similarity NPC138325
0.6286 Remote Similarity NPC34671
0.6154 Remote Similarity NPC92224
0.6154 Remote Similarity NPC282119
0.6154 Remote Similarity NPC38497
0.6 Remote Similarity NPC201753
0.6 Remote Similarity NPC76145
0.6 Remote Similarity NPC34764
0.6 Remote Similarity NPC185839
0.6 Remote Similarity NPC190810
0.5946 Remote Similarity NPC151719
0.5854 Remote Similarity NPC266298
0.5854 Remote Similarity NPC229262
0.5854 Remote Similarity NPC297643
0.5854 Remote Similarity NPC139717
0.5854 Remote Similarity NPC239039
0.5854 Remote Similarity NPC45727
0.5854 Remote Similarity NPC180840
0.5854 Remote Similarity NPC48638
0.5806 Remote Similarity NPC178306
0.58 Remote Similarity NPC476679
0.5714 Remote Similarity NPC29091
0.5714 Remote Similarity NPC182840
0.5714 Remote Similarity NPC10183
0.5714 Remote Similarity NPC103213
0.5714 Remote Similarity NPC255042
0.5641 Remote Similarity NPC12889
0.5625 Remote Similarity NPC106990
0.5625 Remote Similarity NPC96619

  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 NPC13217 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
0.6136 Remote Similarity NPD9675 Approved
0.6136 Remote Similarity NPD9674 Approved
0.6 Remote Similarity NPD319 Phase 1
0.5714 Remote Similarity NPD5783 Phase 3

  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