Structure

Physi-Chem Properties

Molecular Weight:  138.14
Volume:  176.243
LogP:  4.691
LogD:  4.216
LogS:  -4.373
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.521
Synthetic Accessibility Score:  3.292
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.435
MDCK Permeability:  2.3108863388188183e-05
Pgp-inhibitor:  0.246
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.744
30% Bioavailability (F30%):  0.333

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.421
Plasma Protein Binding (PPB):  93.4990234375%
Volume Distribution (VD):  2.735
Pgp-substrate:  8.052942276000977%

ADMET: Metabolism

CYP1A2-inhibitor:  0.875
CYP1A2-substrate:  0.475
CYP2C19-inhibitor:  0.361
CYP2C19-substrate:  0.826
CYP2C9-inhibitor:  0.111
CYP2C9-substrate:  0.852
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.532
CYP3A4-inhibitor:  0.226
CYP3A4-substrate:  0.256

ADMET: Excretion

Clearance (CL):  12.265
Half-life (T1/2):  0.209

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.602
Drug-inuced Liver Injury (DILI):  0.025
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.04
Maximum Recommended Daily Dose:  0.293
Skin Sensitization:  0.92
Carcinogencity:  0.393
Eye Corrosion:  0.935
Eye Irritation:  0.985
Respiratory Toxicity:  0.088

Download Data

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

  Natural Product: NPC206088

Natural Product ID:  NPC206088
Common Name*:   (3S)-3,7-Dimethylocta-1,6-Diene
IUPAC Name:   (3S)-3,7-dimethylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  FUDNBFMOXDUIIE-SNVBAGLBSA-N
Standard InCHI:  InChI=1S/C10H18/c1-5-10(4)8-6-7-9(2)3/h5,7,10H,1,6,8H2,2-4H3/t10-/m1/s1
SMILES:  C=C[C@@H](C)CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183521
PubChem CID:   10887985
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

☑ 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. 1.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2.2 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 NPC206088 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
0.9032 High Similarity NPC213749
0.8788 High Similarity NPC282119
0.871 High Similarity NPC66577
0.8667 High Similarity NPC138113
0.8387 Intermediate Similarity NPC60288
0.8286 Intermediate Similarity NPC45727
0.8286 Intermediate Similarity NPC48638
0.8235 Intermediate Similarity NPC92224
0.8065 Intermediate Similarity NPC123965
0.8065 Intermediate Similarity NPC115959
0.8 Intermediate Similarity NPC190810
0.8 Intermediate Similarity NPC76145
0.8 Intermediate Similarity NPC34764
0.7838 Intermediate Similarity NPC183670
0.7778 Intermediate Similarity NPC297643
0.7778 Intermediate Similarity NPC229262
0.7778 Intermediate Similarity NPC139717
0.7778 Intermediate Similarity NPC266298
0.7778 Intermediate Similarity NPC239039
0.7742 Intermediate Similarity NPC64176
0.7742 Intermediate Similarity NPC262789
0.7742 Intermediate Similarity NPC288991
0.7742 Intermediate Similarity NPC138325
0.7647 Intermediate Similarity NPC305759
0.7647 Intermediate Similarity NPC99088
0.7647 Intermediate Similarity NPC173592
0.7632 Intermediate Similarity NPC120926
0.7632 Intermediate Similarity NPC144023
0.7632 Intermediate Similarity NPC218918
0.7576 Intermediate Similarity NPC471327
0.7576 Intermediate Similarity NPC3649
0.7576 Intermediate Similarity NPC100879
0.75 Intermediate Similarity NPC34671
0.7436 Intermediate Similarity NPC177470
0.7419 Intermediate Similarity NPC10183
0.7179 Intermediate Similarity NPC469969
0.7059 Intermediate Similarity NPC151719
0.7 Intermediate Similarity NPC51758
0.7 Intermediate Similarity NPC209279
0.7 Intermediate Similarity NPC68889
0.7 Intermediate Similarity NPC473912
0.7 Intermediate Similarity NPC194586
0.7 Intermediate Similarity NPC180871
0.7 Intermediate Similarity NPC108494
0.7 Intermediate Similarity NPC88079
0.7 Intermediate Similarity NPC67761
0.6857 Remote Similarity NPC13217
0.6829 Remote Similarity NPC60556
0.6829 Remote Similarity NPC109813
0.6829 Remote Similarity NPC106819
0.6829 Remote Similarity NPC86538
0.6774 Remote Similarity NPC88325
0.675 Remote Similarity NPC188596
0.6744 Remote Similarity NPC323445
0.6667 Remote Similarity NPC248411
0.6667 Remote Similarity NPC202189
0.6591 Remote Similarity NPC124851
0.6579 Remote Similarity NPC185839
0.6571 Remote Similarity NPC196831
0.6562 Remote Similarity NPC31891
0.6562 Remote Similarity NPC266539
0.6562 Remote Similarity NPC266144
0.6562 Remote Similarity NPC287191
0.6552 Remote Similarity NPC178306
0.6512 Remote Similarity NPC296337
0.6512 Remote Similarity NPC241784
0.6512 Remote Similarity NPC86683
0.6512 Remote Similarity NPC13991
0.6512 Remote Similarity NPC49088
0.6512 Remote Similarity NPC114239
0.6512 Remote Similarity NPC210560
0.6512 Remote Similarity NPC24824
0.6512 Remote Similarity NPC165651
0.65 Remote Similarity NPC56917
0.6486 Remote Similarity NPC182392
0.6429 Remote Similarity NPC216921
0.641 Remote Similarity NPC180840
0.6364 Remote Similarity NPC276009
0.6364 Remote Similarity NPC195246
0.6364 Remote Similarity NPC8610
0.6364 Remote Similarity NPC22098
0.6364 Remote Similarity NPC262558
0.6341 Remote Similarity NPC259702
0.6333 Remote Similarity NPC96619
0.6316 Remote Similarity NPC38497
0.625 Remote Similarity NPC255042
0.625 Remote Similarity NPC182840
0.625 Remote Similarity NPC38513
0.625 Remote Similarity NPC29091
0.625 Remote Similarity NPC103213
0.6222 Remote Similarity NPC178644
0.6216 Remote Similarity NPC62779
0.6207 Remote Similarity NPC225855
0.619 Remote Similarity NPC105246
0.619 Remote Similarity NPC190232
0.6176 Remote Similarity NPC179103
0.6176 Remote Similarity NPC76765
0.617 Remote Similarity NPC148056
0.6154 Remote Similarity NPC201753
0.6136 Remote Similarity NPC166788
0.6098 Remote Similarity NPC18205
0.6098 Remote Similarity NPC12319
0.6087 Remote Similarity NPC91765
0.6087 Remote Similarity NPC17810
0.6087 Remote Similarity NPC22765
0.6087 Remote Similarity NPC15912
0.6087 Remote Similarity NPC106990
0.6087 Remote Similarity NPC17518
0.6087 Remote Similarity NPC234597
0.6087 Remote Similarity NPC62755
0.6042 Remote Similarity NPC294358
0.6042 Remote Similarity NPC151919
0.6042 Remote Similarity NPC68014
0.6042 Remote Similarity NPC40417
0.6042 Remote Similarity NPC208638
0.6 Remote Similarity NPC34873
0.6 Remote Similarity NPC92863
0.6 Remote Similarity NPC40434
0.6 Remote Similarity NPC159420
0.6 Remote Similarity NPC155880
0.5957 Remote Similarity NPC27264
0.5957 Remote Similarity NPC329773
0.5957 Remote Similarity NPC26960
0.5957 Remote Similarity NPC32351
0.5957 Remote Similarity NPC474460
0.5957 Remote Similarity NPC289388
0.5957 Remote Similarity NPC118788
0.5957 Remote Similarity NPC182102
0.5952 Remote Similarity NPC269823
0.5918 Remote Similarity NPC14002
0.5918 Remote Similarity NPC476679
0.5909 Remote Similarity NPC138935
0.587 Remote Similarity NPC91962
0.5862 Remote Similarity NPC33192
0.5854 Remote Similarity NPC217923
0.5854 Remote Similarity NPC55269
0.5854 Remote Similarity NPC15934
0.5833 Remote Similarity NPC27438
0.5833 Remote Similarity NPC244038
0.5833 Remote Similarity NPC214584
0.5833 Remote Similarity NPC26906
0.5833 Remote Similarity NPC244452
0.5833 Remote Similarity NPC48162
0.5814 Remote Similarity NPC213538
0.5814 Remote Similarity NPC256766
0.58 Remote Similarity NPC5626
0.5789 Remote Similarity NPC12889
0.5714 Remote Similarity NPC177112
0.5714 Remote Similarity NPC170167
0.5714 Remote Similarity NPC216407
0.5714 Remote Similarity NPC227632
0.5714 Remote Similarity NPC181255
0.5714 Remote Similarity NPC179169
0.5714 Remote Similarity NPC246165
0.5714 Remote Similarity NPC35756
0.5714 Remote Similarity NPC71506
0.5714 Remote Similarity NPC157781
0.5714 Remote Similarity NPC35519
0.5714 Remote Similarity NPC473728
0.5714 Remote Similarity NPC306195
0.5714 Remote Similarity NPC62086
0.5714 Remote Similarity NPC78551
0.5686 Remote Similarity NPC470893
0.5682 Remote Similarity NPC15162
0.5682 Remote Similarity NPC301972
0.5682 Remote Similarity NPC116934
0.5682 Remote Similarity NPC269862
0.5682 Remote Similarity NPC192529
0.5652 Remote Similarity NPC100380
0.5625 Remote Similarity NPC176819
0.5625 Remote Similarity NPC58970
0.5625 Remote Similarity NPC163984
0.5625 Remote Similarity NPC200129
0.56 Remote Similarity NPC23117
0.56 Remote Similarity NPC45283
0.56 Remote Similarity NPC268564
0.56 Remote Similarity NPC37644
0.56 Remote Similarity NPC165755

  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 NPC206088 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
0.8 Intermediate Similarity NPD319 Phase 1
0.625 Remote Similarity NPD5783 Phase 3
0.619 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6098 Remote Similarity NPD1153 Clinical (unspecified phase)
0.6087 Remote Similarity NPD8262 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