Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  335.374
LogP:  6.581
LogD:  5.324
LogS:  -6.106
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.42
Synthetic Accessibility Score:  3.667
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:  -4.739
MDCK Permeability:  2.0796387616428547e-05
Pgp-inhibitor:  0.533
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.037
20% Bioavailability (F20%):  0.727
30% Bioavailability (F30%):  0.198

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.161
Plasma Protein Binding (PPB):  95.01978302001953%
Volume Distribution (VD):  3.208
Pgp-substrate:  0.9955521821975708%

ADMET: Metabolism

CYP1A2-inhibitor:  0.436
CYP1A2-substrate:  0.195
CYP2C19-inhibitor:  0.299
CYP2C19-substrate:  0.073
CYP2C9-inhibitor:  0.55
CYP2C9-substrate:  0.954
CYP2D6-inhibitor:  0.462
CYP2D6-substrate:  0.271
CYP3A4-inhibitor:  0.33
CYP3A4-substrate:  0.142

ADMET: Excretion

Clearance (CL):  4.602
Half-life (T1/2):  0.243

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.064
Drug-inuced Liver Injury (DILI):  0.022
AMES Toxicity:  0.0
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.752
Skin Sensitization:  0.961
Carcinogencity:  0.02
Eye Corrosion:  0.376
Eye Irritation:  0.906
Respiratory Toxicity:  0.004

Download Data

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

  Natural Product: NPC471327

Natural Product ID:  NPC471327
Common Name*:   (E,E,E)-1-Isopropenyl-4,8,12-Trimethylcyclotetradeca-3,7,11-Triene
IUPAC Name:   (1E,5E,9E)-1,5,9-trimethyl-12-propan-2-ylidenecyclotetradeca-1,5,9-triene
Synonyms:  
Standard InCHIKey:  SHVZFTWRFOQOFU-GDVLXBNMSA-N
Standard InCHI:  InChI=1S/C20H32/c1-16(2)20-14-12-18(4)10-6-8-17(3)9-7-11-19(5)13-15-20/h8,11-12H,6-7,9-10,13-15H2,1-5H3/b17-8+,18-12+,19-11+
SMILES:  CC1=CCCC(=CCC(=C(C)C)CCC(=CCC1)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2414206
PubChem CID:   14336535
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[10923847]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[23859780]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae 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
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 >= 20.0 ug.mL-1 PMID[540295]

☑ 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 NPC471327 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
0.931 High Similarity NPC123965
0.931 High Similarity NPC115959
0.8788 High Similarity NPC92224
0.871 High Similarity NPC3649
0.871 High Similarity NPC100879
0.871 High Similarity NPC151719
0.8667 High Similarity NPC34671
0.8333 Intermediate Similarity NPC138325
0.8286 Intermediate Similarity NPC266298
0.8182 Intermediate Similarity NPC99088
0.8182 Intermediate Similarity NPC173592
0.8182 Intermediate Similarity NPC305759
0.8065 Intermediate Similarity NPC138113
0.7941 Intermediate Similarity NPC182392
0.7812 Intermediate Similarity NPC60288
0.7742 Intermediate Similarity NPC76765
0.7742 Intermediate Similarity NPC179103
0.7576 Intermediate Similarity NPC66577
0.7576 Intermediate Similarity NPC206088
0.75 Intermediate Similarity NPC34764
0.75 Intermediate Similarity NPC76145
0.75 Intermediate Similarity NPC190810
0.7353 Intermediate Similarity NPC213749
0.7333 Intermediate Similarity NPC88325
0.7297 Intermediate Similarity NPC239039
0.7297 Intermediate Similarity NPC229262
0.7297 Intermediate Similarity NPC297643
0.7297 Intermediate Similarity NPC139717
0.7222 Intermediate Similarity NPC282119
0.7188 Intermediate Similarity NPC262789
0.7188 Intermediate Similarity NPC64176
0.7188 Intermediate Similarity NPC288991
0.7143 Intermediate Similarity NPC62779
0.7097 Intermediate Similarity NPC266539
0.7097 Intermediate Similarity NPC287191
0.7097 Intermediate Similarity NPC266144
0.7097 Intermediate Similarity NPC31891
0.7059 Intermediate Similarity NPC196831
0.6923 Remote Similarity NPC183670
0.6905 Remote Similarity NPC49088
0.6857 Remote Similarity NPC13217
0.6842 Remote Similarity NPC180840
0.6774 Remote Similarity NPC38513
0.675 Remote Similarity NPC269823
0.675 Remote Similarity NPC120926
0.675 Remote Similarity NPC218918
0.675 Remote Similarity NPC144023
0.6744 Remote Similarity NPC323445
0.6591 Remote Similarity NPC124851
0.6585 Remote Similarity NPC213538
0.6585 Remote Similarity NPC473912
0.6585 Remote Similarity NPC177470
0.6585 Remote Similarity NPC256766
0.6579 Remote Similarity NPC185839
0.6444 Remote Similarity NPC17810
0.6444 Remote Similarity NPC22765
0.6444 Remote Similarity NPC17518
0.6429 Remote Similarity NPC109813
0.6429 Remote Similarity NPC116934
0.6429 Remote Similarity NPC301972
0.6429 Remote Similarity NPC60556
0.6429 Remote Similarity NPC86538
0.641 Remote Similarity NPC48638
0.641 Remote Similarity NPC45727
0.6364 Remote Similarity NPC8610
0.6364 Remote Similarity NPC262558
0.6364 Remote Similarity NPC10183
0.6341 Remote Similarity NPC188596
0.6316 Remote Similarity NPC38497
0.6304 Remote Similarity NPC182102
0.6304 Remote Similarity NPC329773
0.6304 Remote Similarity NPC26960
0.6279 Remote Similarity NPC138935
0.6279 Remote Similarity NPC248411
0.6279 Remote Similarity NPC202189
0.625 Remote Similarity NPC255042
0.625 Remote Similarity NPC182840
0.625 Remote Similarity NPC29091
0.625 Remote Similarity NPC103213
0.625 Remote Similarity NPC217923
0.617 Remote Similarity NPC234829
0.617 Remote Similarity NPC473672
0.617 Remote Similarity NPC474495
0.6154 Remote Similarity NPC201753
0.6136 Remote Similarity NPC86683
0.6136 Remote Similarity NPC114239
0.6136 Remote Similarity NPC241784
0.6136 Remote Similarity NPC140501
0.6136 Remote Similarity NPC296337
0.6136 Remote Similarity NPC76976
0.6136 Remote Similarity NPC160628
0.6136 Remote Similarity NPC13991
0.6136 Remote Similarity NPC191337
0.6098 Remote Similarity NPC18205
0.6098 Remote Similarity NPC12319
0.6042 Remote Similarity NPC208638
0.6 Remote Similarity NPC44363
0.6 Remote Similarity NPC110234
0.6 Remote Similarity NPC92863
0.6 Remote Similarity NPC178306
0.6 Remote Similarity NPC155880
0.6 Remote Similarity NPC308331
0.6 Remote Similarity NPC163751
0.6 Remote Similarity NPC100380
0.5957 Remote Similarity NPC20934
0.5957 Remote Similarity NPC288381
0.5952 Remote Similarity NPC33489
0.5952 Remote Similarity NPC469969
0.5918 Remote Similarity NPC474496
0.5909 Remote Similarity NPC477686
0.5909 Remote Similarity NPC108195
0.5909 Remote Similarity NPC267514
0.5909 Remote Similarity NPC25771
0.5909 Remote Similarity NPC145755
0.587 Remote Similarity NPC318549
0.5854 Remote Similarity NPC15934
0.5833 Remote Similarity NPC16561
0.5814 Remote Similarity NPC67761
0.5814 Remote Similarity NPC68889
0.5814 Remote Similarity NPC298710
0.5814 Remote Similarity NPC51758
0.5814 Remote Similarity NPC180871
0.5814 Remote Similarity NPC67920
0.5814 Remote Similarity NPC287397
0.5814 Remote Similarity NPC108494
0.5814 Remote Similarity NPC194586
0.5814 Remote Similarity NPC88079
0.5814 Remote Similarity NPC209279
0.5814 Remote Similarity NPC149668
0.5806 Remote Similarity NPC96619
0.5789 Remote Similarity NPC12889
0.5778 Remote Similarity NPC24824
0.5778 Remote Similarity NPC165651
0.5778 Remote Similarity NPC210560
0.5778 Remote Similarity NPC239754
0.5778 Remote Similarity NPC276825
0.5778 Remote Similarity NPC269074
0.5745 Remote Similarity NPC145311
0.5745 Remote Similarity NPC106990
0.5745 Remote Similarity NPC98284
0.5714 Remote Similarity NPC27444
0.5714 Remote Similarity NPC103236
0.5714 Remote Similarity NPC329762
0.5714 Remote Similarity NPC56917
0.5686 Remote Similarity NPC469770
0.5686 Remote Similarity NPC470893
0.5686 Remote Similarity NPC223604
0.5686 Remote Similarity NPC281590
0.5686 Remote Similarity NPC329686
0.5682 Remote Similarity NPC216921
0.5682 Remote Similarity NPC252978
0.5682 Remote Similarity NPC292463
0.5682 Remote Similarity NPC106819
0.5667 Remote Similarity NPC225855
0.5652 Remote Similarity NPC195246
0.5652 Remote Similarity NPC22098
0.5652 Remote Similarity NPC128280
0.5652 Remote Similarity NPC55063
0.5652 Remote Similarity NPC197467
0.5652 Remote Similarity NPC276009
0.5652 Remote Similarity NPC180575
0.5652 Remote Similarity NPC19834
0.5625 Remote Similarity NPC15325
0.5625 Remote Similarity NPC249670
0.5625 Remote Similarity NPC59051
0.5625 Remote Similarity NPC474642
0.5625 Remote Similarity NPC474460
0.5625 Remote Similarity NPC32351
0.5625 Remote Similarity NPC473913
0.561 Remote Similarity NPC34873
0.561 Remote Similarity NPC40434
0.56 Remote Similarity NPC476679
0.56 Remote Similarity NPC217188

  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 NPC471327 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
0.75 Intermediate Similarity NPD319 Phase 1
0.7105 Intermediate Similarity NPD5783 Phase 3
0.6444 Remote Similarity NPD8262 Approved
0.6136 Remote Similarity NPD4265 Approved
0.6098 Remote Similarity NPD1153 Clinical (unspecified phase)
0.5778 Remote Similarity NPD39 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