Structure

Physi-Chem Properties

Molecular Weight:  288.25
Volume:  344.164
LogP:  4.493
LogD:  4.054
LogS:  -4.553
# Rotatable Bonds:  3
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.519
Synthetic Accessibility Score:  4.124
Fsp3:  0.6
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:  -4.492
MDCK Permeability:  2.0844188838964328e-05
Pgp-inhibitor:  0.062
Pgp-substrate:  0.042
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.644
Plasma Protein Binding (PPB):  96.27404022216797%
Volume Distribution (VD):  0.719
Pgp-substrate:  3.6448516845703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.31
CYP1A2-substrate:  0.594
CYP2C19-inhibitor:  0.549
CYP2C19-substrate:  0.664
CYP2C9-inhibitor:  0.453
CYP2C9-substrate:  0.976
CYP2D6-inhibitor:  0.881
CYP2D6-substrate:  0.901
CYP3A4-inhibitor:  0.693
CYP3A4-substrate:  0.263

ADMET: Excretion

Clearance (CL):  4.037
Half-life (T1/2):  0.211

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.127
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.947
Skin Sensitization:  0.947
Carcinogencity:  0.046
Eye Corrosion:  0.195
Eye Irritation:  0.794
Respiratory Toxicity:  0.076

Download Data

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

  Natural Product: NPC208638

Natural Product ID:  NPC208638
Common Name*:   Eunicol
IUPAC Name:   (3E,5E)-6-[(1S,3E,7E)-4,8-dimethylcyclodeca-3,7-dien-1-yl]-2-methylhepta-3,5-dien-2-ol
Synonyms:   Eunicol
Standard InCHIKey:  WHRVEMNVMSIMLA-LBDSQGMQSA-N
Standard InCHI:  InChI=1S/C20H32O/c1-16-8-6-9-17(2)12-14-19(13-11-16)18(3)10-7-15-20(4,5)21/h7-8,10,12,15,19,21H,6,9,11,13-14H2,1-5H3/b15-7+,16-8+,17-12+,18-10+/t19-/m0/s1
SMILES:  C/C/1=CC[C@H](CC/C(=C/CC1)/C)/C(=C/C=C/C(O)(C)C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1929559
PubChem CID:   56951445
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
NPO27691 Eunicea fusca Species Plexauridae Eukaryota n.a. Caribbean n.a. PMID[21865038]
NPO26994 Lobophytum pauciflorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[22209732]
NPO27691 Eunicea fusca Species Plexauridae Eukaryota n.a. n.a. n.a. PMID[22734800]
NPO26994 Lobophytum pauciflorum Species Alcyoniidae Eukaryota n.a. Mindoro, Philippines n.a. PMID[9548875]
NPO26994 Lobophytum pauciflorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27691 Eunicea fusca Species Plexauridae 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
NPT762 Cell Line A-431 Homo sapiens IC50 = 350.0 nM PMID[521281]
NPT32 Organism Mus musculus Mus musculus Inhibition = 0.1 % PMID[521282]

☑ 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 NPC208638 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
0.8462 Intermediate Similarity NPC68014
0.8 Intermediate Similarity NPC308844
0.7931 Intermediate Similarity NPC176621
0.7736 Intermediate Similarity NPC182102
0.7736 Intermediate Similarity NPC26960
0.7679 Intermediate Similarity NPC329686
0.7586 Intermediate Similarity NPC181872
0.75 Intermediate Similarity NPC469728
0.7451 Intermediate Similarity NPC138935
0.7407 Intermediate Similarity NPC474460
0.7407 Intermediate Similarity NPC329773
0.74 Intermediate Similarity NPC88079
0.74 Intermediate Similarity NPC108494
0.74 Intermediate Similarity NPC180871
0.74 Intermediate Similarity NPC68889
0.74 Intermediate Similarity NPC194586
0.74 Intermediate Similarity NPC67761
0.74 Intermediate Similarity NPC51758
0.74 Intermediate Similarity NPC209279
0.7241 Intermediate Similarity NPC474643
0.7241 Intermediate Similarity NPC473865
0.7241 Intermediate Similarity NPC55412
0.7241 Intermediate Similarity NPC249645
0.7213 Intermediate Similarity NPC225342
0.72 Intermediate Similarity NPC218918
0.72 Intermediate Similarity NPC120926
0.72 Intermediate Similarity NPC188596
0.7167 Intermediate Similarity NPC475931
0.7143 Intermediate Similarity NPC294358
0.7143 Intermediate Similarity NPC40417
0.7069 Intermediate Similarity NPC474644
0.7 Intermediate Similarity NPC155025
0.7 Intermediate Similarity NPC56917
0.7 Intermediate Similarity NPC226848
0.6984 Remote Similarity NPC300593
0.6964 Remote Similarity NPC244038
0.6949 Remote Similarity NPC4881
0.6939 Remote Similarity NPC266298
0.6935 Remote Similarity NPC210346
0.6935 Remote Similarity NPC64985
0.6923 Remote Similarity NPC278895
0.6885 Remote Similarity NPC122239
0.6875 Remote Similarity NPC92224
0.6875 Remote Similarity NPC282119
0.6863 Remote Similarity NPC269823
0.6852 Remote Similarity NPC180575
0.6833 Remote Similarity NPC11130
0.6786 Remote Similarity NPC131623
0.678 Remote Similarity NPC232247
0.678 Remote Similarity NPC251666
0.678 Remote Similarity NPC297020
0.6774 Remote Similarity NPC99487
0.6774 Remote Similarity NPC471081
0.6731 Remote Similarity NPC256766
0.6731 Remote Similarity NPC213538
0.6716 Remote Similarity NPC239373
0.6716 Remote Similarity NPC329989
0.6667 Remote Similarity NPC59408
0.6667 Remote Similarity NPC474495
0.6667 Remote Similarity NPC261158
0.6667 Remote Similarity NPC473672
0.6667 Remote Similarity NPC214584
0.6667 Remote Similarity NPC71053
0.6667 Remote Similarity NPC306420
0.6667 Remote Similarity NPC317177
0.6667 Remote Similarity NPC317025
0.6667 Remote Similarity NPC329416
0.6667 Remote Similarity NPC326645
0.6667 Remote Similarity NPC26906
0.6667 Remote Similarity NPC104138
0.6667 Remote Similarity NPC24216
0.6667 Remote Similarity NPC73603
0.6667 Remote Similarity NPC183670
0.6613 Remote Similarity NPC312826
0.6604 Remote Similarity NPC116934
0.6567 Remote Similarity NPC272961
0.6562 Remote Similarity NPC174956
0.6562 Remote Similarity NPC474480
0.6562 Remote Similarity NPC473508
0.6552 Remote Similarity NPC35756
0.6552 Remote Similarity NPC306195
0.6552 Remote Similarity NPC179169
0.6552 Remote Similarity NPC71506
0.6552 Remote Similarity NPC157781
0.6552 Remote Similarity NPC35519
0.6552 Remote Similarity NPC177112
0.6552 Remote Similarity NPC181255
0.6538 Remote Similarity NPC144023
0.6515 Remote Similarity NPC279434
0.6508 Remote Similarity NPC323153
0.6508 Remote Similarity NPC66020
0.6508 Remote Similarity NPC240506
0.6508 Remote Similarity NPC127824
0.65 Remote Similarity NPC471992
0.65 Remote Similarity NPC273023
0.65 Remote Similarity NPC227135
0.65 Remote Similarity NPC148216
0.65 Remote Similarity NPC130209
0.65 Remote Similarity NPC148163
0.6491 Remote Similarity NPC473913
0.6491 Remote Similarity NPC474642
0.6491 Remote Similarity NPC249670
0.6471 Remote Similarity NPC15934
0.6471 Remote Similarity NPC255042
0.6471 Remote Similarity NPC182840
0.6471 Remote Similarity NPC103213
0.6471 Remote Similarity NPC29091
0.6462 Remote Similarity NPC150162
0.6441 Remote Similarity NPC474496
0.6441 Remote Similarity NPC61177
0.6441 Remote Similarity NPC303672
0.6429 Remote Similarity NPC130665
0.6418 Remote Similarity NPC254886
0.6418 Remote Similarity NPC259299
0.6415 Remote Similarity NPC177470
0.6415 Remote Similarity NPC206906
0.6406 Remote Similarity NPC68679
0.6406 Remote Similarity NPC207007
0.6406 Remote Similarity NPC321867
0.6393 Remote Similarity NPC48891
0.6379 Remote Similarity NPC27438
0.6377 Remote Similarity NPC203819
0.6364 Remote Similarity NPC165651
0.6364 Remote Similarity NPC140501
0.6364 Remote Similarity NPC160628
0.6364 Remote Similarity NPC19569
0.6364 Remote Similarity NPC210560
0.6364 Remote Similarity NPC269074
0.6364 Remote Similarity NPC24824
0.6349 Remote Similarity NPC5698
0.6338 Remote Similarity NPC470686
0.6333 Remote Similarity NPC110732
0.6333 Remote Similarity NPC189677
0.6333 Remote Similarity NPC474127
0.6324 Remote Similarity NPC224532
0.6324 Remote Similarity NPC305698
0.6316 Remote Similarity NPC85079
0.6316 Remote Similarity NPC31194
0.6316 Remote Similarity NPC248884
0.6316 Remote Similarity NPC153538
0.6308 Remote Similarity NPC81615
0.6308 Remote Similarity NPC190049
0.6296 Remote Similarity NPC15162
0.6286 Remote Similarity NPC95863
0.6286 Remote Similarity NPC471660
0.6286 Remote Similarity NPC472254
0.6275 Remote Similarity NPC48638
0.6275 Remote Similarity NPC239039
0.6275 Remote Similarity NPC45727
0.6271 Remote Similarity NPC195986
0.6269 Remote Similarity NPC255781
0.6269 Remote Similarity NPC230107
0.6269 Remote Similarity NPC191233
0.6269 Remote Similarity NPC267027
0.6269 Remote Similarity NPC311736
0.625 Remote Similarity NPC35141
0.625 Remote Similarity NPC313179
0.625 Remote Similarity NPC252809
0.625 Remote Similarity NPC69383
0.625 Remote Similarity NPC55063
0.625 Remote Similarity NPC19834
0.625 Remote Similarity NPC124183
0.625 Remote Similarity NPC171148
0.625 Remote Similarity NPC308331
0.625 Remote Similarity NPC8610
0.625 Remote Similarity NPC262558
0.6232 Remote Similarity NPC476431
0.6232 Remote Similarity NPC74722
0.6232 Remote Similarity NPC304690
0.623 Remote Similarity NPC298299
0.623 Remote Similarity NPC223604
0.623 Remote Similarity NPC281590
0.6212 Remote Similarity NPC110241
0.6212 Remote Similarity NPC309300
0.6207 Remote Similarity NPC477727
0.6207 Remote Similarity NPC471281
0.6207 Remote Similarity NPC199286
0.6207 Remote Similarity NPC328784
0.6207 Remote Similarity NPC72699
0.6207 Remote Similarity NPC291437
0.6197 Remote Similarity NPC153660
0.6182 Remote Similarity NPC101616
0.6176 Remote Similarity NPC163290
0.6176 Remote Similarity NPC114651
0.6164 Remote Similarity NPC471658
0.6164 Remote Similarity NPC236228
0.6164 Remote Similarity NPC256720
0.6154 Remote Similarity NPC41160
0.6143 Remote Similarity NPC473361
0.6143 Remote Similarity NPC329904
0.614 Remote Similarity NPC91044
0.6133 Remote Similarity NPC471537
0.6129 Remote Similarity NPC96663
0.6129 Remote Similarity NPC274396
0.6122 Remote Similarity NPC305759
0.6122 Remote Similarity NPC99088
0.6122 Remote Similarity NPC173592
0.6119 Remote Similarity NPC220766
0.6119 Remote Similarity NPC187619
0.6119 Remote Similarity NPC107258

  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 NPC208638 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
0.7241 Intermediate Similarity NPD4219 Approved
0.6667 Remote Similarity NPD4194 Approved
0.6667 Remote Similarity NPD4191 Approved
0.6667 Remote Similarity NPD4192 Approved
0.6667 Remote Similarity NPD4193 Approved
0.6607 Remote Similarity NPD4220 Pre-registration
0.65 Remote Similarity NPD342 Phase 1
0.6406 Remote Similarity NPD368 Approved
0.6364 Remote Similarity NPD4265 Approved
0.625 Remote Similarity NPD8264 Approved
0.6216 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6197 Remote Similarity NPD4732 Discontinued
0.6078 Remote Similarity NPD319 Phase 1
0.6053 Remote Similarity NPD7514 Phase 3
0.6053 Remote Similarity NPD7332 Phase 2
0.6034 Remote Similarity NPD8262 Approved
0.6 Remote Similarity NPD4246 Clinical (unspecified phase)
0.597 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5915 Remote Similarity NPD7143 Approved
0.5915 Remote Similarity NPD7144 Approved
0.5849 Remote Similarity NPD5783 Phase 3
0.5833 Remote Similarity NPD7151 Approved
0.5833 Remote Similarity NPD7152 Approved
0.5833 Remote Similarity NPD7150 Approved
0.5789 Remote Similarity NPD7145 Approved
0.5775 Remote Similarity NPD6923 Approved
0.5775 Remote Similarity NPD6922 Approved
0.5769 Remote Similarity NPD6902 Approved
0.5676 Remote Similarity NPD6926 Approved
0.5676 Remote Similarity NPD6924 Approved
0.5658 Remote Similarity NPD6925 Approved
0.5658 Remote Similarity NPD6932 Approved
0.5658 Remote Similarity NPD5776 Phase 2
0.5641 Remote Similarity NPD6931 Approved
0.5641 Remote Similarity NPD6930 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