Structure

Physi-Chem Properties

Molecular Weight:  206.2
Volume:  248.247
LogP:  5.18
LogD:  4.589
LogS:  -5.427
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.499
Synthetic Accessibility Score:  3.893
Fsp3:  0.867
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:  -4.491
MDCK Permeability:  9.78729258349631e-06
Pgp-inhibitor:  0.423
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.958
30% Bioavailability (F30%):  0.561

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.459
Plasma Protein Binding (PPB):  80.04138946533203%
Volume Distribution (VD):  1.193
Pgp-substrate:  26.296836853027344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.36
CYP1A2-substrate:  0.515
CYP2C19-inhibitor:  0.233
CYP2C19-substrate:  0.892
CYP2C9-inhibitor:  0.4
CYP2C9-substrate:  0.436
CYP2D6-inhibitor:  0.056
CYP2D6-substrate:  0.71
CYP3A4-inhibitor:  0.148
CYP3A4-substrate:  0.271

ADMET: Excretion

Clearance (CL):  7.451
Half-life (T1/2):  0.061

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.091
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.239
Maximum Recommended Daily Dose:  0.923
Skin Sensitization:  0.351
Carcinogencity:  0.353
Eye Corrosion:  0.964
Eye Irritation:  0.965
Respiratory Toxicity:  0.959

Download Data

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

  Natural Product: NPC103290

Natural Product ID:  NPC103290
Common Name*:   8(12)Drimene
IUPAC Name:   (4aS,8S,8aR)-4,4,8,8a-tetramethyl-7-methylidene-2,3,4a,5,6,8-hexahydro-1H-naphthalene
Synonyms:   8(12)-Drimene
Standard InCHIKey:  WOBFHHHYXAFVKB-KCQAQPDRSA-N
Standard InCHI:  InChI=1S/C15H26/c1-11-7-8-13-14(3,4)9-6-10-15(13,5)12(11)2/h12-13H,1,6-10H2,2-5H3/t12-,13-,15+/m0/s1
SMILES:  C=C1CC[C@@H]2[C@]([C@H]1C)(C)CCCC2(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507971
PubChem CID:   12184338
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004622] Branched unsaturated hydrocarbons

*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
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[19027298]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[19332371]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[19782567]
NPO28807 Laggera pterodonta Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20506820]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[23422227]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23261 Euphrasia officinalis Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24380 Litsea leefeana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24380 Litsea leefeana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23261 Euphrasia officinalis Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28807 Laggera pterodonta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24380 Litsea leefeana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23261 Euphrasia officinalis Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28807 Laggera pterodonta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23596 Pittosporum tenuifolium Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14969 Hedychium spicatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24141 Satureja thymbra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23514 Nauclea cadamba Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23929 Verongia fistularis n.a. n.a. n.a. 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
NPT1970 Cell Line THP-1 Homo sapiens IC50 = 53890.0 nM PMID[456472]
NPT1083 Cell Line A-375 Homo sapiens IC50 = 50190.0 nM PMID[456472]
NPT81 Cell Line A549 Homo sapiens IC50 = 61290.0 nM PMID[456472]

☑ 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 NPC103290 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
0.9744 High Similarity NPC193180
0.878 High Similarity NPC190232
0.878 High Similarity NPC105246
0.875 High Similarity NPC62086
0.875 High Similarity NPC227632
0.875 High Similarity NPC78551
0.8605 High Similarity NPC86683
0.8444 Intermediate Similarity NPC22765
0.8261 Intermediate Similarity NPC476681
0.814 Intermediate Similarity NPC192529
0.8043 Intermediate Similarity NPC17518
0.7826 Intermediate Similarity NPC124851
0.7755 Intermediate Similarity NPC474416
0.7755 Intermediate Similarity NPC127944
0.7727 Intermediate Similarity NPC227670
0.7727 Intermediate Similarity NPC141777
0.7727 Intermediate Similarity NPC166362
0.76 Intermediate Similarity NPC476683
0.7556 Intermediate Similarity NPC202189
0.7451 Intermediate Similarity NPC469770
0.7442 Intermediate Similarity NPC246165
0.7391 Intermediate Similarity NPC229403
0.7391 Intermediate Similarity NPC241784
0.7391 Intermediate Similarity NPC114239
0.7391 Intermediate Similarity NPC13991
0.7391 Intermediate Similarity NPC296337
0.7308 Intermediate Similarity NPC264779
0.7174 Intermediate Similarity NPC248411
0.717 Intermediate Similarity NPC474415
0.717 Intermediate Similarity NPC475696
0.717 Intermediate Similarity NPC474457
0.717 Intermediate Similarity NPC474528
0.7115 Intermediate Similarity NPC123194
0.7037 Intermediate Similarity NPC60772
0.7037 Intermediate Similarity NPC474769
0.7037 Intermediate Similarity NPC189290
0.7 Intermediate Similarity NPC236623
0.6957 Remote Similarity NPC86538
0.6957 Remote Similarity NPC90803
0.6957 Remote Similarity NPC109813
0.6957 Remote Similarity NPC474118
0.6957 Remote Similarity NPC60556
0.6957 Remote Similarity NPC51762
0.6957 Remote Similarity NPC90506
0.6957 Remote Similarity NPC23145
0.6909 Remote Similarity NPC28755
0.6909 Remote Similarity NPC474420
0.6909 Remote Similarity NPC474454
0.6909 Remote Similarity NPC152211
0.6909 Remote Similarity NPC474455
0.6909 Remote Similarity NPC475716
0.6863 Remote Similarity NPC473728
0.68 Remote Similarity NPC200129
0.6792 Remote Similarity NPC200258
0.6739 Remote Similarity NPC177470
0.6727 Remote Similarity NPC469769
0.6667 Remote Similarity NPC39068
0.6667 Remote Similarity NPC49088
0.6667 Remote Similarity NPC318036
0.6667 Remote Similarity NPC41160
0.66 Remote Similarity NPC17810
0.6591 Remote Similarity NPC139717
0.6591 Remote Similarity NPC229262
0.6591 Remote Similarity NPC297643
0.6579 Remote Similarity NPC133792
0.6579 Remote Similarity NPC10183
0.6579 Remote Similarity NPC7777
0.6552 Remote Similarity NPC202118
0.6552 Remote Similarity NPC474086
0.6552 Remote Similarity NPC197238
0.6545 Remote Similarity NPC11130
0.6545 Remote Similarity NPC173815
0.6531 Remote Similarity NPC323445
0.6522 Remote Similarity NPC473614
0.6522 Remote Similarity NPC144023
0.6491 Remote Similarity NPC311809
0.6491 Remote Similarity NPC127582
0.6481 Remote Similarity NPC470893
0.6441 Remote Similarity NPC144650
0.6441 Remote Similarity NPC101128
0.6441 Remote Similarity NPC476682
0.6441 Remote Similarity NPC52449
0.6441 Remote Similarity NPC469662
0.6441 Remote Similarity NPC169275
0.6441 Remote Similarity NPC68656
0.6429 Remote Similarity NPC324944
0.6383 Remote Similarity NPC473912
0.6379 Remote Similarity NPC469728
0.6364 Remote Similarity NPC190810
0.6364 Remote Similarity NPC76145
0.6364 Remote Similarity NPC34764
0.6333 Remote Similarity NPC474768
0.6333 Remote Similarity NPC282619
0.6333 Remote Similarity NPC258595
0.6333 Remote Similarity NPC27243
0.6333 Remote Similarity NPC208198
0.6333 Remote Similarity NPC475812
0.6333 Remote Similarity NPC107258
0.6333 Remote Similarity NPC64123
0.6333 Remote Similarity NPC2728
0.6333 Remote Similarity NPC476737
0.6333 Remote Similarity NPC268039
0.6333 Remote Similarity NPC60837
0.6333 Remote Similarity NPC11555
0.6333 Remote Similarity NPC172613
0.6316 Remote Similarity NPC472827
0.6316 Remote Similarity NPC309825
0.6304 Remote Similarity NPC183670
0.625 Remote Similarity NPC470369
0.625 Remote Similarity NPC470370
0.623 Remote Similarity NPC39462
0.623 Remote Similarity NPC43300
0.623 Remote Similarity NPC475897
0.623 Remote Similarity NPC476406
0.623 Remote Similarity NPC222366
0.623 Remote Similarity NPC474456
0.623 Remote Similarity NPC476039
0.623 Remote Similarity NPC189917
0.623 Remote Similarity NPC92327
0.623 Remote Similarity NPC286669
0.623 Remote Similarity NPC103734
0.623 Remote Similarity NPC149680
0.623 Remote Similarity NPC185587
0.623 Remote Similarity NPC107704
0.623 Remote Similarity NPC168824
0.623 Remote Similarity NPC473929
0.623 Remote Similarity NPC96812
0.6222 Remote Similarity NPC239039
0.6207 Remote Similarity NPC317778
0.6207 Remote Similarity NPC176621
0.617 Remote Similarity NPC218918
0.617 Remote Similarity NPC120926
0.6167 Remote Similarity NPC285371
0.6167 Remote Similarity NPC475124
0.614 Remote Similarity NPC27610
0.614 Remote Similarity NPC56905
0.6136 Remote Similarity NPC92224
0.6129 Remote Similarity NPC197805
0.6129 Remote Similarity NPC253303
0.6129 Remote Similarity NPC185874
0.6129 Remote Similarity NPC69649
0.6129 Remote Similarity NPC269077
0.6129 Remote Similarity NPC68703
0.6129 Remote Similarity NPC176107
0.6129 Remote Similarity NPC139207
0.6111 Remote Similarity NPC476679
0.6111 Remote Similarity NPC23117
0.6111 Remote Similarity NPC14002
0.6102 Remote Similarity NPC60565
0.6102 Remote Similarity NPC147524
0.6102 Remote Similarity NPC219621
0.6102 Remote Similarity NPC110214
0.6078 Remote Similarity NPC178644
0.6078 Remote Similarity NPC100445
0.6071 Remote Similarity NPC179024
0.6034 Remote Similarity NPC276764
0.6034 Remote Similarity NPC472304
0.6032 Remote Similarity NPC160209
0.6032 Remote Similarity NPC139785
0.6032 Remote Similarity NPC94192
0.6032 Remote Similarity NPC36616
0.6032 Remote Similarity NPC82477
0.6032 Remote Similarity NPC276616
0.6032 Remote Similarity NPC290445
0.6032 Remote Similarity NPC20610
0.6032 Remote Similarity NPC244790
0.6032 Remote Similarity NPC142754
0.6032 Remote Similarity NPC245795
0.6032 Remote Similarity NPC39157
0.6032 Remote Similarity NPC296697
0.6 Remote Similarity NPC81615
0.6 Remote Similarity NPC283247
0.6 Remote Similarity NPC5626
0.5968 Remote Similarity NPC242945
0.5968 Remote Similarity NPC176171
0.5968 Remote Similarity NPC259156
0.5968 Remote Similarity NPC279434
0.5968 Remote Similarity NPC323005
0.5938 Remote Similarity NPC138409
0.5938 Remote Similarity NPC477857
0.5938 Remote Similarity NPC476431
0.5938 Remote Similarity NPC9942
0.5938 Remote Similarity NPC139397
0.5938 Remote Similarity NPC184919
0.5938 Remote Similarity NPC182815
0.5938 Remote Similarity NPC286814
0.5932 Remote Similarity NPC270042
0.5932 Remote Similarity NPC135648
0.5902 Remote Similarity NPC329698
0.5882 Remote Similarity NPC14552
0.5873 Remote Similarity NPC20181
0.5873 Remote Similarity NPC193770
0.5873 Remote Similarity NPC290350
0.5873 Remote Similarity NPC171225
0.5873 Remote Similarity NPC220210
0.5873 Remote Similarity NPC4370
0.587 Remote Similarity NPC266298
0.587 Remote Similarity NPC48638
0.587 Remote Similarity NPC45727
0.5846 Remote Similarity NPC235586

  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 NPC103290 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
0.878 High Similarity NPD1799 Clinical (unspecified phase)
0.66 Remote Similarity NPD8262 Approved
0.6364 Remote Similarity NPD319 Phase 1
0.6032 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5938 Remote Similarity NPD4137 Phase 3
0.5846 Remote Similarity NPD6939 Phase 2
0.5846 Remote Similarity NPD4691 Approved
0.5846 Remote Similarity NPD4747 Approved
0.5846 Remote Similarity NPD6938 Clinical (unspecified phase)
0.5758 Remote Similarity NPD4243 Approved
0.5692 Remote Similarity NPD6923 Approved
0.5692 Remote Similarity NPD6922 Approved
0.5606 Remote Similarity NPD7143 Approved
0.5606 Remote Similarity NPD7144 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