Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  239.69
LogP:  4.483
LogD:  4.355
LogS:  -5.238
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.513
Synthetic Accessibility Score:  5.049
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:  -4.649
MDCK Permeability:  2.908335591200739e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.048

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.135
Plasma Protein Binding (PPB):  88.87549591064453%
Volume Distribution (VD):  1.001
Pgp-substrate:  18.88944435119629%

ADMET: Metabolism

CYP1A2-inhibitor:  0.462
CYP1A2-substrate:  0.508
CYP2C19-inhibitor:  0.464
CYP2C19-substrate:  0.92
CYP2C9-inhibitor:  0.404
CYP2C9-substrate:  0.769
CYP2D6-inhibitor:  0.09
CYP2D6-substrate:  0.475
CYP3A4-inhibitor:  0.487
CYP3A4-substrate:  0.293

ADMET: Excretion

Clearance (CL):  8.7
Half-life (T1/2):  0.215

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.097
Drug-inuced Liver Injury (DILI):  0.023
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.819
Skin Sensitization:  0.925
Carcinogencity:  0.038
Eye Corrosion:  0.959
Eye Irritation:  0.95
Respiratory Toxicity:  0.549

Download Data

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

  Natural Product: NPC178644

Natural Product ID:  NPC178644
Common Name*:   Silphinene
IUPAC Name:   (1R,3aR,5aS,8aR)-1,4,4,5a-tetramethyl-1,2,3,3a,5,6-hexahydrocyclopenta[h]pentalene
Synonyms:   Silphinene
Standard InCHIKey:  VHIAMHVUKUKCHP-UXOAXIEHSA-N
Standard InCHI:  InChI=1S/C15H24/c1-11-6-7-12-13(2,3)10-14(4)8-5-9-15(11,12)14/h5,9,11-12H,6-8,10H2,1-4H3/t11-,12-,14+,15+/m1/s1
SMILES:  C[C@@H]1CC[C@@H]2C(C)(C)C[C@]3(C)CC=C[C@]123
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL458374
PubChem CID:   44567200
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002004] Triquinane sesquiterpenoids
            • [CHEMONTID:0003582] Angular triquinanes

*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
NPO18328 Leontopodium alpinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18328 Leontopodium alpinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18328 Leontopodium alpinum Species Asteraceae 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
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 0.27 ug.cm'-2 PMID[468269]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 2.7 ug.cm'-2 PMID[468269]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata Activity = 24.0 % PMID[468269]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata mortality = 24.0 % PMID[468270]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 2.7 microg/cm2 PMID[468270]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 0.27 microg/cm2 PMID[468270]

☑ 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 NPC178644 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
0.8511 High Similarity NPC323445
0.8298 Intermediate Similarity NPC49088
0.8 Intermediate Similarity NPC200129
0.7872 Intermediate Similarity NPC227670
0.7872 Intermediate Similarity NPC474118
0.7872 Intermediate Similarity NPC166362
0.7872 Intermediate Similarity NPC51762
0.7872 Intermediate Similarity NPC141777
0.766 Intermediate Similarity NPC473912
0.7551 Intermediate Similarity NPC229403
0.7447 Intermediate Similarity NPC473614
0.7234 Intermediate Similarity NPC246165
0.717 Intermediate Similarity NPC471681
0.7143 Intermediate Similarity NPC86538
0.7143 Intermediate Similarity NPC90506
0.7143 Intermediate Similarity NPC23145
0.7143 Intermediate Similarity NPC90803
0.7143 Intermediate Similarity NPC60556
0.7143 Intermediate Similarity NPC109813
0.7 Intermediate Similarity NPC248411
0.6964 Remote Similarity NPC470893
0.6949 Remote Similarity NPC234264
0.6949 Remote Similarity NPC47840
0.6939 Remote Similarity NPC177470
0.6935 Remote Similarity NPC162309
0.6923 Remote Similarity NPC124851
0.6897 Remote Similarity NPC469769
0.6863 Remote Similarity NPC296337
0.6863 Remote Similarity NPC86683
0.6735 Remote Similarity NPC120926
0.6735 Remote Similarity NPC144023
0.6735 Remote Similarity NPC218918
0.6724 Remote Similarity NPC55004
0.6724 Remote Similarity NPC49575
0.6724 Remote Similarity NPC267626
0.6721 Remote Similarity NPC124112
0.6667 Remote Similarity NPC176171
0.6667 Remote Similarity NPC123194
0.6667 Remote Similarity NPC323153
0.6613 Remote Similarity NPC475704
0.661 Remote Similarity NPC472830
0.66 Remote Similarity NPC105246
0.66 Remote Similarity NPC190232
0.6538 Remote Similarity NPC241784
0.6538 Remote Similarity NPC13991
0.6538 Remote Similarity NPC114239
0.6531 Remote Similarity NPC183670
0.65 Remote Similarity NPC5698
0.65 Remote Similarity NPC309825
0.6481 Remote Similarity NPC17518
0.6481 Remote Similarity NPC22765
0.6458 Remote Similarity NPC229262
0.6458 Remote Similarity NPC297643
0.6458 Remote Similarity NPC139717
0.6452 Remote Similarity NPC474086
0.6441 Remote Similarity NPC230823
0.6406 Remote Similarity NPC135650
0.6393 Remote Similarity NPC252809
0.6393 Remote Similarity NPC25853
0.6383 Remote Similarity NPC282119
0.6383 Remote Similarity NPC92224
0.6346 Remote Similarity NPC202189
0.6333 Remote Similarity NPC10017
0.6333 Remote Similarity NPC266295
0.6333 Remote Similarity NPC94991
0.6333 Remote Similarity NPC30215
0.629 Remote Similarity NPC210346
0.625 Remote Similarity NPC190810
0.625 Remote Similarity NPC34764
0.625 Remote Similarity NPC76145
0.623 Remote Similarity NPC259261
0.6222 Remote Similarity NPC206088
0.6222 Remote Similarity NPC66577
0.6207 Remote Similarity NPC95581
0.62 Remote Similarity NPC62086
0.62 Remote Similarity NPC78551
0.62 Remote Similarity NPC227632
0.619 Remote Similarity NPC165695
0.619 Remote Similarity NPC474480
0.6182 Remote Similarity NPC17810
0.6167 Remote Similarity NPC278550
0.6154 Remote Similarity NPC192529
0.6154 Remote Similarity NPC92327
0.6129 Remote Similarity NPC135648
0.6122 Remote Similarity NPC266298
0.6122 Remote Similarity NPC239039
0.6122 Remote Similarity NPC48638
0.6122 Remote Similarity NPC45727
0.6094 Remote Similarity NPC473902
0.6094 Remote Similarity NPC140233
0.6094 Remote Similarity NPC287744
0.6078 Remote Similarity NPC103290
0.6061 Remote Similarity NPC176107
0.6061 Remote Similarity NPC477791
0.6034 Remote Similarity NPC127944
0.6034 Remote Similarity NPC476679
0.6032 Remote Similarity NPC475795
0.6032 Remote Similarity NPC213152
0.6 Remote Similarity NPC187619
0.6 Remote Similarity NPC238352
0.6 Remote Similarity NPC477009
0.6 Remote Similarity NPC183422
0.6 Remote Similarity NPC274396
0.6 Remote Similarity NPC19569
0.5968 Remote Similarity NPC469321
0.5962 Remote Similarity NPC193180
0.5938 Remote Similarity NPC472306
0.5938 Remote Similarity NPC211291
0.5938 Remote Similarity NPC133368
0.5909 Remote Similarity NPC323005
0.5882 Remote Similarity NPC182815
0.5873 Remote Similarity NPC162109
0.5873 Remote Similarity NPC471081
0.587 Remote Similarity NPC151719
0.5857 Remote Similarity NPC234527
0.5857 Remote Similarity NPC14352
0.5846 Remote Similarity NPC212210
0.5846 Remote Similarity NPC309300
0.5846 Remote Similarity NPC469723
0.5833 Remote Similarity NPC298299
0.5833 Remote Similarity NPC469770
0.5833 Remote Similarity NPC310643
0.5821 Remote Similarity NPC136813
0.5806 Remote Similarity NPC60772
0.5797 Remote Similarity NPC40574
0.5797 Remote Similarity NPC9161
0.5797 Remote Similarity NPC49422
0.5797 Remote Similarity NPC254845
0.5797 Remote Similarity NPC475728
0.5781 Remote Similarity NPC63111
0.5781 Remote Similarity NPC15152
0.5781 Remote Similarity NPC147524
0.5781 Remote Similarity NPC97322
0.5781 Remote Similarity NPC274704
0.5781 Remote Similarity NPC219621
0.5775 Remote Similarity NPC309178
0.5763 Remote Similarity NPC165755
0.5763 Remote Similarity NPC296311
0.5763 Remote Similarity NPC14002
0.5745 Remote Similarity NPC213749
0.5738 Remote Similarity NPC20603
0.5735 Remote Similarity NPC167527
0.5735 Remote Similarity NPC20610
0.5735 Remote Similarity NPC160209
0.5714 Remote Similarity NPC471660
0.5714 Remote Similarity NPC115023
0.5714 Remote Similarity NPC472827
0.5714 Remote Similarity NPC470078
0.5714 Remote Similarity NPC234707
0.5714 Remote Similarity NPC143834
0.5694 Remote Similarity NPC313185
0.5692 Remote Similarity NPC167256
0.5692 Remote Similarity NPC32285
0.5692 Remote Similarity NPC279200
0.569 Remote Similarity NPC27438
0.5667 Remote Similarity NPC5626
0.5652 Remote Similarity NPC61702
0.5652 Remote Similarity NPC167272
0.5652 Remote Similarity NPC269877
0.5652 Remote Similarity NPC162867
0.5652 Remote Similarity NPC22301
0.5652 Remote Similarity NPC469677
0.5645 Remote Similarity NPC474415
0.5645 Remote Similarity NPC474528
0.5645 Remote Similarity NPC11130
0.5645 Remote Similarity NPC474457
0.5645 Remote Similarity NPC475696
0.5645 Remote Similarity NPC115385
0.5634 Remote Similarity NPC251705
0.5634 Remote Similarity NPC470045
0.5634 Remote Similarity NPC470044
0.5625 Remote Similarity NPC176621
0.5625 Remote Similarity NPC270042
0.5614 Remote Similarity NPC106990
0.5606 Remote Similarity NPC110241

  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 NPC178644 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
0.66 Remote Similarity NPD1799 Clinical (unspecified phase)
0.625 Remote Similarity NPD319 Phase 1
0.6182 Remote Similarity NPD8262 Approved
0.5797 Remote Similarity NPD7143 Approved
0.5797 Remote Similarity NPD7144 Approved
0.5714 Remote Similarity NPD7151 Approved
0.5714 Remote Similarity NPD7150 Approved
0.5714 Remote Similarity NPD7152 Approved
0.5652 Remote Similarity NPD6922 Approved
0.5652 Remote Similarity NPD6923 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