Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  346.554
LogP:  5.72
LogD:  5.102
LogS:  -5.645
# Rotatable Bonds:  2
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.596
Synthetic Accessibility Score:  5.11
Fsp3:  0.762
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:  -4.716
MDCK Permeability:  4.0715414797887206e-05
Pgp-inhibitor:  0.906
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.861
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.92
Plasma Protein Binding (PPB):  75.14505767822266%
Volume Distribution (VD):  1.506
Pgp-substrate:  28.662446975708008%

ADMET: Metabolism

CYP1A2-inhibitor:  0.794
CYP1A2-substrate:  0.758
CYP2C19-inhibitor:  0.203
CYP2C19-substrate:  0.818
CYP2C9-inhibitor:  0.165
CYP2C9-substrate:  0.085
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.384

ADMET: Excretion

Clearance (CL):  14.492
Half-life (T1/2):  0.246

ADMET: Toxicity

hERG Blockers:  0.11
Human Hepatotoxicity (H-HT):  0.427
Drug-inuced Liver Injury (DILI):  0.902
AMES Toxicity:  0.078
Rat Oral Acute Toxicity:  0.901
Maximum Recommended Daily Dose:  0.626
Skin Sensitization:  0.523
Carcinogencity:  0.718
Eye Corrosion:  0.958
Eye Irritation:  0.579
Respiratory Toxicity:  0.806

Download Data

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

  Natural Product: NPC474416

Natural Product ID:  NPC474416
Common Name*:   (1S,3Ar,3A1R,4S,6S,6As,9As)-1,4-Dimethyl-6-(2-Methylallyl)-7-Methylenedodecahydro-1H-Phenalene-1-Carbonitrile
IUPAC Name:   (1S,3aR,4S,6S,6aS,9aS,9bR)-1,4-dimethyl-7-methylidene-6-(2-methylprop-2-enyl)-3,3a,4,5,6,6a,8,9,9a,9b-decahydro-2H-phenalene-1-carbonitrile
Synonyms:  
Standard InCHIKey:  OSTUOHSDKCQCCA-QJZPXWABSA-N
Standard InCHI:  InChI=1S/C21H31N/c1-13(2)10-16-11-15(4)17-8-9-21(5,12-22)18-7-6-14(3)19(16)20(17)18/h15-20H,1,3,6-11H2,2,4-5H3/t15-,16+,17+,18-,19-,20+,21+/m0/s1
SMILES:  CC1CC(C2C3C1CCC(C3CCC2=C)(C)C#N)CC(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL467611
PubChem CID:   44566843
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003398] Amphilectane, neoamphilectane, cycloamphilectane, and adociane 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
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19199790]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[8759172]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 > 20.0 ug.mL-1 PMID[522227]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.52 ug.mL-1 PMID[522227]
NPT2 Others Unspecified Ratio IC50 > 38.5 n.a. PMID[522227]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.242 ug.mL-1 PMID[522227]
NPT2 Others Unspecified Ratio IC50 > 82.6 n.a. PMID[522227]

☑ 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 NPC474416 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
0.9388 High Similarity NPC476681
0.9245 High Similarity NPC474457
0.8909 High Similarity NPC474420
0.8909 High Similarity NPC474455
0.8909 High Similarity NPC474454
0.8889 High Similarity NPC474528
0.8889 High Similarity NPC474415
0.8889 High Similarity NPC475696
0.8571 High Similarity NPC475716
0.8033 Intermediate Similarity NPC474456
0.7959 Intermediate Similarity NPC193180
0.7833 Intermediate Similarity NPC474086
0.7755 Intermediate Similarity NPC103290
0.7719 Intermediate Similarity NPC318036
0.7586 Intermediate Similarity NPC173815
0.75 Intermediate Similarity NPC476679
0.75 Intermediate Similarity NPC127944
0.7458 Intermediate Similarity NPC324944
0.7407 Intermediate Similarity NPC22765
0.7368 Intermediate Similarity NPC476683
0.7255 Intermediate Similarity NPC190232
0.7255 Intermediate Similarity NPC105246
0.7241 Intermediate Similarity NPC469770
0.7213 Intermediate Similarity NPC317778
0.7091 Intermediate Similarity NPC17518
0.7049 Intermediate Similarity NPC28755
0.7049 Intermediate Similarity NPC152211
0.6909 Remote Similarity NPC124851
0.6863 Remote Similarity NPC62086
0.6863 Remote Similarity NPC78551
0.6863 Remote Similarity NPC227632
0.6852 Remote Similarity NPC86683
0.6792 Remote Similarity NPC192529
0.6774 Remote Similarity NPC472827
0.6667 Remote Similarity NPC123194
0.6618 Remote Similarity NPC138409
0.6618 Remote Similarity NPC184919
0.6562 Remote Similarity NPC219621
0.6406 Remote Similarity NPC311809
0.6364 Remote Similarity NPC476682
0.6364 Remote Similarity NPC202189
0.6349 Remote Similarity NPC469769
0.6324 Remote Similarity NPC476135
0.629 Remote Similarity NPC264779
0.6282 Remote Similarity NPC477289
0.6269 Remote Similarity NPC476737
0.6269 Remote Similarity NPC27243
0.625 Remote Similarity NPC296337
0.625 Remote Similarity NPC241784
0.625 Remote Similarity NPC114239
0.625 Remote Similarity NPC13991
0.6212 Remote Similarity NPC475755
0.6212 Remote Similarity NPC474027
0.6212 Remote Similarity NPC474435
0.6197 Remote Similarity NPC21773
0.6197 Remote Similarity NPC265789
0.619 Remote Similarity NPC470370
0.619 Remote Similarity NPC470369
0.6182 Remote Similarity NPC141777
0.6182 Remote Similarity NPC227670
0.6182 Remote Similarity NPC166362
0.6176 Remote Similarity NPC189917
0.6176 Remote Similarity NPC168824
0.6176 Remote Similarity NPC43300
0.6176 Remote Similarity NPC39462
0.6176 Remote Similarity NPC107704
0.6176 Remote Similarity NPC96812
0.6119 Remote Similarity NPC469662
0.6094 Remote Similarity NPC189290
0.6094 Remote Similarity NPC474769
0.6094 Remote Similarity NPC60772
0.6081 Remote Similarity NPC476308
0.6071 Remote Similarity NPC248411
0.6029 Remote Similarity NPC475812
0.6027 Remote Similarity NPC476904
0.6 Remote Similarity NPC142754
0.6 Remote Similarity NPC82477
0.6 Remote Similarity NPC296697
0.6 Remote Similarity NPC94192
0.6 Remote Similarity NPC39157
0.5972 Remote Similarity NPC476329
0.597 Remote Similarity NPC197238
0.597 Remote Similarity NPC145715
0.597 Remote Similarity NPC202118
0.5965 Remote Similarity NPC229403
0.5942 Remote Similarity NPC37792
0.5942 Remote Similarity NPC222366
0.5942 Remote Similarity NPC286669
0.5942 Remote Similarity NPC92327
0.5942 Remote Similarity NPC476039
0.5926 Remote Similarity NPC246165
0.5915 Remote Similarity NPC286814
0.5915 Remote Similarity NPC477857
0.5902 Remote Similarity NPC473728
0.5902 Remote Similarity NPC212905
0.5882 Remote Similarity NPC473959
0.5873 Remote Similarity NPC200258
0.5873 Remote Similarity NPC470893
0.5867 Remote Similarity NPC7214
0.5857 Remote Similarity NPC220210
0.5857 Remote Similarity NPC197805
0.5857 Remote Similarity NPC20181
0.5857 Remote Similarity NPC176107
0.5844 Remote Similarity NPC211322
0.5833 Remote Similarity NPC477856
0.5833 Remote Similarity NPC45296
0.5833 Remote Similarity NPC214770
0.5833 Remote Similarity NPC200129
0.5821 Remote Similarity NPC469728
0.5821 Remote Similarity NPC41160
0.5806 Remote Similarity NPC472828
0.5797 Remote Similarity NPC64123
0.5797 Remote Similarity NPC474768
0.5781 Remote Similarity NPC39068
0.5775 Remote Similarity NPC476288
0.5775 Remote Similarity NPC20610
0.5775 Remote Similarity NPC139785
0.5753 Remote Similarity NPC164045
0.5753 Remote Similarity NPC190035
0.5753 Remote Similarity NPC111234
0.5753 Remote Similarity NPC301226
0.5738 Remote Similarity NPC236623
0.5735 Remote Similarity NPC474596
0.5714 Remote Similarity NPC323005
0.5694 Remote Similarity NPC472831
0.5694 Remote Similarity NPC139397
0.5694 Remote Similarity NPC182815
0.5692 Remote Similarity NPC11130
0.569 Remote Similarity NPC49088
0.5676 Remote Similarity NPC330659
0.5676 Remote Similarity NPC211009
0.5676 Remote Similarity NPC195489
0.5676 Remote Similarity NPC161187
0.5676 Remote Similarity NPC279241
0.5676 Remote Similarity NPC36310
0.5676 Remote Similarity NPC474743
0.5676 Remote Similarity NPC472506
0.5676 Remote Similarity NPC244708
0.5676 Remote Similarity NPC474488
0.5672 Remote Similarity NPC176621
0.5667 Remote Similarity NPC17810
0.5652 Remote Similarity NPC169275
0.5652 Remote Similarity NPC101128
0.5652 Remote Similarity NPC52449
0.5652 Remote Similarity NPC68656
0.5634 Remote Similarity NPC193770
0.5616 Remote Similarity NPC282593
0.5616 Remote Similarity NPC307176
0.5616 Remote Similarity NPC251929
0.5616 Remote Similarity NPC260040
0.5616 Remote Similarity NPC475728
0.5616 Remote Similarity NPC40574
0.5616 Remote Similarity NPC35734
0.5616 Remote Similarity NPC265782
0.5616 Remote Similarity NPC2634
0.5616 Remote Similarity NPC159577
0.5614 Remote Similarity NPC90803
0.5614 Remote Similarity NPC23145
0.5614 Remote Similarity NPC60556
0.5614 Remote Similarity NPC86538
0.5614 Remote Similarity NPC90506
0.5614 Remote Similarity NPC474118
0.5614 Remote Similarity NPC51762
0.5614 Remote Similarity NPC109813
0.5606 Remote Similarity NPC472830
0.56 Remote Similarity NPC192638
0.56 Remote Similarity NPC25511
0.56 Remote Similarity NPC5046
0.56 Remote Similarity NPC211641
0.56 Remote Similarity NPC196358
0.56 Remote Similarity NPC308440
0.56 Remote Similarity NPC476736
0.56 Remote Similarity NPC145552
0.56 Remote Similarity NPC100334
0.56 Remote Similarity NPC254509
0.56 Remote Similarity NPC472503
0.56 Remote Similarity NPC62657
0.56 Remote Similarity NPC159497
0.56 Remote Similarity NPC49168

  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 NPC474416 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
0.7255 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6316 Remote Similarity NPD8028 Phase 2
0.6286 Remote Similarity NPD6939 Phase 2
0.6286 Remote Similarity NPD6938 Clinical (unspecified phase)
0.5789 Remote Similarity NPD871 Approved
0.5789 Remote Similarity NPD873 Approved
0.5775 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4137 Phase 3
0.5667 Remote Similarity NPD8262 Approved
0.5616 Remote Similarity NPD4691 Approved
0.5616 Remote Similarity NPD4747 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