Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  346.554
LogP:  5.183
LogD:  5.271
LogS:  -6.022
# 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:  5.274
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:  -4.705
MDCK Permeability:  4.762034586747177e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.342

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.841
Plasma Protein Binding (PPB):  92.41686248779297%
Volume Distribution (VD):  0.974
Pgp-substrate:  6.69334602355957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.743
CYP1A2-substrate:  0.638
CYP2C19-inhibitor:  0.535
CYP2C19-substrate:  0.84
CYP2C9-inhibitor:  0.623
CYP2C9-substrate:  0.478
CYP2D6-inhibitor:  0.519
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.955
CYP3A4-substrate:  0.541

ADMET: Excretion

Clearance (CL):  6.077
Half-life (T1/2):  0.375

ADMET: Toxicity

hERG Blockers:  0.305
Human Hepatotoxicity (H-HT):  0.344
Drug-inuced Liver Injury (DILI):  0.902
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.895
Maximum Recommended Daily Dose:  0.46
Skin Sensitization:  0.867
Carcinogencity:  0.249
Eye Corrosion:  0.988
Eye Irritation:  0.915
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC474086

Natural Product ID:  NPC474086
Common Name*:   (2S,2Ar,2A1R,5S,5As,8R,8As)-2,5,8-Trimethyl-8A-((E)-3-Methylbuta-1,3-Dienyl)Dodecahydroacenaphthylene-5-Carbonitrile
IUPAC Name:   (2S,3aR,5S,5aS,8R,8aS,8bR)-2,5,8-trimethyl-8a-[(1E)-3-methylbuta-1,3-dienyl]-1,2,3,3a,4,5a,6,7,8,8b-decahydroacenaphthylene-5-carbonitrile
Synonyms:  
Standard InCHIKey:  SSFDJDHBZVHNKM-SSBPHEBUSA-N
Standard InCHI:  InChI=1S/C21H31N/c1-14(2)8-11-21-12-15(3)17-9-10-20(5,13-22)18(19(17)21)7-6-16(21)4/h8,11,15-19H,1,6-7,9-10,12H2,2-5H3/b11-8+/t15-,16+,17+,18-,19+,20+,21-/m0/s1
SMILES:  N#C[C@@]1(C)CC[C@H]2[C@@H]3[C@@H]1CC[C@H]([C@]3(/C=C/C(=C)C)C[C@@H]2C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL460756
PubChem CID:   44566852
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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 = 19.1 ug.mL-1 PMID[561886]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.09 ug.mL-1 PMID[561886]
NPT2 Others Unspecified Ratio IC50 = 210.0 n.a. PMID[561886]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.0297 ug.mL-1 PMID[561886]
NPT2 Others Unspecified Ratio IC50 = 640.0 n.a. PMID[561886]

☑ 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 NPC474086 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
0.8833 High Similarity NPC475716
0.85 High Similarity NPC474528
0.85 High Similarity NPC474415
0.85 High Similarity NPC475696
0.85 High Similarity NPC474457
0.8448 Intermediate Similarity NPC476679
0.8226 Intermediate Similarity NPC474454
0.8226 Intermediate Similarity NPC474455
0.8226 Intermediate Similarity NPC474420
0.8065 Intermediate Similarity NPC469769
0.7931 Intermediate Similarity NPC476681
0.7833 Intermediate Similarity NPC474416
0.7458 Intermediate Similarity NPC22765
0.7302 Intermediate Similarity NPC470893
0.7302 Intermediate Similarity NPC123194
0.7288 Intermediate Similarity NPC124851
0.7167 Intermediate Similarity NPC17518
0.7121 Intermediate Similarity NPC472827
0.7119 Intermediate Similarity NPC323445
0.7049 Intermediate Similarity NPC200129
0.7 Intermediate Similarity NPC92327
0.6986 Remote Similarity NPC470078
0.6986 Remote Similarity NPC21773
0.6984 Remote Similarity NPC127944
0.6949 Remote Similarity NPC86683
0.6949 Remote Similarity NPC49088
0.6933 Remote Similarity NPC125828
0.6912 Remote Similarity NPC219621
0.6901 Remote Similarity NPC176107
0.68 Remote Similarity NPC476904
0.6769 Remote Similarity NPC469770
0.6765 Remote Similarity NPC317778
0.6761 Remote Similarity NPC176171
0.6757 Remote Similarity NPC265789
0.6724 Remote Similarity NPC193180
0.6724 Remote Similarity NPC190232
0.6724 Remote Similarity NPC105246
0.6716 Remote Similarity NPC472830
0.6712 Remote Similarity NPC182815
0.6667 Remote Similarity NPC469728
0.6623 Remote Similarity NPC7214
0.6622 Remote Similarity NPC475728
0.6622 Remote Similarity NPC9161
0.6622 Remote Similarity NPC49422
0.6613 Remote Similarity NPC17810
0.661 Remote Similarity NPC192529
0.6579 Remote Similarity NPC329866
0.6579 Remote Similarity NPC474796
0.6579 Remote Similarity NPC474797
0.6575 Remote Similarity NPC160209
0.6575 Remote Similarity NPC20610
0.6552 Remote Similarity NPC103290
0.6533 Remote Similarity NPC115023
0.6528 Remote Similarity NPC474456
0.6528 Remote Similarity NPC323005
0.6522 Remote Similarity NPC311809
0.6522 Remote Similarity NPC176621
0.65 Remote Similarity NPC202189
0.6494 Remote Similarity NPC471468
0.6486 Remote Similarity NPC269877
0.6486 Remote Similarity NPC167272
0.6471 Remote Similarity NPC60772
0.6456 Remote Similarity NPC18603
0.6456 Remote Similarity NPC307965
0.6456 Remote Similarity NPC76931
0.6452 Remote Similarity NPC178644
0.6447 Remote Similarity NPC251705
0.6441 Remote Similarity NPC177470
0.641 Remote Similarity NPC469793
0.641 Remote Similarity NPC469796
0.64 Remote Similarity NPC159577
0.64 Remote Similarity NPC477856
0.64 Remote Similarity NPC35734
0.64 Remote Similarity NPC307176
0.64 Remote Similarity NPC282593
0.64 Remote Similarity NPC40574
0.64 Remote Similarity NPC214770
0.6393 Remote Similarity NPC296337
0.6393 Remote Similarity NPC13991
0.6393 Remote Similarity NPC241784
0.6393 Remote Similarity NPC114239
0.6389 Remote Similarity NPC268039
0.6377 Remote Similarity NPC309825
0.6364 Remote Similarity NPC476683
0.6333 Remote Similarity NPC227670
0.6333 Remote Similarity NPC166362
0.6333 Remote Similarity NPC141777
0.6324 Remote Similarity NPC470370
0.6324 Remote Similarity NPC470369
0.6316 Remote Similarity NPC234707
0.6316 Remote Similarity NPC54123
0.6301 Remote Similarity NPC149680
0.6301 Remote Similarity NPC37792
0.6296 Remote Similarity NPC12035
0.6282 Remote Similarity NPC293803
0.6282 Remote Similarity NPC473171
0.6271 Remote Similarity NPC144023
0.6267 Remote Similarity NPC139397
0.6267 Remote Similarity NPC184919
0.6267 Remote Similarity NPC138409
0.6267 Remote Similarity NPC476431
0.625 Remote Similarity NPC469662
0.625 Remote Similarity NPC473959
0.6234 Remote Similarity NPC470044
0.6234 Remote Similarity NPC474228
0.6234 Remote Similarity NPC470045
0.6234 Remote Similarity NPC303613
0.623 Remote Similarity NPC248411
0.622 Remote Similarity NPC118329
0.622 Remote Similarity NPC152039
0.622 Remote Similarity NPC329782
0.622 Remote Similarity NPC474122
0.6203 Remote Similarity NPC129165
0.6203 Remote Similarity NPC134330
0.6203 Remote Similarity NPC474463
0.6203 Remote Similarity NPC69408
0.6203 Remote Similarity NPC113733
0.6184 Remote Similarity NPC2634
0.6184 Remote Similarity NPC260040
0.6184 Remote Similarity NPC251929
0.6184 Remote Similarity NPC265782
0.6176 Remote Similarity NPC318036
0.6173 Remote Similarity NPC211322
0.6167 Remote Similarity NPC473912
0.6154 Remote Similarity NPC309852
0.6154 Remote Similarity NPC329090
0.6154 Remote Similarity NPC27395
0.6145 Remote Similarity NPC283277
0.6145 Remote Similarity NPC215474
0.6145 Remote Similarity NPC472312
0.6143 Remote Similarity NPC152211
0.6143 Remote Similarity NPC28755
0.6133 Remote Similarity NPC32055
0.6129 Remote Similarity NPC229403
0.6125 Remote Similarity NPC474230
0.6125 Remote Similarity NPC91665
0.6111 Remote Similarity NPC145715
0.6111 Remote Similarity NPC202118
0.6111 Remote Similarity NPC197238
0.6104 Remote Similarity NPC305501
0.6102 Remote Similarity NPC183670
0.6087 Remote Similarity NPC173815
0.6081 Remote Similarity NPC222366
0.6081 Remote Similarity NPC476039
0.6081 Remote Similarity NPC286669
0.6076 Remote Similarity NPC141071
0.6076 Remote Similarity NPC285893
0.6076 Remote Similarity NPC288035
0.6076 Remote Similarity NPC471723
0.6076 Remote Similarity NPC136188
0.6076 Remote Similarity NPC22105
0.6076 Remote Similarity NPC304309
0.6076 Remote Similarity NPC328104
0.6076 Remote Similarity NPC319090
0.6076 Remote Similarity NPC28657
0.6076 Remote Similarity NPC230301
0.6076 Remote Similarity NPC257347
0.6076 Remote Similarity NPC255650
0.6076 Remote Similarity NPC134847
0.6076 Remote Similarity NPC162742
0.6071 Remote Similarity NPC171639
0.6071 Remote Similarity NPC21667
0.6061 Remote Similarity NPC473728
0.6053 Remote Similarity NPC472831
0.6049 Remote Similarity NPC82635
0.6049 Remote Similarity NPC186191
0.6049 Remote Similarity NPC205455
0.6049 Remote Similarity NPC470052
0.6049 Remote Similarity NPC105197
0.6026 Remote Similarity NPC474140
0.6 Remote Similarity NPC300324
0.6 Remote Similarity NPC324944
0.6 Remote Similarity NPC120926
0.6 Remote Similarity NPC247325
0.6 Remote Similarity NPC244488
0.6 Remote Similarity NPC259989
0.6 Remote Similarity NPC321016
0.6 Remote Similarity NPC237460
0.6 Remote Similarity NPC240604
0.6 Remote Similarity NPC321381
0.6 Remote Similarity NPC474231
0.6 Remote Similarity NPC477289
0.6 Remote Similarity NPC470362
0.6 Remote Similarity NPC174803
0.6 Remote Similarity NPC189883
0.6 Remote Similarity NPC193770
0.6 Remote Similarity NPC315261
0.6 Remote Similarity NPC107059
0.6 Remote Similarity NPC197805
0.6 Remote Similarity NPC218918
0.5976 Remote Similarity NPC190211
0.5976 Remote Similarity NPC170793
0.597 Remote Similarity NPC472828
0.5952 Remote Similarity NPC469804
0.5952 Remote Similarity NPC469805
0.5952 Remote Similarity NPC469799
0.5952 Remote Similarity NPC469806
0.5949 Remote Similarity NPC255021
0.593 Remote Similarity NPC75810
0.593 Remote Similarity NPC24733

  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 NPC474086 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
0.7083 Intermediate Similarity NPD6939 Phase 2
0.7083 Intermediate Similarity NPD6938 Clinical (unspecified phase)
0.6724 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6622 Remote Similarity NPD7144 Approved
0.6622 Remote Similarity NPD7143 Approved
0.6613 Remote Similarity NPD8262 Approved
0.6579 Remote Similarity NPD4687 Approved
0.6579 Remote Similarity NPD4058 Approved
0.6533 Remote Similarity NPD7150 Approved
0.6533 Remote Similarity NPD7152 Approved
0.6533 Remote Similarity NPD7151 Approved
0.6486 Remote Similarity NPD6923 Approved
0.6486 Remote Similarity NPD6922 Approved
0.64 Remote Similarity NPD4747 Approved
0.6364 Remote Similarity NPD5733 Approved
0.6364 Remote Similarity NPD4784 Approved
0.6364 Remote Similarity NPD4785 Approved
0.6351 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6322 Remote Similarity NPD4096 Approved
0.6316 Remote Similarity NPD5276 Approved
0.6316 Remote Similarity NPD4243 Approved
0.6267 Remote Similarity NPD4137 Phase 3
0.6265 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6184 Remote Similarity NPD4691 Approved
0.6154 Remote Similarity NPD6924 Approved
0.6154 Remote Similarity NPD6926 Approved
0.6125 Remote Similarity NPD6932 Approved
0.6076 Remote Similarity NPD6942 Approved
0.6076 Remote Similarity NPD5275 Approved
0.6076 Remote Similarity NPD7339 Approved
0.6076 Remote Similarity NPD4190 Phase 3
0.6049 Remote Similarity NPD7145 Approved
0.6024 Remote Similarity NPD8028 Phase 2
0.6 Remote Similarity NPD6933 Approved
0.5976 Remote Similarity NPD4195 Approved
0.5926 Remote Similarity NPD5776 Phase 2
0.5926 Remote Similarity NPD6925 Approved
0.5904 Remote Similarity NPD7514 Phase 3
0.5854 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6902 Approved
0.5802 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5783 Remote Similarity NPD6683 Phase 2
0.5783 Remote Similarity NPD6929 Approved
0.573 Remote Similarity NPD5675 Discontinued
0.573 Remote Similarity NPD4723 Approved
0.573 Remote Similarity NPD4722 Approved
0.5714 Remote Similarity NPD7332 Phase 2
0.5714 Remote Similarity NPD6930 Phase 2
0.5714 Remote Similarity NPD4219 Approved
0.5714 Remote Similarity NPD6931 Approved
0.5714 Remote Similarity NPD7525 Registered
0.5632 Remote Similarity NPD4544 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