Structure

Physi-Chem Properties

Molecular Weight:  238.18
Volume:  266.756
LogP:  5.516
LogD:  5.251
LogS:  -5.261
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.496
Synthetic Accessibility Score:  4.478
Fsp3:  0.867
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:  -4.386
MDCK Permeability:  2.0145509552094154e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.587
30% Bioavailability (F30%):  0.23

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.049
Plasma Protein Binding (PPB):  99.01691436767578%
Volume Distribution (VD):  4.042
Pgp-substrate:  2.1199119091033936%

ADMET: Metabolism

CYP1A2-inhibitor:  0.787
CYP1A2-substrate:  0.694
CYP2C19-inhibitor:  0.273
CYP2C19-substrate:  0.918
CYP2C9-inhibitor:  0.546
CYP2C9-substrate:  0.517
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.262
CYP3A4-inhibitor:  0.209
CYP3A4-substrate:  0.481

ADMET: Excretion

Clearance (CL):  6.835
Half-life (T1/2):  0.292

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.416
Drug-inuced Liver Injury (DILI):  0.684
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.046
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.06
Carcinogencity:  0.05
Eye Corrosion:  0.128
Eye Irritation:  0.249
Respiratory Toxicity:  0.082

Download Data

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

  Natural Product: NPC473728

Natural Product ID:  NPC473728
Common Name*:   (1R,4S,4Ar,8Ar)-4-Isopropyl-1,6-Dimethyl-1,2,3,4,4A,7,8,8A-Octahydronaphthalene-1-Thiol
IUPAC Name:   (1R,4S,4aR,8aR)-1,6-dimethyl-4-propan-2-yl-3,4,4a,7,8,8a-hexahydro-2H-naphthalene-1-thiol
Synonyms:  
Standard InCHIKey:  NHIPRVZTDBRCSA-BYNSBNAKSA-N
Standard InCHI:  InChI=1S/C15H26S/c1-10(2)12-7-8-15(4,16)14-6-5-11(3)9-13(12)14/h9-10,12-14,16H,5-8H2,1-4H3/t12-,13-,14+,15+/m0/s1
SMILES:  CC1=CC2C(CCC(C2CC1)(C)S)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450466
PubChem CID:   44566866
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 > 20.0 ug.mL-1 PMID[447487]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 3.61 ug.mL-1 PMID[447487]
NPT2 Others Unspecified Ratio IC50 > 5.5 n.a. PMID[447487]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 2.89 ug.mL-1 PMID[447487]
NPT2 Others Unspecified Ratio IC50 > 6.9 n.a. PMID[447487]

☑ 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 NPC473728 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
0.8163 Intermediate Similarity NPC202189
0.8 Intermediate Similarity NPC86683
0.7885 Intermediate Similarity NPC17518
0.76 Intermediate Similarity NPC192529
0.7547 Intermediate Similarity NPC22765
0.7358 Intermediate Similarity NPC124851
0.7308 Intermediate Similarity NPC13991
0.7308 Intermediate Similarity NPC296337
0.7308 Intermediate Similarity NPC114239
0.7308 Intermediate Similarity NPC241784
0.7292 Intermediate Similarity NPC229262
0.7292 Intermediate Similarity NPC297643
0.7292 Intermediate Similarity NPC139717
0.7119 Intermediate Similarity NPC470369
0.7119 Intermediate Similarity NPC470370
0.7115 Intermediate Similarity NPC248411
0.7083 Intermediate Similarity NPC190810
0.7083 Intermediate Similarity NPC76145
0.7083 Intermediate Similarity NPC34764
0.7069 Intermediate Similarity NPC469770
0.7059 Intermediate Similarity NPC105246
0.7059 Intermediate Similarity NPC177470
0.7059 Intermediate Similarity NPC193180
0.7059 Intermediate Similarity NPC190232
0.6897 Remote Similarity NPC476683
0.6863 Remote Similarity NPC103290
0.6863 Remote Similarity NPC144023
0.6833 Remote Similarity NPC474415
0.6833 Remote Similarity NPC474528
0.6833 Remote Similarity NPC475696
0.6825 Remote Similarity NPC145715
0.6786 Remote Similarity NPC200129
0.678 Remote Similarity NPC123194
0.6774 Remote Similarity NPC311809
0.6721 Remote Similarity NPC469769
0.6719 Remote Similarity NPC473959
0.6667 Remote Similarity NPC183670
0.6613 Remote Similarity NPC472304
0.6613 Remote Similarity NPC474455
0.6613 Remote Similarity NPC475716
0.6613 Remote Similarity NPC474454
0.6613 Remote Similarity NPC276764
0.6613 Remote Similarity NPC474420
0.66 Remote Similarity NPC239039
0.6557 Remote Similarity NPC474457
0.6415 Remote Similarity NPC473912
0.6406 Remote Similarity NPC469728
0.6406 Remote Similarity NPC79576
0.6406 Remote Similarity NPC282694
0.6406 Remote Similarity NPC194208
0.6346 Remote Similarity NPC227632
0.6346 Remote Similarity NPC62086
0.6346 Remote Similarity NPC78551
0.6316 Remote Similarity NPC17810
0.6308 Remote Similarity NPC174956
0.6296 Remote Similarity NPC60556
0.6296 Remote Similarity NPC109813
0.6296 Remote Similarity NPC86538
0.6275 Remote Similarity NPC48638
0.6275 Remote Similarity NPC45727
0.6271 Remote Similarity NPC306195
0.6271 Remote Similarity NPC181255
0.6271 Remote Similarity NPC35519
0.6271 Remote Similarity NPC179169
0.6271 Remote Similarity NPC157781
0.625 Remote Similarity NPC213749
0.625 Remote Similarity NPC127582
0.625 Remote Similarity NPC317778
0.6232 Remote Similarity NPC184919
0.623 Remote Similarity NPC470893
0.6226 Remote Similarity NPC218918
0.6226 Remote Similarity NPC120926
0.6212 Remote Similarity NPC285371
0.6212 Remote Similarity NPC475124
0.6212 Remote Similarity NPC469662
0.62 Remote Similarity NPC92224
0.619 Remote Similarity NPC60772
0.6102 Remote Similarity NPC214584
0.6102 Remote Similarity NPC26906
0.6071 Remote Similarity NPC49088
0.6066 Remote Similarity NPC5626
0.6061 Remote Similarity NPC474086
0.6061 Remote Similarity NPC197238
0.6061 Remote Similarity NPC202118
0.6042 Remote Similarity NPC3649
0.6032 Remote Similarity NPC11130
0.6029 Remote Similarity NPC242945
0.6029 Remote Similarity NPC37792
0.6029 Remote Similarity NPC176171
0.6029 Remote Similarity NPC222366
0.6029 Remote Similarity NPC259156
0.6029 Remote Similarity NPC279434
0.6029 Remote Similarity NPC476039
0.6029 Remote Similarity NPC92327
0.6029 Remote Similarity NPC202017
0.6029 Remote Similarity NPC286669
0.6 Remote Similarity NPC177112
0.6 Remote Similarity NPC71506
0.6 Remote Similarity NPC176621
0.5965 Remote Similarity NPC323445
0.5962 Remote Similarity NPC266298
0.5942 Remote Similarity NPC290350
0.5942 Remote Similarity NPC197805
0.5942 Remote Similarity NPC4370
0.5942 Remote Similarity NPC176107
0.5942 Remote Similarity NPC193770
0.5942 Remote Similarity NPC171225
0.5938 Remote Similarity NPC27610
0.5938 Remote Similarity NPC56905
0.5932 Remote Similarity NPC476681
0.5909 Remote Similarity NPC219621
0.5909 Remote Similarity NPC60565
0.5902 Remote Similarity NPC474416
0.5902 Remote Similarity NPC14002
0.5902 Remote Similarity NPC127944
0.5902 Remote Similarity NPC268564
0.5902 Remote Similarity NPC476679
0.5902 Remote Similarity NPC23117
0.5882 Remote Similarity NPC282119
0.5882 Remote Similarity NPC163678
0.5873 Remote Similarity NPC179024
0.5857 Remote Similarity NPC216460
0.5857 Remote Similarity NPC208999
0.5857 Remote Similarity NPC20610
0.5857 Remote Similarity NPC82477
0.5857 Remote Similarity NPC310992
0.5857 Remote Similarity NPC142754
0.5857 Remote Similarity NPC260474
0.5857 Remote Similarity NPC39157
0.5857 Remote Similarity NPC296697
0.5857 Remote Similarity NPC476945
0.5857 Remote Similarity NPC188292
0.5846 Remote Similarity NPC472827
0.5846 Remote Similarity NPC152211
0.5846 Remote Similarity NPC28755
0.5846 Remote Similarity NPC309825
0.5833 Remote Similarity NPC244038
0.5833 Remote Similarity NPC471681
0.5821 Remote Similarity NPC81615
0.5821 Remote Similarity NPC283247
0.5797 Remote Similarity NPC323005
0.5797 Remote Similarity NPC255781
0.5775 Remote Similarity NPC139397
0.5775 Remote Similarity NPC138409
0.5775 Remote Similarity NPC286814
0.5775 Remote Similarity NPC474248
0.5775 Remote Similarity NPC182815
0.5758 Remote Similarity NPC135648
0.5735 Remote Similarity NPC6697
0.5735 Remote Similarity NPC52449
0.5735 Remote Similarity NPC169275
0.5714 Remote Similarity NPC141777
0.5714 Remote Similarity NPC166362
0.5714 Remote Similarity NPC220210
0.5714 Remote Similarity NPC227670
0.5714 Remote Similarity NPC200258
0.5714 Remote Similarity NPC20181
0.5714 Remote Similarity NPC206088
0.5694 Remote Similarity NPC282593
0.5694 Remote Similarity NPC307176
0.5694 Remote Similarity NPC475728
0.5694 Remote Similarity NPC260040
0.5694 Remote Similarity NPC92801
0.5694 Remote Similarity NPC251929
0.5694 Remote Similarity NPC2634
0.5694 Remote Similarity NPC34834
0.5694 Remote Similarity NPC265782
0.5694 Remote Similarity NPC35734
0.5694 Remote Similarity NPC159577
0.5692 Remote Similarity NPC170799
0.5692 Remote Similarity NPC308108
0.5672 Remote Similarity NPC213152
0.5652 Remote Similarity NPC268039
0.5652 Remote Similarity NPC251118
0.5652 Remote Similarity NPC107258
0.5634 Remote Similarity NPC94192
0.5634 Remote Similarity NPC32055
0.5634 Remote Similarity NPC96484
0.5634 Remote Similarity NPC160209
0.5634 Remote Similarity NPC87141
0.5634 Remote Similarity NPC155198
0.5625 Remote Similarity NPC318036
0.5625 Remote Similarity NPC39068
0.5625 Remote Similarity NPC141699
0.5625 Remote Similarity NPC264779
0.5616 Remote Similarity NPC190035
0.5616 Remote Similarity NPC160817
0.5616 Remote Similarity NPC54123
0.5616 Remote Similarity NPC470078
0.5616 Remote Similarity NPC23954
0.5616 Remote Similarity NPC242992
0.5616 Remote Similarity NPC265789
0.5616 Remote Similarity NPC164022
0.5616 Remote Similarity NPC115023
0.5616 Remote Similarity NPC474562
0.5616 Remote Similarity NPC21773

  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 NPC473728 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 NPD319 Phase 1
0.7059 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6316 Remote Similarity NPD8262 Approved
0.5857 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5775 Remote Similarity NPD4137 Phase 3
0.5694 Remote Similarity NPD4747 Approved
0.5694 Remote Similarity NPD6938 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4691 Approved
0.5694 Remote Similarity NPD6939 Phase 2
0.5692 Remote Similarity NPD287 Approved
0.5616 Remote Similarity NPD4243 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