Structure

Physi-Chem Properties

Molecular Weight:  263.17
Volume:  289.776
LogP:  5.82
LogD:  5.069
LogS:  -5.16
# Rotatable Bonds:  2
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.393
Synthetic Accessibility Score:  5.28
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.643
MDCK Permeability:  2.8409247534000315e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.757
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.855
Plasma Protein Binding (PPB):  88.76461791992188%
Volume Distribution (VD):  1.1
Pgp-substrate:  6.894429683685303%

ADMET: Metabolism

CYP1A2-inhibitor:  0.35
CYP1A2-substrate:  0.136
CYP2C19-inhibitor:  0.064
CYP2C19-substrate:  0.843
CYP2C9-inhibitor:  0.318
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.179
CYP2D6-substrate:  0.11
CYP3A4-inhibitor:  0.863
CYP3A4-substrate:  0.465

ADMET: Excretion

Clearance (CL):  7.074
Half-life (T1/2):  0.118

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.114
Drug-inuced Liver Injury (DILI):  0.632
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.839
Maximum Recommended Daily Dose:  0.312
Skin Sensitization:  0.813
Carcinogencity:  0.325
Eye Corrosion:  0.925
Eye Irritation:  0.496
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC37792

Natural Product ID:  NPC37792
Common Name*:   (5S,6R,7S,10R)-7-Isopropyl-6-Isothiocyanato-2,10-Dimethylspiro[4.5]Dec-1-Ene
IUPAC Name:   (5S,6R,9S,10R)-10-isothiocyanato-3,6-dimethyl-9-propan-2-ylspiro[4.5]dec-3-ene
Synonyms:  
Standard InCHIKey:  QEUKPIZJCSOXDW-QKPAOTATSA-N
Standard InCHI:  InChI=1S/C16H25NS/c1-11(2)14-6-5-13(4)16(15(14)17-10-18)8-7-12(3)9-16/h9,11,13-15H,5-8H2,1-4H3/t13-,14+,15-,16-/m1/s1
SMILES:  CC(C)[C@@H]1CC[C@@H](C)[C@]2(CCC(=C2)C)[C@@H]1N=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507622
PubChem CID:   23425033
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

*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
NPO4958 Acanthella klethra Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[1294700]
NPO4958 Acanthella klethra Species Melastomataceae 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
NPT91 Cell Line KB Homo sapiens IC50 > 20.0 ug.mL-1 PMID[486221]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 12.34 ug.mL-1 PMID[486221]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 3.11 ug.mL-1 PMID[486221]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum EC50 = 11800.0 nM PMID[486222]

☑ 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 NPC37792 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
0.9032 High Similarity NPC219621
0.8308 Intermediate Similarity NPC145715
0.8281 Intermediate Similarity NPC311809
0.8182 Intermediate Similarity NPC473959
0.8125 Intermediate Similarity NPC152211
0.8125 Intermediate Similarity NPC28755
0.8116 Intermediate Similarity NPC184919
0.7397 Intermediate Similarity NPC265789
0.7361 Intermediate Similarity NPC138409
0.7333 Intermediate Similarity NPC125828
0.7313 Intermediate Similarity NPC472827
0.7273 Intermediate Similarity NPC470369
0.7273 Intermediate Similarity NPC470370
0.7206 Intermediate Similarity NPC317778
0.72 Intermediate Similarity NPC476904
0.7164 Intermediate Similarity NPC472830
0.7162 Intermediate Similarity NPC21773
0.7123 Intermediate Similarity NPC472831
0.7013 Intermediate Similarity NPC476308
0.6962 Remote Similarity NPC211322
0.6944 Remote Similarity NPC474456
0.6933 Remote Similarity NPC476329
0.6901 Remote Similarity NPC476682
0.6795 Remote Similarity NPC7214
0.6707 Remote Similarity NPC283277
0.6667 Remote Similarity NPC250632
0.6667 Remote Similarity NPC124851
0.6618 Remote Similarity NPC318036
0.6588 Remote Similarity NPC166458
0.6585 Remote Similarity NPC329782
0.6562 Remote Similarity NPC22765
0.6562 Remote Similarity NPC17518
0.6522 Remote Similarity NPC474415
0.6522 Remote Similarity NPC173815
0.6522 Remote Similarity NPC475696
0.6522 Remote Similarity NPC474457
0.6522 Remote Similarity NPC474528
0.6506 Remote Similarity NPC472312
0.6471 Remote Similarity NPC24733
0.6471 Remote Similarity NPC152684
0.6463 Remote Similarity NPC12035
0.6429 Remote Similarity NPC171639
0.6429 Remote Similarity NPC324944
0.642 Remote Similarity NPC79704
0.6418 Remote Similarity NPC475272
0.64 Remote Similarity NPC476135
0.6395 Remote Similarity NPC157479
0.6386 Remote Similarity NPC474122
0.6386 Remote Similarity NPC118329
0.6386 Remote Similarity NPC152039
0.6386 Remote Similarity NPC475724
0.6349 Remote Similarity NPC86683
0.6338 Remote Similarity NPC474454
0.6338 Remote Similarity NPC475716
0.6338 Remote Similarity NPC474420
0.6338 Remote Similarity NPC474455
0.631 Remote Similarity NPC215474
0.6301 Remote Similarity NPC474596
0.6301 Remote Similarity NPC474086
0.6212 Remote Similarity NPC472829
0.6207 Remote Similarity NPC474458
0.6176 Remote Similarity NPC476679
0.6129 Remote Similarity NPC190232
0.6129 Remote Similarity NPC105246
0.6118 Remote Similarity NPC224072
0.6118 Remote Similarity NPC39966
0.6094 Remote Similarity NPC296337
0.6094 Remote Similarity NPC241784
0.6094 Remote Similarity NPC114239
0.6094 Remote Similarity NPC13991
0.6092 Remote Similarity NPC311769
0.6092 Remote Similarity NPC182106
0.6092 Remote Similarity NPC147513
0.6092 Remote Similarity NPC75810
0.6081 Remote Similarity NPC477740
0.6067 Remote Similarity NPC259252
0.6067 Remote Similarity NPC34754
0.6047 Remote Similarity NPC21667
0.6032 Remote Similarity NPC192529
0.6029 Remote Similarity NPC473728
0.6023 Remote Similarity NPC56107
0.6 Remote Similarity NPC249312
0.6 Remote Similarity NPC123194
0.6 Remote Similarity NPC257962
0.6 Remote Similarity NPC469770
0.5972 Remote Similarity NPC469769
0.597 Remote Similarity NPC200129
0.597 Remote Similarity NPC476681
0.5942 Remote Similarity NPC472828
0.5942 Remote Similarity NPC474416
0.5938 Remote Similarity NPC248411
0.5938 Remote Similarity NPC202189
0.5938 Remote Similarity NPC275686
0.5934 Remote Similarity NPC84171
0.593 Remote Similarity NPC471868
0.5895 Remote Similarity NPC167419
0.5873 Remote Similarity NPC193180
0.5867 Remote Similarity NPC475755
0.5867 Remote Similarity NPC472544
0.5857 Remote Similarity NPC476683
0.5851 Remote Similarity NPC311164
0.5851 Remote Similarity NPC272732
0.5846 Remote Similarity NPC49088
0.5833 Remote Similarity NPC140685
0.5821 Remote Similarity NPC106990
0.5806 Remote Similarity NPC476753
0.5806 Remote Similarity NPC476752
0.5806 Remote Similarity NPC93027
0.5758 Remote Similarity NPC323445
0.5758 Remote Similarity NPC90538
0.5753 Remote Similarity NPC231129
0.575 Remote Similarity NPC472543
0.5745 Remote Similarity NPC280710
0.5745 Remote Similarity NPC243985
0.5745 Remote Similarity NPC476754
0.5733 Remote Similarity NPC477739
0.5714 Remote Similarity NPC475812
0.5714 Remote Similarity NPC324405
0.5714 Remote Similarity NPC103290
0.5676 Remote Similarity NPC21781
0.5676 Remote Similarity NPC82919
0.5657 Remote Similarity NPC226509
0.5657 Remote Similarity NPC247060
0.5644 Remote Similarity NPC55462
0.5632 Remote Similarity NPC90150
0.5625 Remote Similarity NPC476903
0.5618 Remote Similarity NPC471867
0.5616 Remote Similarity NPC11130
0.56 Remote Similarity NPC474583
0.56 Remote Similarity NPC176621

  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 NPC37792 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
0.6154 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6939 Phase 2
0.6129 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6076 Remote Similarity NPD5365 Phase 2
0.5914 Remote Similarity NPD5771 Approved
0.5914 Remote Similarity NPD5769 Clinical (unspecified phase)

  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