Structure

Physi-Chem Properties

Molecular Weight:  251.17
Volume:  275.116
LogP:  6.151
LogD:  4.678
LogS:  -5.593
# 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:  0.658
Synthetic Accessibility Score:  4.691
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:  -4.427
MDCK Permeability:  2.120279532391578e-05
Pgp-inhibitor:  0.061
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.958
30% Bioavailability (F30%):  0.931

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.086
Plasma Protein Binding (PPB):  97.32415008544922%
Volume Distribution (VD):  3.543
Pgp-substrate:  3.539398193359375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.76
CYP1A2-substrate:  0.489
CYP2C19-inhibitor:  0.579
CYP2C19-substrate:  0.937
CYP2C9-inhibitor:  0.716
CYP2C9-substrate:  0.12
CYP2D6-inhibitor:  0.051
CYP2D6-substrate:  0.141
CYP3A4-inhibitor:  0.591
CYP3A4-substrate:  0.581

ADMET: Excretion

Clearance (CL):  11.98
Half-life (T1/2):  0.083

ADMET: Toxicity

hERG Blockers:  0.053
Human Hepatotoxicity (H-HT):  0.261
Drug-inuced Liver Injury (DILI):  0.659
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.419
Maximum Recommended Daily Dose:  0.276
Skin Sensitization:  0.622
Carcinogencity:  0.376
Eye Corrosion:  0.622
Eye Irritation:  0.247
Respiratory Toxicity:  0.953

Download Data

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

  Natural Product: NPC470370

Natural Product ID:  NPC470370
Common Name*:   (1R,4S,7S,10S)-10-Isothiocyanato-4-Amorphene
IUPAC Name:   (1S,4S,4aR,8aS)-4,7-dimethyl-1-propan-2-yl-4-thionitroso-2,3,4a,5,6,8a-hexahydro-1H-naphthalene
Synonyms:  
Standard InCHIKey:  NBLCYHOPKZIVLV-YJNKXOJESA-N
Standard InCHI:  InChI=1S/C15H25NS/c1-10(2)12-7-8-15(4,16-17)14-6-5-11(3)9-13(12)14/h9-10,12-14H,5-8H2,1-4H3/t12-,13+,14+,15-/m0/s1
SMILES:  S=N[C@@]1(C)CC[C@H]([C@@H]2[C@H]1CCC(=C2)C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2021438
PubChem CID:   70693902
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
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. At the 20 m depth, the coast of Jeju Island, Korea 2002-OCT PMID[16643027]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. the coast of Jeju Island, Korea 2002-OCT PMID[16643027]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[17190456]
NPO6254 Axinyssa sp. Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[18288806]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[19653640]
NPO21731 Acanthella cavernosa Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[2045823]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[2045823]
NPO40734 Axinyssa fenestratus Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[2045823]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[20806907]
NPO32840 topsentia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[8145229]
NPO6254 Axinyssa sp. Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21731 Acanthella cavernosa Species Axinellidae 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
NPT81 Cell Line A549 Homo sapiens GI50 = 33400.0 nM PMID[572120]

☑ 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 NPC470370 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
1.0 High Similarity NPC470369
0.8814 High Similarity NPC145715
0.8667 High Similarity NPC473959
0.8475 Intermediate Similarity NPC317778
0.8 Intermediate Similarity NPC184919
0.7869 Intermediate Similarity NPC311809
0.7797 Intermediate Similarity NPC318036
0.7727 Intermediate Similarity NPC138409
0.7541 Intermediate Similarity NPC324944
0.746 Intermediate Similarity NPC219621
0.7419 Intermediate Similarity NPC152211
0.7419 Intermediate Similarity NPC28755
0.7407 Intermediate Similarity NPC202189
0.7377 Intermediate Similarity NPC173815
0.7273 Intermediate Similarity NPC86683
0.7273 Intermediate Similarity NPC37792
0.7246 Intermediate Similarity NPC476329
0.7193 Intermediate Similarity NPC17518
0.7119 Intermediate Similarity NPC473728
0.7097 Intermediate Similarity NPC475696
0.7097 Intermediate Similarity NPC474415
0.7097 Intermediate Similarity NPC474528
0.7083 Intermediate Similarity NPC476308
0.6933 Remote Similarity NPC250632
0.6909 Remote Similarity NPC192529
0.6897 Remote Similarity NPC22765
0.6897 Remote Similarity NPC106990
0.6875 Remote Similarity NPC472827
0.6875 Remote Similarity NPC474420
0.6875 Remote Similarity NPC474455
0.6875 Remote Similarity NPC474454
0.6875 Remote Similarity NPC475716
0.6825 Remote Similarity NPC474457
0.6806 Remote Similarity NPC476904
0.6761 Remote Similarity NPC21773
0.6724 Remote Similarity NPC124851
0.6712 Remote Similarity NPC125828
0.6667 Remote Similarity NPC476135
0.6667 Remote Similarity NPC114239
0.6667 Remote Similarity NPC13991
0.6667 Remote Similarity NPC241784
0.6667 Remote Similarity NPC296337
0.6623 Remote Similarity NPC475724
0.6604 Remote Similarity NPC139717
0.6604 Remote Similarity NPC297643
0.6604 Remote Similarity NPC229262
0.6528 Remote Similarity NPC265789
0.6508 Remote Similarity NPC469770
0.6491 Remote Similarity NPC248411
0.6471 Remote Similarity NPC476682
0.6429 Remote Similarity NPC193180
0.6429 Remote Similarity NPC177470
0.6429 Remote Similarity NPC105246
0.6429 Remote Similarity NPC190232
0.6415 Remote Similarity NPC34764
0.6415 Remote Similarity NPC190810
0.6415 Remote Similarity NPC76145
0.64 Remote Similarity NPC7214
0.6324 Remote Similarity NPC474086
0.6286 Remote Similarity NPC474456
0.625 Remote Similarity NPC123194
0.625 Remote Similarity NPC103290
0.625 Remote Similarity NPC144023
0.623 Remote Similarity NPC200129
0.623 Remote Similarity NPC476681
0.622 Remote Similarity NPC474458
0.6212 Remote Similarity NPC469769
0.6203 Remote Similarity NPC329782
0.619 Remote Similarity NPC474416
0.619 Remote Similarity NPC476679
0.6154 Remote Similarity NPC211322
0.6125 Remote Similarity NPC472312
0.6119 Remote Similarity NPC472304
0.6119 Remote Similarity NPC276764
0.6087 Remote Similarity NPC472544
0.6076 Remote Similarity NPC12035
0.6071 Remote Similarity NPC183670
0.6049 Remote Similarity NPC171639
0.6032 Remote Similarity NPC212905
0.6027 Remote Similarity NPC472831
0.6 Remote Similarity NPC118329
0.6 Remote Similarity NPC239039
0.6 Remote Similarity NPC152039
0.597 Remote Similarity NPC472830
0.5942 Remote Similarity NPC469728
0.5942 Remote Similarity NPC282694
0.5942 Remote Similarity NPC79576
0.5942 Remote Similarity NPC194208
0.5926 Remote Similarity NPC215474
0.5926 Remote Similarity NPC283277
0.5862 Remote Similarity NPC473912
0.5857 Remote Similarity NPC174956
0.5854 Remote Similarity NPC21667
0.5846 Remote Similarity NPC476683
0.5833 Remote Similarity NPC470365
0.5823 Remote Similarity NPC79704
0.5806 Remote Similarity NPC17810
0.5802 Remote Similarity NPC474122
0.5797 Remote Similarity NPC127582
0.5789 Remote Similarity NPC78551
0.5789 Remote Similarity NPC227632
0.5789 Remote Similarity NPC62086
0.5781 Remote Similarity NPC179169
0.5781 Remote Similarity NPC157781
0.5781 Remote Similarity NPC35519
0.5781 Remote Similarity NPC306195
0.5781 Remote Similarity NPC181255
0.5775 Remote Similarity NPC469662
0.5775 Remote Similarity NPC285371
0.5775 Remote Similarity NPC475124
0.5763 Remote Similarity NPC86538
0.5763 Remote Similarity NPC60556
0.5763 Remote Similarity NPC109813
0.5758 Remote Similarity NPC470893
0.5735 Remote Similarity NPC231129
0.5735 Remote Similarity NPC60772
0.5714 Remote Similarity NPC45727
0.5714 Remote Similarity NPC24733
0.5714 Remote Similarity NPC48638
0.569 Remote Similarity NPC120926
0.569 Remote Similarity NPC218918
0.566 Remote Similarity NPC213749
0.5652 Remote Similarity NPC82919
0.5647 Remote Similarity NPC157479
0.5636 Remote Similarity NPC92224
0.5634 Remote Similarity NPC202118
0.5634 Remote Similarity NPC197238
0.5625 Remote Similarity NPC214584
0.5625 Remote Similarity NPC26906
0.5616 Remote Similarity NPC476039
0.5616 Remote Similarity NPC176171
0.5616 Remote Similarity NPC242945
0.5616 Remote Similarity NPC92327
0.5616 Remote Similarity NPC259156
0.5616 Remote Similarity NPC202017
0.5616 Remote Similarity NPC286669
0.5616 Remote Similarity NPC279434
0.5616 Remote Similarity NPC222366
0.5606 Remote Similarity NPC5626

  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 NPC470370 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
0.6429 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6415 Remote Similarity NPD319 Phase 1
0.6164 Remote Similarity NPD6939 Phase 2
0.6164 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6081 Remote Similarity NPD5365 Phase 2
0.5806 Remote Similarity NPD8262 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