Structure

Physi-Chem Properties

Molecular Weight:  279.17
Volume:  298.566
LogP:  4.796
LogD:  3.763
LogS:  -5.049
# Rotatable Bonds:  2
TPSA:  32.59
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.471
Synthetic Accessibility Score:  5.031
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.449
MDCK Permeability:  2.2679090761812404e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.033

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.919
Plasma Protein Binding (PPB):  57.27733612060547%
Volume Distribution (VD):  1.392
Pgp-substrate:  37.2047119140625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.123
CYP1A2-substrate:  0.613
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.889
CYP2C9-inhibitor:  0.046
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.107
CYP3A4-inhibitor:  0.818
CYP3A4-substrate:  0.56

ADMET: Excretion

Clearance (CL):  6.63
Half-life (T1/2):  0.175

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.081
Drug-inuced Liver Injury (DILI):  0.277
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.549
Maximum Recommended Daily Dose:  0.418
Skin Sensitization:  0.433
Carcinogencity:  0.644
Eye Corrosion:  0.926
Eye Irritation:  0.849
Respiratory Toxicity:  0.95

Download Data

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

  Natural Product: NPC475724

Natural Product ID:  NPC475724
Common Name*:   Axinisothiocyanate J
IUPAC Name:   (2R,4aR,5S,8S)-5-isothiocyanato-2,5-dimethyl-8-propan-2-yl-3,4,4a,6,7,8-hexahydronaphthalen-2-ol
Synonyms:   Axinisothiocyanate J
Standard InCHIKey:  RDQPBBPUCUTPAG-XZDPQHSOSA-N
Standard InCHI:  InChI=1S/C16H25NOS/c1-11(2)12-5-8-16(4,17-10-19)14-6-7-15(3,18)9-13(12)14/h9,11-12,14,18H,5-8H2,1-4H3/t12-,14+,15+,16-/m0/s1
SMILES:  CC(C)C1CCC(C2C1=CC(CC2)(C)O)(C)N=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL512911
PubChem CID:   24862172
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
NPO6254 Axinyssa sp. Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[18288806]
NPO6254 Axinyssa sp. Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 = 10400.0 nM PMID[470329]
NPT82 Cell Line MDA-MB-231 Homo sapiens TGI = 14300.0 nM PMID[470329]
NPT81 Cell Line A549 Homo sapiens GI50 = 11800.0 nM PMID[470329]
NPT81 Cell Line A549 Homo sapiens TGI = 19000.0 nM PMID[470329]
NPT139 Cell Line HT-29 Homo sapiens GI50 = 11800.0 nM PMID[470329]
NPT139 Cell Line HT-29 Homo sapiens TGI = 14000.0 nM PMID[470329]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens Inhibition = 50.0 % PMID[470330]
NPT27 Others Unspecified IC50 > 50000.0 nM PMID[470330]

☑ 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 NPC475724 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
0.8452 Intermediate Similarity NPC474458
0.75 Intermediate Similarity NPC174956
0.75 Intermediate Similarity NPC145715
0.75 Intermediate Similarity NPC79704
0.7403 Intermediate Similarity NPC473959
0.7222 Intermediate Similarity NPC470365
0.7215 Intermediate Similarity NPC279434
0.7051 Intermediate Similarity NPC81615
0.7013 Intermediate Similarity NPC311809
0.7 Intermediate Similarity NPC202017
0.6951 Remote Similarity NPC184919
0.6932 Remote Similarity NPC250632
0.6923 Remote Similarity NPC194208
0.6923 Remote Similarity NPC79576
0.6923 Remote Similarity NPC282694
0.6882 Remote Similarity NPC34754
0.6867 Remote Similarity NPC34834
0.6832 Remote Similarity NPC90538
0.6786 Remote Similarity NPC476329
0.6786 Remote Similarity NPC23954
0.6778 Remote Similarity NPC224072
0.6747 Remote Similarity NPC474248
0.6747 Remote Similarity NPC138409
0.6707 Remote Similarity NPC171225
0.6706 Remote Similarity NPC220939
0.6706 Remote Similarity NPC265485
0.6701 Remote Similarity NPC473314
0.6667 Remote Similarity NPC476308
0.6628 Remote Similarity NPC476366
0.6628 Remote Similarity NPC201048
0.6627 Remote Similarity NPC96484
0.6623 Remote Similarity NPC470370
0.6623 Remote Similarity NPC470369
0.6593 Remote Similarity NPC39966
0.6582 Remote Similarity NPC66020
0.6569 Remote Similarity NPC471083
0.6552 Remote Similarity NPC32832
0.6548 Remote Similarity NPC471560
0.6535 Remote Similarity NPC275686
0.6526 Remote Similarity NPC316186
0.6506 Remote Similarity NPC69649
0.6506 Remote Similarity NPC114651
0.6506 Remote Similarity NPC68703
0.65 Remote Similarity NPC41160
0.65 Remote Similarity NPC469728
0.6494 Remote Similarity NPC179024
0.6477 Remote Similarity NPC265588
0.6477 Remote Similarity NPC472305
0.6477 Remote Similarity NPC244488
0.6477 Remote Similarity NPC247325
0.6477 Remote Similarity NPC470749
0.6471 Remote Similarity NPC475728
0.6456 Remote Similarity NPC28755
0.6456 Remote Similarity NPC152211
0.6444 Remote Similarity NPC170394
0.6429 Remote Similarity NPC94192
0.6429 Remote Similarity NPC208999
0.6408 Remote Similarity NPC50815
0.6408 Remote Similarity NPC247060
0.6404 Remote Similarity NPC470758
0.6404 Remote Similarity NPC91594
0.6404 Remote Similarity NPC470711
0.6404 Remote Similarity NPC132542
0.6404 Remote Similarity NPC34110
0.64 Remote Similarity NPC181255
0.64 Remote Similarity NPC306195
0.64 Remote Similarity NPC157781
0.64 Remote Similarity NPC35519
0.64 Remote Similarity NPC179169
0.6386 Remote Similarity NPC37792
0.6375 Remote Similarity NPC240506
0.6375 Remote Similarity NPC135648
0.6375 Remote Similarity NPC317778
0.6364 Remote Similarity NPC280710
0.6364 Remote Similarity NPC243985
0.6364 Remote Similarity NPC477290
0.6364 Remote Similarity NPC133580
0.6353 Remote Similarity NPC476431
0.6353 Remote Similarity NPC473893
0.6346 Remote Similarity NPC293299
0.6346 Remote Similarity NPC45365
0.6341 Remote Similarity NPC96793
0.6341 Remote Similarity NPC323424
0.6341 Remote Similarity NPC107540
0.6337 Remote Similarity NPC240650
0.6337 Remote Similarity NPC4834
0.6333 Remote Similarity NPC471409
0.6333 Remote Similarity NPC83351
0.6333 Remote Similarity NPC179028
0.6333 Remote Similarity NPC275494
0.6333 Remote Similarity NPC167891
0.6322 Remote Similarity NPC130665
0.6322 Remote Similarity NPC474743
0.6316 Remote Similarity NPC166458
0.631 Remote Similarity NPC197805
0.631 Remote Similarity NPC476135
0.6304 Remote Similarity NPC264245
0.6292 Remote Similarity NPC151622
0.6292 Remote Similarity NPC253190
0.6292 Remote Similarity NPC7629
0.6282 Remote Similarity NPC39068
0.6282 Remote Similarity NPC264779
0.6267 Remote Similarity NPC26906
0.6267 Remote Similarity NPC214584
0.6264 Remote Similarity NPC109546
0.6264 Remote Similarity NPC81306
0.6264 Remote Similarity NPC47982
0.6264 Remote Similarity NPC143182
0.6264 Remote Similarity NPC30986
0.6264 Remote Similarity NPC84694
0.6264 Remote Similarity NPC28862
0.6264 Remote Similarity NPC209430
0.625 Remote Similarity NPC306727
0.6237 Remote Similarity NPC49964
0.6237 Remote Similarity NPC87489
0.6235 Remote Similarity NPC216460
0.6226 Remote Similarity NPC55462
0.6222 Remote Similarity NPC266193
0.6222 Remote Similarity NPC474826
0.6222 Remote Similarity NPC477425
0.6222 Remote Similarity NPC477427
0.6222 Remote Similarity NPC257666
0.6222 Remote Similarity NPC477426
0.6207 Remote Similarity NPC164022
0.6207 Remote Similarity NPC167706
0.6207 Remote Similarity NPC242992
0.6196 Remote Similarity NPC209944
0.6196 Remote Similarity NPC295131
0.6196 Remote Similarity NPC164840
0.6196 Remote Similarity NPC234193
0.6196 Remote Similarity NPC472301
0.6196 Remote Similarity NPC241290
0.619 Remote Similarity NPC222366
0.619 Remote Similarity NPC476039
0.619 Remote Similarity NPC286669
0.619 Remote Similarity NPC476406
0.619 Remote Similarity NPC267027
0.6173 Remote Similarity NPC176621
0.617 Remote Similarity NPC475789
0.617 Remote Similarity NPC474634
0.6154 Remote Similarity NPC148163
0.6154 Remote Similarity NPC148216
0.6154 Remote Similarity NPC130209
0.6154 Remote Similarity NPC474216
0.6154 Remote Similarity NPC476314
0.6145 Remote Similarity NPC476682
0.6139 Remote Similarity NPC272732
0.6139 Remote Similarity NPC311164
0.6136 Remote Similarity NPC35656
0.6136 Remote Similarity NPC259049
0.6136 Remote Similarity NPC474140
0.6136 Remote Similarity NPC182717
0.6136 Remote Similarity NPC471799
0.6129 Remote Similarity NPC47761
0.6129 Remote Similarity NPC209620
0.6129 Remote Similarity NPC249423
0.6129 Remote Similarity NPC23852
0.6129 Remote Similarity NPC476646
0.6125 Remote Similarity NPC189290
0.6125 Remote Similarity NPC474769
0.6105 Remote Similarity NPC238485
0.6105 Remote Similarity NPC231310
0.6105 Remote Similarity NPC474047
0.6105 Remote Similarity NPC205845
0.6105 Remote Similarity NPC83702
0.6098 Remote Similarity NPC68679
0.6098 Remote Similarity NPC321867
0.6098 Remote Similarity NPC207007
0.6098 Remote Similarity NPC210346
0.6095 Remote Similarity NPC469598
0.6092 Remote Similarity NPC92801
0.6092 Remote Similarity NPC145498
0.6087 Remote Similarity NPC242767
0.6087 Remote Similarity NPC233295
0.6078 Remote Similarity NPC476903
0.6071 Remote Similarity NPC258595
0.6071 Remote Similarity NPC163678
0.6071 Remote Similarity NPC64123
0.6067 Remote Similarity NPC471797
0.6067 Remote Similarity NPC100334
0.6067 Remote Similarity NPC469534
0.6067 Remote Similarity NPC469533
0.6067 Remote Similarity NPC469593
0.6064 Remote Similarity NPC202389
0.6064 Remote Similarity NPC189972
0.6064 Remote Similarity NPC92226
0.6064 Remote Similarity NPC296701
0.6064 Remote Similarity NPC50964
0.6064 Remote Similarity NPC224455
0.6064 Remote Similarity NPC101462
0.6064 Remote Similarity NPC2524
0.6064 Remote Similarity NPC218616
0.6064 Remote Similarity NPC155521
0.6047 Remote Similarity NPC471238
0.6047 Remote Similarity NPC476945
0.6047 Remote Similarity NPC160209
0.6047 Remote Similarity NPC32055
0.6044 Remote Similarity NPC74995
0.6044 Remote Similarity NPC318495
0.6044 Remote Similarity NPC198968

  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 NPC475724 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
0.6701 Remote Similarity NPD5771 Approved
0.6395 Remote Similarity NPD4243 Approved
0.625 Remote Similarity NPD4785 Approved
0.625 Remote Similarity NPD4784 Approved
0.6214 Remote Similarity NPD6404 Discontinued
0.6186 Remote Similarity NPD4722 Approved
0.6186 Remote Similarity NPD4723 Approved
0.618 Remote Similarity NPD5275 Approved
0.618 Remote Similarity NPD4190 Phase 3
0.6154 Remote Similarity NPD342 Phase 1
0.6098 Remote Similarity NPD368 Approved
0.6 Remote Similarity NPD7339 Approved
0.6 Remote Similarity NPD6942 Approved
0.5979 Remote Similarity NPD4623 Approved
0.5979 Remote Similarity NPD4519 Discontinued
0.5934 Remote Similarity NPD1346 Approved
0.5934 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5918 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5914 Remote Similarity NPD4195 Approved
0.5824 Remote Similarity NPD8264 Approved
0.5795 Remote Similarity NPD791 Approved
0.5795 Remote Similarity NPD15 Approved
0.5745 Remote Similarity NPD7645 Phase 2
0.5729 Remote Similarity NPD4221 Approved
0.5729 Remote Similarity NPD4223 Phase 3
0.5728 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6926 Approved
0.5714 Remote Similarity NPD6924 Approved
0.5684 Remote Similarity NPD6931 Approved
0.5684 Remote Similarity NPD6930 Phase 2
0.5684 Remote Similarity NPD7525 Registered
0.5638 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4197 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