Structure

Physi-Chem Properties

Molecular Weight:  277.15
Volume:  295.929
LogP:  4.408
LogD:  3.791
LogS:  -4.269
# Rotatable Bonds:  2
TPSA:  29.43
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.562
Synthetic Accessibility Score:  4.726
Fsp3:  0.75
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:  -4.641
MDCK Permeability:  2.3738744857837446e-05
Pgp-inhibitor:  0.072
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.14

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.843
Plasma Protein Binding (PPB):  72.05460357666016%
Volume Distribution (VD):  1.073
Pgp-substrate:  18.59002685546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.139
CYP1A2-substrate:  0.458
CYP2C19-inhibitor:  0.05
CYP2C19-substrate:  0.931
CYP2C9-inhibitor:  0.136
CYP2C9-substrate:  0.084
CYP2D6-inhibitor:  0.046
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.804
CYP3A4-substrate:  0.523

ADMET: Excretion

Clearance (CL):  6.052
Half-life (T1/2):  0.5

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.145
Drug-inuced Liver Injury (DILI):  0.363
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.228
Maximum Recommended Daily Dose:  0.85
Skin Sensitization:  0.912
Carcinogencity:  0.197
Eye Corrosion:  0.907
Eye Irritation:  0.895
Respiratory Toxicity:  0.924

Download Data

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

  Natural Product: NPC250632

Natural Product ID:  NPC250632
Common Name*:   Axinisothiocyanate L
IUPAC Name:   (4aS,5R,8R,8aR)-8-isothiocyanato-3,8-dimethyl-5-propan-2-yl-1,4a,5,6,7,8a-hexahydronaphthalen-2-one
Synonyms:   Axinisothiocyanate L
Standard InCHIKey:  ODUZQPVIXXXOEL-IXYNUQLISA-N
Standard InCHI:  InChI=1S/C16H23NOS/c1-10(2)12-5-6-16(4,17-9-19)14-8-15(18)11(3)7-13(12)14/h7,10,12-14H,5-6,8H2,1-4H3/t12-,13-,14-,16-/m1/s1
SMILES:  S=C=N[C@]1(C)CC[C@@H]([C@@H]2[C@H]1CC(=O)C(=C2)C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL457457
PubChem CID:   24862229
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
NPT81 Cell Line A549 Homo sapiens GI50 = 31400.0 nM PMID[469450]
NPT139 Cell Line HT-29 Homo sapiens GI50 = 31400.0 nM PMID[469450]

☑ 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 NPC250632 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
0.7838 Intermediate Similarity NPC145715
0.7733 Intermediate Similarity NPC473959
0.7432 Intermediate Similarity NPC472304
0.7432 Intermediate Similarity NPC276764
0.725 Intermediate Similarity NPC184919
0.725 Intermediate Similarity NPC138409
0.7191 Intermediate Similarity NPC311769
0.7191 Intermediate Similarity NPC182106
0.7143 Intermediate Similarity NPC259252
0.7125 Intermediate Similarity NPC188292
0.7125 Intermediate Similarity NPC310992
0.7125 Intermediate Similarity NPC260474
0.7105 Intermediate Similarity NPC311809
0.7105 Intermediate Similarity NPC127582
0.7065 Intermediate Similarity NPC249312
0.7051 Intermediate Similarity NPC285371
0.7051 Intermediate Similarity NPC475124
0.6962 Remote Similarity NPC251118
0.6951 Remote Similarity NPC265782
0.6951 Remote Similarity NPC251929
0.6951 Remote Similarity NPC2634
0.6933 Remote Similarity NPC470369
0.6933 Remote Similarity NPC470370
0.6932 Remote Similarity NPC475724
0.6914 Remote Similarity NPC87141
0.6914 Remote Similarity NPC155198
0.6867 Remote Similarity NPC54123
0.6854 Remote Similarity NPC477581
0.6854 Remote Similarity NPC477583
0.6842 Remote Similarity NPC476753
0.6842 Remote Similarity NPC27610
0.6842 Remote Similarity NPC56905
0.6842 Remote Similarity NPC476752
0.6835 Remote Similarity NPC469662
0.6829 Remote Similarity NPC139397
0.6829 Remote Similarity NPC256846
0.6786 Remote Similarity NPC474228
0.6786 Remote Similarity NPC303613
0.6786 Remote Similarity NPC251705
0.6786 Remote Similarity NPC470045
0.6786 Remote Similarity NPC470044
0.6778 Remote Similarity NPC21667
0.6771 Remote Similarity NPC476754
0.6753 Remote Similarity NPC152211
0.6753 Remote Similarity NPC28755
0.6747 Remote Similarity NPC159577
0.6747 Remote Similarity NPC35734
0.6747 Remote Similarity NPC260040
0.6747 Remote Similarity NPC282593
0.6747 Remote Similarity NPC307176
0.6742 Remote Similarity NPC477582
0.6709 Remote Similarity NPC197238
0.6709 Remote Similarity NPC202118
0.6709 Remote Similarity NPC288253
0.6667 Remote Similarity NPC317778
0.6667 Remote Similarity NPC234707
0.6667 Remote Similarity NPC37792
0.6667 Remote Similarity NPC476329
0.6667 Remote Similarity NPC474562
0.6667 Remote Similarity NPC115023
0.6667 Remote Similarity NPC190035
0.6667 Remote Similarity NPC225467
0.6634 Remote Similarity NPC226509
0.6634 Remote Similarity NPC152718
0.6633 Remote Similarity NPC247220
0.6628 Remote Similarity NPC476346
0.6628 Remote Similarity NPC293803
0.6625 Remote Similarity NPC6697
0.6625 Remote Similarity NPC212210
0.6622 Remote Similarity NPC268564
0.6593 Remote Similarity NPC477584
0.6588 Remote Similarity NPC130016
0.6588 Remote Similarity NPC180015
0.6588 Remote Similarity NPC109576
0.6588 Remote Similarity NPC56747
0.6585 Remote Similarity NPC290350
0.6585 Remote Similarity NPC4370
0.6582 Remote Similarity NPC213152
0.6582 Remote Similarity NPC60565
0.6559 Remote Similarity NPC474458
0.6552 Remote Similarity NPC1254
0.6552 Remote Similarity NPC476308
0.6552 Remote Similarity NPC69408
0.6512 Remote Similarity NPC255021
0.6512 Remote Similarity NPC329866
0.6512 Remote Similarity NPC309852
0.6512 Remote Similarity NPC474796
0.6512 Remote Similarity NPC474797
0.6506 Remote Similarity NPC142754
0.6506 Remote Similarity NPC82477
0.6506 Remote Similarity NPC20610
0.6506 Remote Similarity NPC39157
0.6506 Remote Similarity NPC296697
0.65 Remote Similarity NPC140685
0.65 Remote Similarity NPC165695
0.6494 Remote Similarity NPC115385
0.6471 Remote Similarity NPC5701
0.6471 Remote Similarity NPC305501
0.6463 Remote Similarity NPC323005
0.6452 Remote Similarity NPC76283
0.6442 Remote Similarity NPC230677
0.6437 Remote Similarity NPC65650
0.6437 Remote Similarity NPC473171
0.6429 Remote Similarity NPC286814
0.6429 Remote Similarity NPC182815
0.641 Remote Similarity NPC308108
0.641 Remote Similarity NPC311852
0.641 Remote Similarity NPC60772
0.641 Remote Similarity NPC170799
0.6404 Remote Similarity NPC189485
0.6404 Remote Similarity NPC115515
0.64 Remote Similarity NPC184033
0.6386 Remote Similarity NPC220210
0.6386 Remote Similarity NPC20181
0.6386 Remote Similarity NPC475523
0.6364 Remote Similarity NPC469796
0.6364 Remote Similarity NPC180886
0.6364 Remote Similarity NPC469793
0.6364 Remote Similarity NPC76966
0.6364 Remote Similarity NPC473733
0.6364 Remote Similarity NPC186554
0.6346 Remote Similarity NPC469958
0.6341 Remote Similarity NPC470329
0.6333 Remote Similarity NPC90965
0.6333 Remote Similarity NPC170793
0.6333 Remote Similarity NPC27817
0.6322 Remote Similarity NPC211641
0.6322 Remote Similarity NPC128346
0.6322 Remote Similarity NPC20025
0.6322 Remote Similarity NPC219232
0.6292 Remote Similarity NPC472300
0.6279 Remote Similarity NPC470078
0.6279 Remote Similarity NPC133253
0.6279 Remote Similarity NPC21944
0.6265 Remote Similarity NPC92327
0.6265 Remote Similarity NPC176171
0.6264 Remote Similarity NPC474509
0.6264 Remote Similarity NPC476809
0.6264 Remote Similarity NPC108955
0.6263 Remote Similarity NPC477290
0.625 Remote Similarity NPC474563
0.625 Remote Similarity NPC25853
0.625 Remote Similarity NPC255650
0.6234 Remote Similarity NPC200258
0.6222 Remote Similarity NPC207772
0.6222 Remote Similarity NPC79704
0.6222 Remote Similarity NPC275494
0.6222 Remote Similarity NPC471409
0.6222 Remote Similarity NPC74410
0.6216 Remote Similarity NPC58970
0.6216 Remote Similarity NPC176819
0.6216 Remote Similarity NPC163984
0.6216 Remote Similarity NPC32351
0.6214 Remote Similarity NPC34193
0.6207 Remote Similarity NPC474488
0.6203 Remote Similarity NPC30215
0.6203 Remote Similarity NPC94991
0.6203 Remote Similarity NPC266295
0.6196 Remote Similarity NPC149237
0.6196 Remote Similarity NPC278459
0.6196 Remote Similarity NPC475833
0.6196 Remote Similarity NPC116797
0.6196 Remote Similarity NPC55869
0.6196 Remote Similarity NPC99308
0.6196 Remote Similarity NPC474085
0.619 Remote Similarity NPC193770
0.619 Remote Similarity NPC476135
0.619 Remote Similarity NPC176107
0.6184 Remote Similarity NPC23117
0.618 Remote Similarity NPC7629
0.618 Remote Similarity NPC19907
0.618 Remote Similarity NPC151622
0.618 Remote Similarity NPC472305
0.6163 Remote Similarity NPC246722
0.6163 Remote Similarity NPC477856
0.6163 Remote Similarity NPC214770
0.6163 Remote Similarity NPC151045
0.6154 Remote Similarity NPC476177
0.6154 Remote Similarity NPC318036
0.6154 Remote Similarity NPC469598
0.6129 Remote Similarity NPC3511
0.6129 Remote Similarity NPC472867
0.6129 Remote Similarity NPC472239
0.6129 Remote Similarity NPC142253
0.6125 Remote Similarity NPC285594
0.6125 Remote Similarity NPC259261
0.6125 Remote Similarity NPC96551
0.6111 Remote Similarity NPC97377
0.6111 Remote Similarity NPC257666
0.6111 Remote Similarity NPC266193
0.6111 Remote Similarity NPC34110
0.6111 Remote Similarity NPC175585
0.6111 Remote Similarity NPC165711
0.6104 Remote Similarity NPC5626
0.6098 Remote Similarity NPC472306
0.6098 Remote Similarity NPC32285
0.6092 Remote Similarity NPC181204
0.6092 Remote Similarity NPC223187
0.6087 Remote Similarity NPC472478
0.6087 Remote Similarity NPC2482

  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 NPC250632 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
0.7 Intermediate Similarity NPD7812 Clinical (unspecified phase)
0.6951 Remote Similarity NPD4691 Approved
0.6829 Remote Similarity NPD4137 Phase 3
0.6778 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6747 Remote Similarity NPD4747 Approved
0.6706 Remote Similarity NPD4058 Approved
0.6556 Remote Similarity NPD8028 Phase 2
0.6512 Remote Similarity NPD4687 Approved
0.6512 Remote Similarity NPD5733 Approved
0.6506 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6471 Remote Similarity NPD5276 Approved
0.6429 Remote Similarity NPD5769 Clinical (unspecified phase)
0.641 Remote Similarity NPD287 Approved
0.6117 Remote Similarity NPD6404 Discontinued
0.6087 Remote Similarity NPD4695 Discontinued
0.5957 Remote Similarity NPD4223 Phase 3
0.5957 Remote Similarity NPD4221 Approved
0.5876 Remote Similarity NPD5690 Phase 2
0.5833 Remote Similarity NPD3666 Approved
0.5833 Remote Similarity NPD3665 Phase 1
0.5833 Remote Similarity NPD3133 Approved
0.5833 Remote Similarity NPD4197 Approved
0.5816 Remote Similarity NPD3573 Approved
0.58 Remote Similarity NPD4096 Approved
0.5773 Remote Similarity NPD5329 Approved
0.5714 Remote Similarity NPD4519 Discontinued
0.5714 Remote Similarity NPD4690 Approved
0.5714 Remote Similarity NPD7146 Approved
0.5714 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4688 Approved
0.5714 Remote Similarity NPD4689 Approved
0.5714 Remote Similarity NPD3618 Phase 1
0.5714 Remote Similarity NPD5205 Approved
0.5714 Remote Similarity NPD7521 Approved
0.5714 Remote Similarity NPD4623 Approved
0.5714 Remote Similarity NPD7334 Approved
0.5714 Remote Similarity NPD4693 Phase 3
0.5714 Remote Similarity NPD4138 Approved
0.5714 Remote Similarity NPD5330 Approved
0.5714 Remote Similarity NPD6684 Approved
0.5714 Remote Similarity NPD4694 Approved
0.5714 Remote Similarity NPD6409 Approved
0.5714 Remote Similarity NPD5280 Approved
0.5699 Remote Similarity NPD3617 Approved
0.5698 Remote Similarity NPD7331 Phase 2
0.5673 Remote Similarity NPD7732 Phase 3
0.5673 Remote Similarity NPD7614 Phase 1
0.567 Remote Similarity NPD3668 Phase 3
0.5625 Remote Similarity NPD3667 Approved
0.56 Remote Similarity NPD5737 Approved
0.56 Remote Similarity NPD6672 Approved
0.56 Remote Similarity NPD7513 Clinical (unspecified phase)
0.56 Remote Similarity NPD6903 Approved
0.56 Remote Similarity NPD5208 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