Structure

Physi-Chem Properties

Molecular Weight:  178.08
Volume:  183.942
LogP:  3.975
LogD:  4.263
LogS:  -4.161
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.584
Synthetic Accessibility Score:  3.951
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.18
MDCK Permeability:  1.1601577170949895e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.383

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.871
Plasma Protein Binding (PPB):  85.97858428955078%
Volume Distribution (VD):  1.863
Pgp-substrate:  16.857030868530273%

ADMET: Metabolism

CYP1A2-inhibitor:  0.932
CYP1A2-substrate:  0.898
CYP2C19-inhibitor:  0.518
CYP2C19-substrate:  0.913
CYP2C9-inhibitor:  0.512
CYP2C9-substrate:  0.717
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.711
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.26

ADMET: Excretion

Clearance (CL):  13.822
Half-life (T1/2):  0.334

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.062
Drug-inuced Liver Injury (DILI):  0.853
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.195
Maximum Recommended Daily Dose:  0.078
Skin Sensitization:  0.715
Carcinogencity:  0.466
Eye Corrosion:  0.566
Eye Irritation:  0.986
Respiratory Toxicity:  0.757

Download Data

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

  Natural Product: NPC254529

Natural Product ID:  NPC254529
Common Name*:   2-(Butan-2-Yldisulfanyl)Butane
IUPAC Name:   2-(butan-2-yldisulfanyl)butane
Synonyms:  
Standard InCHIKey:  QTWKINKGAHTPFJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H18S2/c1-5-7(3)9-10-8(4)6-2/h7-8H,5-6H2,1-4H3
SMILES:  CCC(SSC(CC)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3189103
PubChem CID:   94314
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0002800] Organic disulfides
        • [CHEMONTID:0004089] Dialkyldisulfides

*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
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. root n.a. PMID[15043424]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15043424]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. root n.a. PMID[15467238]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15787437]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[16378364]
NPO3083 Ferula assafoetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3083 Ferula assafoetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3083 Ferula assafoetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3412 Ferula sinkiangensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3780 Ferula fukanensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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
NPT2 Others Unspecified Potency n.a. 173.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 109.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 8634.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 43641.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61644.8 nM PubChem BioAssay data set

☑ 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 NPC254529 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
0.8333 Intermediate Similarity NPC239277
0.8095 Intermediate Similarity NPC476550
0.75 Intermediate Similarity NPC476549
0.7222 Intermediate Similarity NPC49871
0.7222 Intermediate Similarity NPC264395
0.7143 Intermediate Similarity NPC476548
0.7143 Intermediate Similarity NPC326758
0.7 Intermediate Similarity NPC266796
0.6522 Remote Similarity NPC142438
0.65 Remote Similarity NPC196982
0.6087 Remote Similarity NPC220140
0.6087 Remote Similarity NPC184203

  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 NPC254529 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
NPD

  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