Structure

Physi-Chem Properties

Molecular Weight:  68.06
Volume:  89.763
LogP:  2.244
LogD:  1.316
LogS:  -2.19
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.411
Synthetic Accessibility Score:  3.033
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.274
MDCK Permeability:  4.3856653064722195e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.965
Plasma Protein Binding (PPB):  58.682228088378906%
Volume Distribution (VD):  1.829
Pgp-substrate:  51.621639251708984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.363
CYP1A2-substrate:  0.533
CYP2C19-inhibitor:  0.05
CYP2C19-substrate:  0.871
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.286
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.763
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.239

ADMET: Excretion

Clearance (CL):  9.037
Half-life (T1/2):  0.783

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.173
Drug-inuced Liver Injury (DILI):  0.325
AMES Toxicity:  0.1
Rat Oral Acute Toxicity:  0.877
Maximum Recommended Daily Dose:  0.301
Skin Sensitization:  0.903
Carcinogencity:  0.867
Eye Corrosion:  0.984
Eye Irritation:  0.994
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC96619

Natural Product ID:  NPC96619
Common Name*:   2-Methylbuta-1,3-Diene
IUPAC Name:   2-methylbuta-1,3-diene
Synonyms:  
Standard InCHIKey:  RRHGJUQNOFWUDK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
SMILES:  C=CC(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1566132
PubChem CID:   6557
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004622] Branched unsaturated hydrocarbons

*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
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO41795 Streptomyces avermitilis NEAU12TP5P4 [TP5] Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[32695892]
NPO41772 Saccharomyces cerevisiae WPK12 [n.a.] Strain Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[33869813]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 3060.7 nM PubChem BioAssay data set
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 3088.8 nM PubChem BioAssay data set
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 1534 nM PubChem BioAssay data set
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 39810.7 nM PMID[515135]
NPT539 Individual Protein Cellular tumor antigen p53 Homo sapiens Potency = 5.0 nM PMID[515135]
NPT102 Individual Protein Interleukin-8 Homo sapiens Potency n.a. 33491.5 nM PMID[515135]
NPT2 Others Unspecified Potency n.a. 34341.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68519.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 15339.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54427.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 9767.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21667.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24311.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6106.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27278.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 38.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 8705.4 nM PubChem BioAssay data set
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 25118.9 nM PMID[515135]
NPT2 Others Unspecified Potency = 12589.3 nM PMID[515135]

☑ 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 NPC96619 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
0.8095 Intermediate Similarity NPC225855
0.7727 Intermediate Similarity NPC178306
0.7692 Intermediate Similarity NPC288991
0.7692 Intermediate Similarity NPC262789
0.7692 Intermediate Similarity NPC64176
0.7619 Intermediate Similarity NPC33192
0.7407 Intermediate Similarity NPC138113
0.7143 Intermediate Similarity NPC60288
0.6538 Remote Similarity NPC88325
0.6452 Remote Similarity NPC173592
0.6452 Remote Similarity NPC305759
0.6452 Remote Similarity NPC99088
0.6333 Remote Similarity NPC206088
0.6333 Remote Similarity NPC66577
0.6296 Remote Similarity NPC266144
0.6296 Remote Similarity NPC287191
0.6296 Remote Similarity NPC266539
0.6296 Remote Similarity NPC31891
0.6207 Remote Similarity NPC123965
0.6207 Remote Similarity NPC115959
0.6071 Remote Similarity NPC10183
0.6061 Remote Similarity NPC282119
0.5926 Remote Similarity NPC38513
0.5862 Remote Similarity NPC76765
0.5862 Remote Similarity NPC138325
0.5862 Remote Similarity NPC179103
0.5806 Remote Similarity NPC3649
0.5806 Remote Similarity NPC471327
0.5806 Remote Similarity NPC100879
0.5769 Remote Similarity NPC142438
0.5714 Remote Similarity NPC45727
0.5714 Remote Similarity NPC48638
0.5667 Remote Similarity NPC34671
0.5625 Remote Similarity NPC213749
0.5625 Remote Similarity NPC13217
0.5625 Remote Similarity NPC266979

  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 NPC96619 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 NPD8834 Discontinued

  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