Structure

Physi-Chem Properties

Molecular Weight:  112.13
Volume:  144.288
LogP:  3.81
LogD:  3.539
LogS:  -3.923
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.457
Synthetic Accessibility Score:  2.646
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.359
MDCK Permeability:  2.3233193132909946e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.948
30% Bioavailability (F30%):  0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  66.17800903320312%
Volume Distribution (VD):  2.107
Pgp-substrate:  54.56410598754883%

ADMET: Metabolism

CYP1A2-inhibitor:  0.259
CYP1A2-substrate:  0.657
CYP2C19-inhibitor:  0.282
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.056
CYP2C9-substrate:  0.844
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.76
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.194

ADMET: Excretion

Clearance (CL):  10.637
Half-life (T1/2):  0.609

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.051
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.134
Carcinogencity:  0.441
Eye Corrosion:  0.987
Eye Irritation:  0.986
Respiratory Toxicity:  0.112

Download Data

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

  Natural Product: NPC10183

Natural Product ID:  NPC10183
Common Name*:   2,4,4-Trimethylpent-1-Ene
IUPAC Name:   2,4,4-trimethylpent-1-ene
Synonyms:  
Standard InCHIKey:  FXNDIJDIPNCZQJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H16/c1-7(2)6-8(3,4)5/h1,6H2,2-5H3
SMILES:  C=C(C)CC(C)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3186786
PubChem CID:   7868
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
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27661 Radix codonopsis pilosulae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae 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
NPT2 Others Unspecified Potency n.a. 6852 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 NPC10183 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
0.8 Intermediate Similarity NPC66577
0.7419 Intermediate Similarity NPC206088
0.7188 Intermediate Similarity NPC213749
0.6774 Remote Similarity NPC138113
0.6774 Remote Similarity NPC123965
0.6774 Remote Similarity NPC115959
0.6757 Remote Similarity NPC78551
0.6757 Remote Similarity NPC227632
0.6757 Remote Similarity NPC246165
0.6757 Remote Similarity NPC62086
0.6579 Remote Similarity NPC103290
0.6571 Remote Similarity NPC282119
0.6571 Remote Similarity NPC92224
0.6562 Remote Similarity NPC60288
0.6552 Remote Similarity NPC88325
0.6538 Remote Similarity NPC252008
0.641 Remote Similarity NPC193180
0.641 Remote Similarity NPC190232
0.641 Remote Similarity NPC105246
0.6389 Remote Similarity NPC190810
0.6389 Remote Similarity NPC76145
0.6389 Remote Similarity NPC34764
0.6364 Remote Similarity NPC471327
0.6364 Remote Similarity NPC100879
0.6364 Remote Similarity NPC3649
0.6333 Remote Similarity NPC266144
0.6333 Remote Similarity NPC287191
0.6333 Remote Similarity NPC31891
0.6333 Remote Similarity NPC266539
0.6296 Remote Similarity NPC178306
0.625 Remote Similarity NPC227670
0.625 Remote Similarity NPC23145
0.625 Remote Similarity NPC60556
0.625 Remote Similarity NPC474118
0.625 Remote Similarity NPC166362
0.625 Remote Similarity NPC51762
0.625 Remote Similarity NPC141777
0.625 Remote Similarity NPC86538
0.625 Remote Similarity NPC109813
0.625 Remote Similarity NPC90506
0.625 Remote Similarity NPC90803
0.6216 Remote Similarity NPC239039
0.6216 Remote Similarity NPC229262
0.6216 Remote Similarity NPC266298
0.6216 Remote Similarity NPC48638
0.6216 Remote Similarity NPC45727
0.6216 Remote Similarity NPC297643
0.6216 Remote Similarity NPC139717
0.6098 Remote Similarity NPC248411
0.6071 Remote Similarity NPC96619
0.6 Remote Similarity NPC173592
0.6 Remote Similarity NPC38513
0.6 Remote Similarity NPC305759
0.6 Remote Similarity NPC99088
0.5952 Remote Similarity NPC114239
0.5952 Remote Similarity NPC229403
0.5952 Remote Similarity NPC241784
0.5952 Remote Similarity NPC49088
0.5952 Remote Similarity NPC86683
0.5952 Remote Similarity NPC296337
0.5952 Remote Similarity NPC13991
0.5938 Remote Similarity NPC138325
0.5938 Remote Similarity NPC288991
0.5938 Remote Similarity NPC262789
0.5938 Remote Similarity NPC179103
0.5938 Remote Similarity NPC76765
0.5938 Remote Similarity NPC64176
0.5926 Remote Similarity NPC225855
0.5897 Remote Similarity NPC183670
0.5854 Remote Similarity NPC216921
0.5814 Remote Similarity NPC323445
0.5769 Remote Similarity NPC152459
0.5758 Remote Similarity NPC34671
0.575 Remote Similarity NPC473614
0.575 Remote Similarity NPC144023
0.575 Remote Similarity NPC188596
0.575 Remote Similarity NPC120926
0.575 Remote Similarity NPC218918
0.575 Remote Similarity NPC469969
0.5714 Remote Similarity NPC13217
0.5682 Remote Similarity NPC124851
0.561 Remote Similarity NPC209279
0.561 Remote Similarity NPC180871
0.561 Remote Similarity NPC68889
0.561 Remote Similarity NPC67761
0.561 Remote Similarity NPC473912
0.561 Remote Similarity NPC88079
0.561 Remote Similarity NPC177470
0.561 Remote Similarity NPC51758
0.561 Remote Similarity NPC194586
0.561 Remote Similarity NPC108494

  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 NPC10183 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
0.641 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6389 Remote Similarity NPD319 Phase 1

  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