Structure

Physi-Chem Properties

Molecular Weight:  232.08
Volume:  215.459
LogP:  5.748
LogD:  3.936
LogS:  -5.799
# Rotatable Bonds:  9
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.308
Synthetic Accessibility Score:  2.183
Fsp3:  0.818
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.599
MDCK Permeability:  1.5557654478470795e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.146
30% Bioavailability (F30%):  0.735

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.972
Plasma Protein Binding (PPB):  97.75765228271484%
Volume Distribution (VD):  1.612
Pgp-substrate:  3.626542806625366%

ADMET: Metabolism

CYP1A2-inhibitor:  0.915
CYP1A2-substrate:  0.365
CYP2C19-inhibitor:  0.6
CYP2C19-substrate:  0.168
CYP2C9-inhibitor:  0.369
CYP2C9-substrate:  0.897
CYP2D6-inhibitor:  0.18
CYP2D6-substrate:  0.786
CYP3A4-inhibitor:  0.537
CYP3A4-substrate:  0.12

ADMET: Excretion

Clearance (CL):  2.575
Half-life (T1/2):  0.217

ADMET: Toxicity

hERG Blockers:  0.063
Human Hepatotoxicity (H-HT):  0.088
Drug-inuced Liver Injury (DILI):  0.16
AMES Toxicity:  0.422
Rat Oral Acute Toxicity:  0.107
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.95
Carcinogencity:  0.357
Eye Corrosion:  0.99
Eye Irritation:  0.993
Respiratory Toxicity:  0.866

Download Data

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

  Natural Product: NPC16561

Natural Product ID:  NPC16561
Common Name*:   11-Bromoundec-1-Ene
IUPAC Name:   11-bromoundec-1-ene
Synonyms:  
Standard InCHIKey:  YPLVPFUSXYSHJD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H21Br/c1-2-3-4-5-6-7-8-9-10-11-12/h2H,1,3-11H2
SMILES:  C=CCCCCCCCCCBr
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1702186
PubChem CID:   284148
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0001515] Organobromides

*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
NPO30946 Pumex n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO26698 Pumex n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO6456 Concretio silicea bambusae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO2437 Herba elephantopi scaberis n.a. n.a. n.a. 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
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 25118.9 nM PMID[475855]
NPT199 Individual Protein DNA polymerase kappa Homo sapiens Potency n.a. 29934.9 nM PMID[475855]

☑ 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 NPC16561 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
0.8214 Intermediate Similarity NPC38513
0.7931 Intermediate Similarity NPC266539
0.7931 Intermediate Similarity NPC31891
0.7931 Intermediate Similarity NPC287191
0.7931 Intermediate Similarity NPC266144
0.7586 Intermediate Similarity NPC88325
0.7419 Intermediate Similarity NPC76765
0.7419 Intermediate Similarity NPC179103
0.6765 Remote Similarity NPC151719
0.6552 Remote Similarity NPC127355
0.6389 Remote Similarity NPC62779
0.6341 Remote Similarity NPC160588
0.6216 Remote Similarity NPC182392
0.6207 Remote Similarity NPC178306
0.6176 Remote Similarity NPC34671
0.6098 Remote Similarity NPC469969
0.6071 Remote Similarity NPC33192
0.5897 Remote Similarity NPC216416
0.5882 Remote Similarity NPC138325
0.587 Remote Similarity NPC475153
0.5862 Remote Similarity NPC225855
0.5833 Remote Similarity NPC471327
0.5833 Remote Similarity NPC196831
0.5833 Remote Similarity NPC3649
0.5833 Remote Similarity NPC100879
0.5814 Remote Similarity NPC99746
0.5745 Remote Similarity NPC475071
0.5714 Remote Similarity NPC138113
0.5641 Remote Similarity NPC213767

  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 NPC16561 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