Structure

Physi-Chem Properties

Molecular Weight:  441.81
Volume:  267.153
LogP:  5.381
LogD:  3.714
LogS:  -5.576
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.467
Synthetic Accessibility Score:  5.186
Fsp3:  0.8
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:  -4.457
MDCK Permeability:  1.6414605852332897e-05
Pgp-inhibitor:  0.072
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.075
20% Bioavailability (F20%):  0.252
30% Bioavailability (F30%):  0.23

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.906
Plasma Protein Binding (PPB):  99.86582946777344%
Volume Distribution (VD):  2.49
Pgp-substrate:  3.5124058723449707%

ADMET: Metabolism

CYP1A2-inhibitor:  0.933
CYP1A2-substrate:  0.818
CYP2C19-inhibitor:  0.906
CYP2C19-substrate:  0.909
CYP2C9-inhibitor:  0.898
CYP2C9-substrate:  0.621
CYP2D6-inhibitor:  0.379
CYP2D6-substrate:  0.712
CYP3A4-inhibitor:  0.889
CYP3A4-substrate:  0.695

ADMET: Excretion

Clearance (CL):  1.369
Half-life (T1/2):  0.127

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.3
Drug-inuced Liver Injury (DILI):  0.762
AMES Toxicity:  0.09
Rat Oral Acute Toxicity:  0.608
Maximum Recommended Daily Dose:  0.94
Skin Sensitization:  0.858
Carcinogencity:  0.405
Eye Corrosion:  0.994
Eye Irritation:  0.973
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC99746

Natural Product ID:  NPC99746
Common Name*:   Anverene
IUPAC Name:   (E,3R,4S,6S)-1,4,7-tribromo-3,6-dichloro-3,7-dimethyloct-1-ene
Synonyms:   Anverene
Standard InCHIKey:  WKBBLSRQTDAPOH-PXGKHDNCSA-N
Standard InCHI:  InChI=1S/C10H15Br3Cl2/c1-9(2,13)8(14)6-7(12)10(3,15)4-5-11/h4-5,7-8H,6H2,1-3H3/b5-4+/t7-,8-,10+/m0/s1
SMILES:  Br/C=C/[C@]([C@H](C[C@@H](C(Br)(C)C)Cl)Br)(Cl)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455882
PubChem CID:   11178318
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002868] Vinyl halides
        • [CHEMONTID:0002864] Vinyl bromides

*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
NPO32988 antarctic peninsula Species n.a. n.a. n.a. n.a. n.a. PMID[15332845]

☑ 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
NPT1531 Organism Enterococcus faecium Enterococcus faecium IZ = 8.0 mm PMID[521647]

☑ 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 NPC99746 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
0.9268 High Similarity NPC160588
0.9268 High Similarity NPC180409
0.878 High Similarity NPC51086
0.8372 Intermediate Similarity NPC474773
0.7407 Intermediate Similarity NPC183031
0.7333 Intermediate Similarity NPC107849
0.7059 Intermediate Similarity NPC469971
0.7037 Intermediate Similarity NPC469962
0.6957 Remote Similarity NPC469969
0.6957 Remote Similarity NPC259702
0.6897 Remote Similarity NPC52966
0.6889 Remote Similarity NPC55269
0.6727 Remote Similarity NPC469967
0.6522 Remote Similarity NPC101811
0.62 Remote Similarity NPC473533
0.6167 Remote Similarity NPC110214
0.6087 Remote Similarity NPC201753
0.5962 Remote Similarity NPC159420
0.5814 Remote Similarity NPC16561
0.5606 Remote Similarity NPC301725

  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 NPC99746 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