Structure

Physi-Chem Properties

Molecular Weight:  408.06
Volume:  375.775
LogP:  4.912
LogD:  5.264
LogS:  -4.705
# Rotatable Bonds:  9
TPSA:  42.32
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.31
Synthetic Accessibility Score:  4.417
Fsp3:  0.588
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.647
MDCK Permeability:  8.424391126027331e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.337
Plasma Protein Binding (PPB):  98.88932037353516%
Volume Distribution (VD):  1.087
Pgp-substrate:  2.489563226699829%

ADMET: Metabolism

CYP1A2-inhibitor:  0.972
CYP1A2-substrate:  0.845
CYP2C19-inhibitor:  0.893
CYP2C19-substrate:  0.775
CYP2C9-inhibitor:  0.837
CYP2C9-substrate:  0.27
CYP2D6-inhibitor:  0.403
CYP2D6-substrate:  0.386
CYP3A4-inhibitor:  0.844
CYP3A4-substrate:  0.874

ADMET: Excretion

Clearance (CL):  2.311
Half-life (T1/2):  0.167

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.58
Drug-inuced Liver Injury (DILI):  0.561
AMES Toxicity:  0.189
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.419
Skin Sensitization:  0.05
Carcinogencity:  0.288
Eye Corrosion:  0.004
Eye Irritation:  0.029
Respiratory Toxicity:  0.982

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

  Natural Product: NPC278902

Natural Product ID:  NPC278902
Common Name*:   Herbamide B
IUPAC Name:   (2E,4E,7S)-8,8,8-trichloro-2,7-dimethyl-N-[(1S)-2-methyl-1-(1,3-thiazol-2-yl)propyl]octa-2,4-dienamide
Synonyms:  
Standard InCHIKey:  SASMNYHOQIJNIJ-CBZHAUGTSA-N
Standard InCHI:  InChI=1S/C17H23Cl3N2OS/c1-11(2)14(16-21-9-10-24-16)22-15(23)12(3)7-5-6-8-13(4)17(18,19)20/h5-7,9-11,13-14H,8H2,1-4H3,(H,22,23)/b6-5+,12-7+/t13-,14-/m0/s1
SMILES:  CC(C)[C@@H](c1nccs1)N=C(/C(=C/C=C/C[C@H](C)C(Cl)(Cl)Cl)/C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1088458
PubChem CID:   44627702
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10514329]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10654420]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10691708]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. palauan n.a. PMID[10691729]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10843570]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10924172]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10978206]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076571]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076573]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076574]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11277744]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11389621]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11430000]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11473443]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11922791]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[12762816]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[12828459]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[14575437]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[1517734]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[16643028]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17125217]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17441769]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18444683]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Singapore n.a. PMID[19093843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19489598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. eastern Caribbean n.a. PMID[19739598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19839606]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20030365]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. panamanian n.a. PMID[20158242]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Floridian n.a. PMID[20166701]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20936843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21138309]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[2128518]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21341718]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21539315]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21806011]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21999614]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[22035372]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29792428]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[3924698]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[7623050]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[8699186]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9584405]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599278]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599279]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9784156]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10000.0 nM PMID[549928]
NPT633 Organism Leishmania donovani Leishmania donovani IC50 = 5900.0 nM PMID[549928]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 > 10000.0 nM PMID[549928]

☑ 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 NPC278902 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
0.7462 Intermediate Similarity NPC145047
0.7462 Intermediate Similarity NPC137705
0.7462 Intermediate Similarity NPC86490
0.6781 Remote Similarity NPC478251
0.6781 Remote Similarity NPC478252
0.6761 Remote Similarity NPC478254
0.6761 Remote Similarity NPC478253
0.6726 Remote Similarity NPC261708
0.6709 Remote Similarity NPC475920
0.6014 Remote Similarity NPC475568
0.6 Remote Similarity NPC475604
0.6 Remote Similarity NPC275393
0.5929 Remote Similarity NPC214375
0.5845 Remote Similarity NPC135558
0.5843 Remote Similarity NPC473886
0.5806 Remote Similarity NPC469801
0.5805 Remote Similarity NPC161143
0.5796 Remote Similarity NPC319751
0.5732 Remote Similarity NPC315252
0.5724 Remote Similarity NPC51692
0.5723 Remote Similarity NPC473398
0.5687 Remote Similarity NPC119481
0.5621 Remote Similarity NPC474070
0.5616 Remote Similarity NPC267605

  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 NPC278902 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
0.5668 Remote Similarity NPD2299 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