Structure

Physi-Chem Properties

Molecular Weight:  499.2
Volume:  490.246
LogP:  4.889
LogD:  4.117
LogS:  -5.151
# Rotatable Bonds:  21
TPSA:  55.84
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.091
Synthetic Accessibility Score:  3.89
Fsp3:  0.826
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:  -4.654
MDCK Permeability:  4.091254231752828e-05
Pgp-inhibitor:  0.881
Pgp-substrate:  0.033
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.949
Plasma Protein Binding (PPB):  96.96116638183594%
Volume Distribution (VD):  1.187
Pgp-substrate:  1.3910713195800781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.126
CYP2C19-inhibitor:  0.241
CYP2C19-substrate:  0.888
CYP2C9-inhibitor:  0.078
CYP2C9-substrate:  0.13
CYP2D6-inhibitor:  0.196
CYP2D6-substrate:  0.172
CYP3A4-inhibitor:  0.914
CYP3A4-substrate:  0.272

ADMET: Excretion

Clearance (CL):  3.701
Half-life (T1/2):  0.651

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.399
Drug-inuced Liver Injury (DILI):  0.034
AMES Toxicity:  0.831
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.715
Skin Sensitization:  0.895
Carcinogencity:  0.397
Eye Corrosion:  0.003
Eye Irritation:  0.017
Respiratory Toxicity:  0.603

Download Data

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

  Natural Product: NPC477524

Natural Product ID:  NPC477524
Common Name*:   Columbamide B
IUPAC Name:   [(2S)-3-methoxy-2-[methyl-[(E)-10,16,16-trichlorohexadec-4-enoyl]amino]propyl] acetate
Synonyms:  
Standard InCHIKey:  JBEYLLUXESVNSE-QOZDHKFNSA-N
Standard InCHI:  InChI=1S/C23H40Cl3NO4/c1-19(28)31-18-21(17-30-3)27(2)23(29)16-12-7-5-4-6-9-13-20(24)14-10-8-11-15-22(25)26/h5,7,20-22H,4,6,8-18H2,1-3H3/b7-5+/t20?,21-/m0/s1
SMILES:  CC(=O)OC[C@H](COC)N(C)C(=O)CC/C=C/CCCCC(CCCCCC(Cl)Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   122183470
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
NPO4779 Moorea bouillonii Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[26149623]
NPO4779 Moorea bouillonii 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
NPT1287 Individual Protein Cannabinoid CB2 receptor Homo sapiens Ki = 860 nM PMID[26149623]
NPT232 Individual Protein Cannabinoid CB1 receptor Homo sapiens Ki = 410 nM PMID[26149623]
NPT2 Others Unspecified Ratio Ki = 2 n.a. PMID[26149623]

☑ 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 NPC477524 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
0.9867 High Similarity NPC477523
0.7722 Intermediate Similarity NPC97614
0.6809 Remote Similarity NPC81195
0.6737 Remote Similarity NPC53240
0.6535 Remote Similarity NPC233932
0.6437 Remote Similarity NPC470994
0.6222 Remote Similarity NPC325936
0.6154 Remote Similarity NPC188785
0.5978 Remote Similarity NPC474833
0.5833 Remote Similarity NPC178758
0.5833 Remote Similarity NPC196102
0.5824 Remote Similarity NPC281154
0.5795 Remote Similarity NPC45060
0.5795 Remote Similarity NPC280065
0.5765 Remote Similarity NPC206660
0.5758 Remote Similarity NPC324506
0.5729 Remote Similarity NPC474312
0.5714 Remote Similarity NPC252684
0.5682 Remote Similarity NPC249713
0.5682 Remote Similarity NPC474812
0.5664 Remote Similarity NPC476875
0.5649 Remote Similarity NPC469426
0.5649 Remote Similarity NPC469427

  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 NPC477524 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
0.6 Remote Similarity NPD1452 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