Structure

Physi-Chem Properties

Molecular Weight:  239.26
Volume:  287.733
LogP:  5.654
LogD:  3.857
LogS:  -4.832
# Rotatable Bonds:  0
TPSA:  12.03
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.633
Synthetic Accessibility Score:  2.819
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.798
MDCK Permeability:  1.3110075997246895e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.703
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.37
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.605
Plasma Protein Binding (PPB):  85.65885925292969%
Volume Distribution (VD):  1.231
Pgp-substrate:  9.336366653442383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.532
CYP1A2-substrate:  0.217
CYP2C19-inhibitor:  0.429
CYP2C19-substrate:  0.488
CYP2C9-inhibitor:  0.083
CYP2C9-substrate:  0.139
CYP2D6-inhibitor:  0.98
CYP2D6-substrate:  0.662
CYP3A4-inhibitor:  0.499
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  5.127
Half-life (T1/2):  0.093

ADMET: Toxicity

hERG Blockers:  0.407
Human Hepatotoxicity (H-HT):  0.521
Drug-inuced Liver Injury (DILI):  0.177
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.582
Maximum Recommended Daily Dose:  0.19
Skin Sensitization:  0.964
Carcinogencity:  0.055
Eye Corrosion:  0.99
Eye Irritation:  0.764
Respiratory Toxicity:  0.96

Download Data

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

  Natural Product: NPC15231

Natural Product ID:  NPC15231
Common Name*:   Haliclorensin C
IUPAC Name:   (3S)-3-methyl-azacyclohexadecane
Synonyms:   Haliclorensin C
Standard InCHIKey:  BOCVLEJSICULOK-INIZCTEOSA-N
Standard InCHI:  InChI=1S/C16H33N/c1-16-13-11-9-7-5-3-2-4-6-8-10-12-14-17-15-16/h16-17H,2-15H2,1H3/t16-/m0/s1
SMILES:  C[C@H]1CCCCCCCCCCCCCNC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1080039
PubChem CID:   45379848
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002451] Secondary amines
            • [CHEMONTID:0002228] Dialkylamines

*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
NPO4186 Haliclona tulearensis Species Chalinidae Eukaryota n.a. n.a. n.a. PMID[19894692]
NPO4186 Haliclona tulearensis Species Chalinidae 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
NPT176 Organism Artemia salina Artemia salina LD50 = 2.1 mM PMID[505589]

☑ 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 NPC15231 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
0.9211 High Similarity NPC473035
0.7805 Intermediate Similarity NPC326791
0.7317 Intermediate Similarity NPC74599
0.7209 Intermediate Similarity NPC167301
0.6905 Remote Similarity NPC203203
0.6842 Remote Similarity NPC270175
0.6842 Remote Similarity NPC313882
0.675 Remote Similarity NPC320889
0.641 Remote Similarity NPC152949
0.6271 Remote Similarity NPC472544
0.6154 Remote Similarity NPC201713
0.6098 Remote Similarity NPC21157
0.6098 Remote Similarity NPC95589
0.6066 Remote Similarity NPC469970
0.6 Remote Similarity NPC193536
0.5962 Remote Similarity NPC153803
0.5902 Remote Similarity NPC53276
0.5789 Remote Similarity NPC83032
0.5789 Remote Similarity NPC125872
0.5781 Remote Similarity NPC271640
0.575 Remote Similarity NPC27675
0.5745 Remote Similarity NPC471575
0.5745 Remote Similarity NPC471440
0.5682 Remote Similarity NPC323644
0.566 Remote Similarity NPC133178
0.5641 Remote Similarity NPC172053
0.561 Remote Similarity NPC232311

  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 NPC15231 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
0.7907 Intermediate Similarity NPD718 Approved
0.7907 Intermediate Similarity NPD390 Approved
0.7805 Intermediate Similarity NPD2707 Clinical (unspecified phase)
0.7551 Intermediate Similarity NPD3721 Approved
0.7551 Intermediate Similarity NPD3722 Approved
0.7179 Intermediate Similarity NPD5385 Approved
0.7179 Intermediate Similarity NPD5384 Approved
0.6923 Remote Similarity NPD3734 Approved
0.6923 Remote Similarity NPD2705 Approved
0.6923 Remote Similarity NPD2706 Approved
0.675 Remote Similarity NPD2274 Approved
0.675 Remote Similarity NPD2275 Approved
0.6667 Remote Similarity NPD2273 Clinical (unspecified phase)
0.6471 Remote Similarity NPD4834 Discontinued
0.6415 Remote Similarity NPD4839 Approved
0.64 Remote Similarity NPD5379 Clinical (unspecified phase)
0.6341 Remote Similarity NPD1156 Clinical (unspecified phase)
0.62 Remote Similarity NPD874 Approved
0.62 Remote Similarity NPD872 Approved
0.619 Remote Similarity NPD2276 Clinical (unspecified phase)
0.6098 Remote Similarity NPD401 Approved
0.6071 Remote Similarity NPD627 Approved
0.6071 Remote Similarity NPD625 Approved
0.6071 Remote Similarity NPD628 Phase 3
0.6071 Remote Similarity NPD626 Phase 3
0.6038 Remote Similarity NPD5793 Discontinued
0.6 Remote Similarity NPD3727 Discontinued
0.5758 Remote Similarity NPD5365 Phase 2
0.5714 Remote Similarity NPD9458 Approved

  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