Structure

Physi-Chem Properties

Molecular Weight:  288.26
Volume:  335.095
LogP:  8.896
LogD:  4.142
LogS:  -7.114
# Rotatable Bonds:  16
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.204
Synthetic Accessibility Score:  1.59
Fsp3:  1.0
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:  -4.849
MDCK Permeability:  8.149731911544222e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.037
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.022
Plasma Protein Binding (PPB):  99.30823516845703%
Volume Distribution (VD):  4.499
Pgp-substrate:  1.2217503786087036%

ADMET: Metabolism

CYP1A2-inhibitor:  0.149
CYP1A2-substrate:  0.177
CYP2C19-inhibitor:  0.294
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.072
CYP2C9-substrate:  0.953
CYP2D6-inhibitor:  0.317
CYP2D6-substrate:  0.062
CYP3A4-inhibitor:  0.18
CYP3A4-substrate:  0.042

ADMET: Excretion

Clearance (CL):  4.34
Half-life (T1/2):  0.077

ADMET: Toxicity

hERG Blockers:  0.244
Human Hepatotoxicity (H-HT):  0.039
Drug-inuced Liver Injury (DILI):  0.55
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.041
Skin Sensitization:  0.949
Carcinogencity:  0.068
Eye Corrosion:  0.99
Eye Irritation:  0.966
Respiratory Toxicity:  0.819

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

  Natural Product: NPC29199

Natural Product ID:  NPC29199
Common Name*:   1-Chlorooctadecane
IUPAC Name:   1-chlorooctadecane
Synonyms:  
Standard InCHIKey:  VUQPJRPDRDVQMN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H37Cl/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19/h2-18H2,1H3
SMILES:  CCCCCCCCCCCCCCCCCCCl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187568
PubChem CID:   18815
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0001516] Organochlorides

*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
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota rhizomes n.a. n.a. PMID[19585998]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. PMID[19919095]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota flower buds and leaves Khon Kaen province, Thailand 2010 PMID[23270663]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Leaves n.a. n.a. PMID[23642481]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Flowers n.a. n.a. PMID[26462418]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3478 Nelumbo nucifera Species Nelumbonaceae 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
NPT2 Others Unspecified Potency n.a. 298.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 674.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 3349.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2985.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 841.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 848.9 nM PubChem BioAssay data set

☑ 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 NPC29199 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
0.7083 Intermediate Similarity NPC26229
0.7083 Intermediate Similarity NPC77249
0.7083 Intermediate Similarity NPC239406
0.7083 Intermediate Similarity NPC26974
0.7083 Intermediate Similarity NPC154477
0.6667 Remote Similarity NPC89422
0.6296 Remote Similarity NPC234888
0.625 Remote Similarity NPC227986
0.625 Remote Similarity NPC64370
0.625 Remote Similarity NPC278711
0.625 Remote Similarity NPC136996
0.625 Remote Similarity NPC302327
0.625 Remote Similarity NPC273385
0.625 Remote Similarity NPC82648
0.6071 Remote Similarity NPC47161
0.5833 Remote Similarity NPC224874
0.5667 Remote Similarity NPC172053

  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 NPC29199 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