Structure

Physi-Chem Properties

Molecular Weight:  352.16
Volume:  310.569
LogP:  8.654
LogD:  4.414
LogS:  -7.146
# Rotatable Bonds:  14
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.181
Synthetic Accessibility Score:  1.779
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:  -4.828
MDCK Permeability:  8.58526982483454e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.174
30% Bioavailability (F30%):  0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.06
Plasma Protein Binding (PPB):  98.74285888671875%
Volume Distribution (VD):  3.441
Pgp-substrate:  1.2715184688568115%

ADMET: Metabolism

CYP1A2-inhibitor:  0.254
CYP1A2-substrate:  0.193
CYP2C19-inhibitor:  0.372
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.088
CYP2C9-substrate:  0.942
CYP2D6-inhibitor:  0.268
CYP2D6-substrate:  0.085
CYP3A4-inhibitor:  0.188
CYP3A4-substrate:  0.049

ADMET: Excretion

Clearance (CL):  3.996
Half-life (T1/2):  0.057

ADMET: Toxicity

hERG Blockers:  0.228
Human Hepatotoxicity (H-HT):  0.047
Drug-inuced Liver Injury (DILI):  0.574
AMES Toxicity:  0.034
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.948
Carcinogencity:  0.07
Eye Corrosion:  0.996
Eye Irritation:  0.964
Respiratory Toxicity:  0.906

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

  Natural Product: NPC234888

Natural Product ID:  NPC234888
Common Name*:   1-Iodohexadecane
IUPAC Name:   1-iodohexadecane
Synonyms:  
Standard InCHIKey:  KMWHQYDMBYABKL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H33I/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17/h2-16H2,1H3
SMILES:  CCCCCCCCCCCCCCCCI
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1233571
PubChem CID:   11007
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0001518] Organoiodides

*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
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[21314165]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[21314165]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13080 Gomphrena globosa Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13080 Gomphrena globosa Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13080 Gomphrena globosa Species Amaranthaceae 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. 13335.8 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 NPC234888 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
0.85 High Similarity NPC26974
0.85 High Similarity NPC239406
0.85 High Similarity NPC154477
0.85 High Similarity NPC77249
0.85 High Similarity NPC26229
0.8 Intermediate Similarity NPC89422
0.75 Intermediate Similarity NPC136996
0.75 Intermediate Similarity NPC82648
0.75 Intermediate Similarity NPC64370
0.75 Intermediate Similarity NPC227986
0.75 Intermediate Similarity NPC278711
0.75 Intermediate Similarity NPC302327
0.75 Intermediate Similarity NPC273385
0.7083 Intermediate Similarity NPC47161
0.7 Intermediate Similarity NPC224874
0.6538 Remote Similarity NPC172053
0.65 Remote Similarity NPC98925
0.6296 Remote Similarity NPC256060
0.6296 Remote Similarity NPC29199
0.6 Remote Similarity NPC127355
0.5926 Remote Similarity NPC287807
0.5862 Remote Similarity NPC76765
0.5862 Remote Similarity NPC179103

  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 NPC234888 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