Structure

Physi-Chem Properties

Molecular Weight:  250.23
Volume:  297.549
LogP:  4.713
LogD:  4.058
LogS:  -3.488
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.512
Synthetic Accessibility Score:  2.599
Fsp3:  0.824
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:  -4.846
MDCK Permeability:  2.1647689209203236e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.71
Plasma Protein Binding (PPB):  96.6489028930664%
Volume Distribution (VD):  1.958
Pgp-substrate:  1.063351035118103%

ADMET: Metabolism

CYP1A2-inhibitor:  0.326
CYP1A2-substrate:  0.254
CYP2C19-inhibitor:  0.317
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.228
CYP2C9-substrate:  0.94
CYP2D6-inhibitor:  0.105
CYP2D6-substrate:  0.881
CYP3A4-inhibitor:  0.39
CYP3A4-substrate:  0.072

ADMET: Excretion

Clearance (CL):  4.693
Half-life (T1/2):  0.874

ADMET: Toxicity

hERG Blockers:  0.127
Human Hepatotoxicity (H-HT):  0.146
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.148
Skin Sensitization:  0.946
Carcinogencity:  0.17
Eye Corrosion:  0.458
Eye Irritation:  0.969
Respiratory Toxicity:  0.851

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

  Natural Product: NPC8587

Natural Product ID:  NPC8587
Common Name*:   ZKVZSBSZTMPBQR-UPHRSURJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZKVZSBSZTMPBQR-UPHRSURJSA-N
Standard InCHI:  InChI=1S/C17H30O/c18-17-15-13-11-9-7-5-3-1-2-4-6-8-10-12-14-16-17/h1-2H,3-16H2/b2-1-
SMILES:  C1=CCCCCCCCC(=O)CCCCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315941
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO19917 Corymbia peltata Species Myrtaceae Eukaryota flowers n.a. n.a. PMID[18412395]
NPO16405 Uncaria nervosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17501 Viverra zibetha Species Viverridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19332 Croomia japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17501 Viverra zibetha Species Viverridae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27623 Citrus japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16405 Uncaria nervosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17501 Viverra zibetha Species Viverridae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19332 Croomia japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19957 Urmenetea atacamensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24358 Phyllanthus muellerianus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25877 Eupatorium glehni Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22680 Ectomyelois ceratoniae Species Pyralidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19917 Corymbia peltata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24437 Isodon umbrosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16405 Uncaria nervosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27623 Citrus japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11681 Aria latifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17501 Viverra zibetha Species Viverridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19976 Fistulina hepatica Species Fistulinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24167 Plocamium coccineum Species Plocamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20887 Coryne sarcoides Species Corynidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21953 Athyrium yokoscense Species Athyriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20803 Limacia oblonga Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24322 Plagiomnium acutum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23785 Narcissus bicolor Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19332 Croomia japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23950 Eugenia aquea Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24397 Mucuna holtoni Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22400 Laurencia nana Species Rhodomelaceae 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

☑ 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 NPC8587 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

  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 NPC8587 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

  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