Structure

Physi-Chem Properties

Molecular Weight:  123.07
Volume:  132.95
LogP:  0.444
LogD:  0.756
LogS:  -0.636
# Rotatable Bonds:  1
TPSA:  46.25
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.541
Synthetic Accessibility Score:  1.769
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.603
MDCK Permeability:  0.00037260446697473526
Pgp-inhibitor:  0.0
Pgp-substrate:  0.383
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.02
30% Bioavailability (F30%):  0.071

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.402
Plasma Protein Binding (PPB):  24.473482131958008%
Volume Distribution (VD):  1.405
Pgp-substrate:  75.35260009765625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.491
CYP1A2-substrate:  0.268
CYP2C19-inhibitor:  0.078
CYP2C19-substrate:  0.685
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.105
CYP2D6-inhibitor:  0.103
CYP2D6-substrate:  0.852
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  7.269
Half-life (T1/2):  0.834

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.03
Drug-inuced Liver Injury (DILI):  0.243
AMES Toxicity:  0.51
Rat Oral Acute Toxicity:  0.165
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.819
Carcinogencity:  0.302
Eye Corrosion:  0.059
Eye Irritation:  0.993
Respiratory Toxicity:  0.904

Download Data

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

  Natural Product: NPC169597

Natural Product ID:  NPC169597
Common Name*:   VYFOAVADNIHPTR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VYFOAVADNIHPTR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H9NO/c8-7-4-2-1-3-6(7)5-9/h1-4,9H,5,8H2
SMILES:  c1ccc(c(c1)CO)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21439
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000033] Benzyl alcohols

*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
NPO12570 Salacia macrosperma Species Celastraceae Eukaryota n.a. n.a. n.a. DOI[10.1039/P19790000349]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota rhizomes n.a. n.a. PMID[11000020]
NPO2082 Chromobacterium violaceum Species Chromobacteriaceae Bacteria n.a. n.a. n.a. PMID[17176066]
NPO2082 Chromobacterium violaceum Species Chromobacteriaceae Bacteria n.a. n.a. n.a. PMID[20490411]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. rhizome n.a. PMID[21401114]
NPO2082 Chromobacterium violaceum Species Chromobacteriaceae Bacteria n.a. n.a. n.a. PMID[21779844]
NPO503 Trigonostemon lii Species Euphorbiaceae Eukaryota leaves n.a. n.a. PMID[22342628]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. PMID[27439360]
NPO5865 Justicia gendarussa Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[28613071]
NPO14489 Hyoscyamus albus Species Solanaceae Eukaryota Hairy roots n.a. n.a. PMID[9868154]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5865 Justicia gendarussa Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16014 Angelica porphyrocaulis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO503 Trigonostemon lii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27100 Evernia olivetorina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14489 Hyoscyamus albus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5616 Cissampelos ovalifolia Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5414 Microsorium brachylepis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2640 Bignonia suberosa Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22035 Kielmeyera elata Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2082 Chromobacterium violaceum Species Chromobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12570 Salacia macrosperma Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14091 Lecidea confluens Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8637 Brassica elongata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1263 Marine bacillus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6311 0vodinia antillensis Species 0vodiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13935 Dendrobium ochreatum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7880 Greyia flanaganii Species Melianthaceae 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
NPT1444 Individual Protein PI3-kinase p110-alpha subunit Homo sapiens Inhibition < 25.0 % PMID[549432]
NPT71 Cell Line HEK293 Homo sapiens IC50 = 3600000.0 nM PMID[549433]
NPT71 Cell Line HEK293 Homo sapiens Activity = 43.1 % PMID[549433]
NPT71 Cell Line HEK293 Homo sapiens Activity = 20.8 % PMID[549433]
NPT6559 Protein Complex PI3-kinase p110-alpha/p85-alpha Homo sapiens Inhibition < 25.0 % PMID[549432]
NPT22322 SINGLE PROTEIN Pendrin Homo sapiens Ratio = 100.0 n.a. PMID[549433]
NPT22322 SINGLE PROTEIN Pendrin Homo sapiens Ratio = 1.8 n.a. PMID[549433]
NPT22322 SINGLE PROTEIN Pendrin Homo sapiens Ratio = 0.9 n.a. PMID[549433]

☑ 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 NPC169597 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 NPC169597 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