Structure

Physi-Chem Properties

Molecular Weight:  133.05
Volume:  144.973
LogP:  0.786
LogD:  0.949
LogS:  -1.106
# Rotatable Bonds:  1
TPSA:  44.02
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.586
Synthetic Accessibility Score:  2.424
Fsp3:  0.125
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.65
MDCK Permeability:  6.956182915018871e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.142
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  45.70136260986328%
Volume Distribution (VD):  1.229
Pgp-substrate:  68.09573364257812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.373
CYP1A2-substrate:  0.165
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.28
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.131
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.292

ADMET: Excretion

Clearance (CL):  7.897
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.328
Drug-inuced Liver Injury (DILI):  0.952
AMES Toxicity:  0.367
Rat Oral Acute Toxicity:  0.973
Maximum Recommended Daily Dose:  0.996
Skin Sensitization:  0.918
Carcinogencity:  0.123
Eye Corrosion:  0.961
Eye Irritation:  0.993
Respiratory Toxicity:  0.985

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  Natural Product: NPC208363

Natural Product ID:  NPC208363
Common Name*:   NNICRUQPODTGRU-MRVPVSSYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NNICRUQPODTGRU-MRVPVSSYSA-N
Standard InCHI:  InChI=1S/C8H7NO/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8,10H/t8-/m1/s1
SMILES:  c1ccc(cc1)[C@@H](C#N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   439767
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives

*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
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. kernel n.a. PMID[10670815]
NPO6978 Boronella koniambiensis Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[16038554]
NPO651 Aconitum vilmorinianum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[17226159]
NPO13952 Streptomyces lavendulae Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17237222]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits Malatya Fruit Research Institute between the first and third weeks of 2005-Jul. PMID[18038980]
NPO4083 Brevibacillus laterosporus Species Paenibacillaceae Bacteria n.a. n.a. n.a. PMID[18044840]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. stem n.a. PMID[21381684]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. leaf n.a. PMID[21381684]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[21381684]
NPO13952 Streptomyces lavendulae Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[22187429]
NPO651 Aconitum vilmorinianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[23784883]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[24400858]
NPO10899 Ophioparma ventosa Species Ophioparmaceae Eukaryota n.a. n.a. n.a. PMID[26934105]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. root n.a. PMID[27133212]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14111 Maytenus serrata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16307 Murraya kwangsiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5482 Gymnanthemum amygdalinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16307 Murraya kwangsiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14111 Maytenus serrata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16307 Murraya kwangsiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13427 Erinaceus europaeus Species Erinaceidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14111 Maytenus serrata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20032 Prunus sibirica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25099 Prunus mandshurica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10452 Odontites rubra Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12470 Brachyspira hyodysenteriae Species Brachyspiraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14914 Esox saurus Species Esocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8671 Physalis solanaceus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15434 Rhodomicrobium vannielii Species Hyphomicrobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1723 Sideritis syriaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6978 Boronella koniambiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15178 Psychotria bahiensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16109 Actinidia kolomikta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26256 Zanthoxylum chiriquinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10899 Ophioparma ventosa Species Ophioparmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11962 Garcinia macrophylla Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15159 Podocarpus salignus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5750 Monomorium floricola Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22056.1 Streptomyces fervens Subspecies Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16307 Murraya kwangsiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14604 Dipteronia dyeriana Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO651 Aconitum vilmorinianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20032 Prunus sibirica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2607 Ophiorrhiza blumeana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12547 Viburnum chingii Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5482 Gymnanthemum amygdalinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13740 Aconitum kamtschaticum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14442 Gouania microcarpa Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13582 Leucopaxillus giganteus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15679 Amyris marshii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3697 Ongokea klaineana Species Aptandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12951 Talaromyces coalescens Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15570 Plectranthus mollis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14747 Usnea florida Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11644 Prosopis ruscifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16625 Phalaenopsis aphrodite Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22053 Vepris pilosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13427 Erinaceus europaeus Species Erinaceidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16541 Veratrum stenophyllum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7077 Canarium strictum Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12457 Siphocampylus verticillatus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13952 Streptomyces lavendulae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7792 Coreopsis grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13273 Maytenus loeseneri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15312 Coelogorgia palmosa Species Coelogorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4083 Brevibacillus laterosporus Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11376 Schistostephium rotundifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9386 Ectropis bicolor Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16311 Rusavskia elegans Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14111 Maytenus serrata Species Celastraceae 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 NPC208363 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 NPC208363 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