Structure

Physi-Chem Properties

Molecular Weight:  170.13
Volume:  187.904
LogP:  3.484
LogD:  2.839
LogS:  -3.412
# Rotatable Bonds:  5
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.468
Synthetic Accessibility Score:  2.683
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.47
MDCK Permeability:  4.476317189983092e-05
Pgp-inhibitor:  0.871
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.216
30% Bioavailability (F30%):  0.965

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.849
Plasma Protein Binding (PPB):  90.8659896850586%
Volume Distribution (VD):  0.893
Pgp-substrate:  10.632647514343262%

ADMET: Metabolism

CYP1A2-inhibitor:  0.672
CYP1A2-substrate:  0.476
CYP2C19-inhibitor:  0.245
CYP2C19-substrate:  0.207
CYP2C9-inhibitor:  0.182
CYP2C9-substrate:  0.913
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.21
CYP3A4-inhibitor:  0.186
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  6.958
Half-life (T1/2):  0.685

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.2
Drug-inuced Liver Injury (DILI):  0.392
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.888
Skin Sensitization:  0.945
Carcinogencity:  0.647
Eye Corrosion:  0.972
Eye Irritation:  0.976
Respiratory Toxicity:  0.488

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  Natural Product: NPC80475

Natural Product ID:  NPC80475
Common Name*:   IFYYFLINQYPWGJ-SECBINFHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IFYYFLINQYPWGJ-SECBINFHSA-N
Standard InCHI:  InChI=1S/C10H18O2/c1-2-3-4-5-6-9-7-8-10(11)12-9/h9H,2-8H2,1H3/t9-/m1/s1
SMILES:  CCCCCC[C@@H]1CCC(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   183870
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO6978 Boronella koniambiensis Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[16038554]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
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]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
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. n.a. n.a. PMID[21381684]
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]
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]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
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]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
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]
NPO11438 Angelica gigas Species Apiaceae 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]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO15462 Angelica sinensis Species Apiaceae 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]
NPO16307 Murraya kwangsiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4795 Prunus armeniaca Species Rosaceae 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]
NPO15462 Angelica sinensis Species Apiaceae 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]
NPO11438 Angelica gigas 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]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae 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]
NPO15570 Plectranthus mollis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8671 Physalis solanaceus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16625 Phalaenopsis aphrodite Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6978 Boronella koniambiensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16541 Veratrum stenophyllum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15312 Coelogorgia palmosa Species Coelogorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15159 Podocarpus salignus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7792 Coreopsis grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16109 Actinidia kolomikta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7718 Peucedanum palustre Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11376 Schistostephium rotundifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10899 Ophioparma ventosa Species Ophioparmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO651 Aconitum vilmorinianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14111 Maytenus serrata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22056.1 Streptomyces fervens Subspecies Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15178 Psychotria bahiensis 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]
NPO13582 Leucopaxillus giganteus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14914 Esox saurus Species Esocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12951 Talaromyces coalescens Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1723 Sideritis syriaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13952 Streptomyces lavendulae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11962 Garcinia macrophylla Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11644 Prosopis ruscifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4083 Brevibacillus laterosporus Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14604 Dipteronia dyeriana Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16307 Murraya kwangsiensis 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]
NPO26256 Zanthoxylum chiriquinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16311 Rusavskia elegans Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2607 Ophiorrhiza blumeana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12457 Siphocampylus verticillatus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5750 Monomorium floricola Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13273 Maytenus loeseneri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3697 Ongokea klaineana Species Aptandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14442 Gouania microcarpa Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15884 Dodonaea polyandra Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14747 Usnea florida Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5482 Gymnanthemum amygdalinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12470 Brachyspira hyodysenteriae Species Brachyspiraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13740 Aconitum kamtschaticum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9386 Ectropis bicolor Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15434 Rhodomicrobium vannielii Species Hyphomicrobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22053 Vepris pilosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7077 Canarium strictum Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15679 Amyris marshii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10452 Odontites rubra Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4795 Prunus armeniaca Species Rosaceae 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 NPC80475 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 NPC80475 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