Structure

Physi-Chem Properties

Molecular Weight:  267.1
Volume:  235.446
LogP:  -2.28
LogD:  -0.914
LogS:  -1.714
# Rotatable Bonds:  2
TPSA:  140.27
# H-Bond Aceptor:  9
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.42
Synthetic Accessibility Score:  4.159
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.693
MDCK Permeability:  1.6082027286756784e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.963
Human Intestinal Absorption (HIA):  0.993
20% Bioavailability (F20%):  0.757
30% Bioavailability (F30%):  0.64

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.746
Plasma Protein Binding (PPB):  13.252840995788574%
Volume Distribution (VD):  1.134
Pgp-substrate:  77.32337188720703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.232
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.422
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.077
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.034

ADMET: Excretion

Clearance (CL):  3.596
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.762
Drug-inuced Liver Injury (DILI):  0.975
AMES Toxicity:  0.13
Rat Oral Acute Toxicity:  0.658
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.096
Carcinogencity:  0.096
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.961

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  Natural Product: NPC322476

Natural Product ID:  NPC322476
Common Name*:   OIRDTQYFTABQOQ-VKZRYZQFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OIRDTQYFTABQOQ-VKZRYZQFSA-N
Standard InCHI:  InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10?/m0/s1
SMILES:  C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)CO)O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   121484514
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]

*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
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28146.2 Liriope spicata (thunb.) lour. var. prolifera y. t. ma Varieties Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30006 Lsatis indigotica n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2838 Verbena officinalis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8101 Rehmannia glutinosa Species Orobanchaceae 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 NPC322476 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 NPC322476 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