Structure

Physi-Chem Properties

Molecular Weight:  206.11
Volume:  210.728
LogP:  -1.161
LogD:  0.633
LogS:  -1.761
# Rotatable Bonds:  3
TPSA:  75.35
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.689
Synthetic Accessibility Score:  3.179
Fsp3:  0.364
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:  -5.807
MDCK Permeability:  0.00025717710377648473
Pgp-inhibitor:  0.0
Pgp-substrate:  0.483
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.752
Plasma Protein Binding (PPB):  29.570819854736328%
Volume Distribution (VD):  0.403
Pgp-substrate:  71.47063446044922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.034
CYP1A2-substrate:  0.052
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.079
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.855
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.369
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.088

ADMET: Excretion

Clearance (CL):  10.483
Half-life (T1/2):  0.655

ADMET: Toxicity

hERG Blockers:  0.127
Human Hepatotoxicity (H-HT):  0.173
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.426
Rat Oral Acute Toxicity:  0.579
Maximum Recommended Daily Dose:  0.905
Skin Sensitization:  0.57
Carcinogencity:  0.375
Eye Corrosion:  0.005
Eye Irritation:  0.039
Respiratory Toxicity:  0.827

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  Natural Product: NPC209054

Natural Product ID:  NPC209054
Common Name*:   SPHNJDOWMOXSMT-APPZFPTMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SPHNJDOWMOXSMT-APPZFPTMSA-N
Standard InCHI:  InChI=1S/C11H14N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,7,9,13H,5-6,12H2,(H,14,15)/t7-,9+/m1/s1
SMILES:  c1ccc2c(c1)[C@H](C[C@@H](C(=O)O)N)CN2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   56844224
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0001290] Indolyl carboxylic acids and 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
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. seed n.a. PMID[10898633]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11040054]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[11076555]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[11459643]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[11678654]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[12467621]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[1517743]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15787451]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. root n.a. PMID[16212233]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16724856]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. PMID[18071251]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. faeces n.a. PMID[18323202]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[19900811]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota Roots Anhui, China n.a. PMID[22694318]
NPO17823 Lycium chinense Species Solanaceae Eukaryota root bark n.a. n.a. PMID[23282106]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO17823 Lycium chinense Species Solanaceae Eukaryota Root Bark n.a. n.a. PMID[26982999]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. PMID[30892891]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. aerial part n.a. PMID[8237383]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[8277318]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8368081]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[9090870]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23234 Ageratum conyzoides Species Asteraceae 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 NPC209054 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 NPC209054 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