Structure

Physi-Chem Properties

Molecular Weight:  339.22
Volume:  382.077
LogP:  3.932
LogD:  3.633
LogS:  -4.61
# Rotatable Bonds:  9
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.673
Synthetic Accessibility Score:  3.061
Fsp3:  0.409
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.629
MDCK Permeability:  3.516453580232337e-05
Pgp-inhibitor:  0.259
Pgp-substrate:  0.058
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.182
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.914
Plasma Protein Binding (PPB):  90.6966323852539%
Volume Distribution (VD):  6.281
Pgp-substrate:  9.392395973205566%

ADMET: Metabolism

CYP1A2-inhibitor:  0.139
CYP1A2-substrate:  0.141
CYP2C19-inhibitor:  0.25
CYP2C19-substrate:  0.985
CYP2C9-inhibitor:  0.169
CYP2C9-substrate:  0.06
CYP2D6-inhibitor:  0.988
CYP2D6-substrate:  0.825
CYP3A4-inhibitor:  0.646
CYP3A4-substrate:  0.908

ADMET: Excretion

Clearance (CL):  12.363
Half-life (T1/2):  0.327

ADMET: Toxicity

hERG Blockers:  0.905
Human Hepatotoxicity (H-HT):  0.795
Drug-inuced Liver Injury (DILI):  0.403
AMES Toxicity:  0.44
Rat Oral Acute Toxicity:  0.209
Maximum Recommended Daily Dose:  0.424
Skin Sensitization:  0.933
Carcinogencity:  0.083
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.959

Download Data

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

  Natural Product: NPC112367

Natural Product ID:  NPC112367
Common Name*:   NFOLVAGTJPDWEQ-JURULQHISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NFOLVAGTJPDWEQ-JURULQHISA-N
Standard InCHI:  InChI=1S/C22H29NO2.C9H8O4.C8H10N4O2.ClH/c1-5-21(24)25-22(18(2)17-23(3)4,20-14-10-7-11-15-20)16-19-12-8-6-9-13-19;1-6(10)13-8-5-3-2-4-7(8)9(11)12;1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2;/h6-15,18H,5,16-17H2,1-4H3;2-5H,1H3,(H,11,12);4H,1-3H3;1H/t18-,22-;;;/m1.../s1
SMILES:  CCC(=O)O[C@](Cc1ccccc1)([C@H](C)CN(C)C)c1ccccc1.CC(=O)Oc1ccccc1C(=O)O.Cn1cnc2c1c(=O)n(C)c(=O)n2C.Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24847964
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

*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
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.foodchem.2013.08.121]
NPO12068 Firmiana simplex Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[16124753]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Flowers n.a. n.a. PMID[16180814]
NPO8258 Camellia sinensis Species Theaceae Eukaryota seeds Shizuoka prefecture, Japan n.a. PMID[16499314]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota leaves Mato Leitao, RS, Brazil n.a. PMID[18192087]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[21434603]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. flower n.a. PMID[21922925]
NPO8258 Camellia sinensis Species Theaceae Eukaryota flower buds n.a. n.a. PMID[21925888]
NPO8258 Camellia sinensis Species Theaceae Eukaryota leaves n.a. n.a. PMID[22377672]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. leaf n.a. PMID[23265489]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaves Bandung, West Java, Indonesia PMID[23621359]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. PMID[25955847]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12068 Firmiana simplex Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30962 Folium camelliae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6084 Scurrura atropurpurea n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8258.1 Camellia sinensis var. assamica Varieties Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26505 Cola acuminata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8258.1 Camellia sinensis var. assamica Varieties Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6084 Scurrura atropurpurea n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26505 Cola acuminata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12068 Firmiana simplex Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12068 Firmiana simplex Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20116 Ilex cornuta Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26505 Cola acuminata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12068 Firmiana simplex Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9788 Coffea arabica Species Rubiaceae 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 NPC112367 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 NPC112367 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