Structure

Physi-Chem Properties

Molecular Weight:  338.12
Volume:  354.95
LogP:  2.786
LogD:  2.923
LogS:  -3.611
# Rotatable Bonds:  7
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.597
Synthetic Accessibility Score:  2.363
Fsp3:  0.1
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.793
MDCK Permeability:  1.5965102647896856e-05
Pgp-inhibitor:  0.176
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.139
Plasma Protein Binding (PPB):  100.0168228149414%
Volume Distribution (VD):  0.321
Pgp-substrate:  0.5453693866729736%

ADMET: Metabolism

CYP1A2-inhibitor:  0.777
CYP1A2-substrate:  0.117
CYP2C19-inhibitor:  0.438
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.769
CYP2C9-substrate:  0.945
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.881
CYP3A4-inhibitor:  0.613
CYP3A4-substrate:  0.39

ADMET: Excretion

Clearance (CL):  14.79
Half-life (T1/2):  0.949

ADMET: Toxicity

hERG Blockers:  0.217
Human Hepatotoxicity (H-HT):  0.418
Drug-inuced Liver Injury (DILI):  0.877
AMES Toxicity:  0.41
Rat Oral Acute Toxicity:  0.87
Maximum Recommended Daily Dose:  0.683
Skin Sensitization:  0.96
Carcinogencity:  0.611
Eye Corrosion:  0.008
Eye Irritation:  0.867
Respiratory Toxicity:  0.914

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  Natural Product: NPC71941

Natural Product ID:  NPC71941
Common Name*:   HJTVQHVGMGKONQ-LUZURFALSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HJTVQHVGMGKONQ-LUZURFALSA-N
Standard InCHI:  InChI=1S/C20H18O5/c1-25-20-12-15(6-11-19(20)24)5-10-18(23)13-17(22)9-4-14-2-7-16(21)8-3-14/h2-12,21,24H,13H2,1H3/b9-4+,10-5+
SMILES:  COc1cc(/C=C/C(=O)CC(=O)/C=C/c2ccc(cc2)O)ccc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5469424
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002651] Linear diarylheptanoids
          • [CHEMONTID:0000356] Curcuminoids

*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
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. rhizome n.a. DOI[10.1021/np100392m]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12350137]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota rhizome n.a. n.a. PMID[12617587]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[15730265]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[20879743]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[21807513]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[23153397]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[23738470]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. root n.a. PMID[23738470]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[23755850]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. leaf n.a. PMID[23901173]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[25275213]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota Flowers Johor, Malaysia PMID[26399961]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota Flowers Kelantan, Malaysia PMID[26399961]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota Flowers Pahang, Malaysia PMID[26399961]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[28068085]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota Radix n.a. n.a. PMID[29236488]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9584408]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9868158]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome Essent. Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28019 Oleum curcumae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9241 Adiantum capillus-veneris Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7308 Fraxinus quadrangulata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28019 Oleum curcumae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO9241 Adiantum capillus-veneris Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3251 Jacobaea maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7308 Fraxinus quadrangulata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9241 Adiantum capillus-veneris Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25160 Goniothalamus borneensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3532 Tridentata marginata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7308 Fraxinus quadrangulata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3251 Jacobaea maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9241 Adiantum capillus-veneris Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5878 Etlingera elatior Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7929 Curcuma zedoaria Species Zingiberaceae 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
NPO24124 NPC71941 Dried Or Powder n.a. 1982.5 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO24124 NPC71941 n.a. n.a. 1982.5 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]

☑ 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
NPT579 Cell Line DLD-1 Homo sapiens IC50 > 40000.0 nM PMID[29605808]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 92100.0 nM PMID[29605808]
NPT1527 Cell Line WRL68 Homo sapiens IC50 = 26300.0 nM PMID[29605808]
NPT762 Cell Line A-431 Homo sapiens IC50 > 100000.0 nM PMID[29605808]
NPT81 Cell Line A549 Homo sapiens IC50 = 28200.0 nM PMID[29605808]
NPT453 Cell Line HT-1080 Homo sapiens IC50 = 7500.0 nM PMID[31336310]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 9000000.0 nM PMID[31336310]
NPT146 Cell Line SK-OV-3 Homo sapiens Activity = 70.7 % PMID[31336310]
NPT146 Cell Line SK-OV-3 Homo sapiens Activity = 35.1 % PMID[31336310]
NPT146 Cell Line SK-OV-3 Homo sapiens Activity = 51.5 % PMID[31336310]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = -6.76 % DOI[10.6019/CHEMBL4495564]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.28 % DOI[10.6019/CHEMBL4495565]

☑ 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 NPC71941 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 NPC71941 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