NPASS Compound

Structure

NPC278548 OpenBabel06302215412D 44 49 0 0 1 0 0 0 0 0999 V2000 -3.3948 3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 2.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 0.9800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9800 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8487 1.4700 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6974 0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6974 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5461 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5461 -1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6974 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -2.4500 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8487 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -5.3900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -3.4300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -2.4500 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3948 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 -0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2435 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0922 -0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0922 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2435 -2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9409 -2.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9409 -0.4900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -1.9600 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6974 -0.9800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -6.3700 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -3.4300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6974 -2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3948 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 2.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 3.9200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 44 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 6 1 6 0 0 0 10 11 1 0 0 0 0 10 40 1 0 0 0 0 11 12 1 0 0 0 0 11 43 1 1 0 0 0 12 13 1 0 0 0 0 13 39 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 42 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 41 1 0 0 0 0 17 39 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 35 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 38 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 37 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 26 35 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 34 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 35 36 1 6 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	608.15
Volume:	576.029
LogP:	2.408
LogD:	1.687
LogS:	-4.587
# Rotatable Bonds:	4
TPSA:	229.99
# H-Bond Aceptor:	13
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.15
Synthetic Accessibility Score:	4.646
Fsp3:	0.226
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.926
MDCK Permeability:	4.487290880206274e-06
Pgp-inhibitor:	0.071
Pgp-substrate:	0.05
Human Intestinal Absorption (HIA):	0.88
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	87.2761459350586%
Volume Distribution (VD):	0.46
Pgp-substrate:	12.650932312011719%

ADMET: Metabolism

CYP1A2-inhibitor:	0.041
CYP1A2-substrate:	0.289
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.629
CYP2C9-substrate:	0.892
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.188
CYP3A4-inhibitor:	0.125
CYP3A4-substrate:	0.35

ADMET: Excretion

Clearance (CL):	10.786
Half-life (T1/2):	0.791

ADMET: Toxicity

hERG Blockers:	0.057
Human Hepatotoxicity (H-HT):	0.125
Drug-inuced Liver Injury (DILI):	0.733
AMES Toxicity:	0.258
Rat Oral Acute Toxicity:	0.481
Maximum Recommended Daily Dose:	0.939
Skin Sensitization:	0.96
Carcinogencity:	0.022
Eye Corrosion:	0.003
Eye Irritation:	0.905
Respiratory Toxicity:	0.03

Download Data

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

Natural Product: NPC278548

Natural Product ID:	NPC278548
*Common Name:**	ADKHKBZKHGJXDZ-UKWJTHFESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ADKHKBZKHGJXDZ-UKWJTHFESA-N
Standard InCHI:	InChI=1S/C31H28O13/c1-42-31-20(38)5-12(6-21(31)39)28-22(40)9-14-16(34)10-19(37)25(30(14)44-28)26-24-18(36)7-13(32)8-23(24)43-29(27(26)41)11-2-3-15(33)17(35)4-11/h2-8,10,22,26-29,32-41H,9H2,1H3/t22-,26+,27+,28+,29+/m0/s1
SMILES:	COc1c(cc(cc1O)[C@@H]1[C@H](Cc2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4ccc(c(c4)O)O)[C@@H]3O)O)O)c2O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	53344583
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[21080642]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	bark	Santa Maria, Rio Grande do Sul, Brazil	2007-OCT	PMID[21080642]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[21553897]
NPO21327	Ramalina stenospora	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23614	Ovophis okinavensis	Species	Viperidae	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 NPC278548 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 NPC278548 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