NPASS Compound

Structure

NPC302762 OpenBabel06302215402D 30 33 0 0 0 0 0 0 0 0999 V2000 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 29 1 0 0 0 0 7 8 1 0 0 0 0 8 16 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 12 1 0 0 0 0 10 11 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 28 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 27 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 28 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	404.16
Volume:	424.317
LogP:	6.307
LogD:	3.785
LogS:	-2.561
# Rotatable Bonds:	3
TPSA:	79.9
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.558
Synthetic Accessibility Score:	3.127
Fsp3:	0.24
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.791
MDCK Permeability:	2.0379437046358362e-05
Pgp-inhibitor:	0.97
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.199
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008
Plasma Protein Binding (PPB):	98.33512878417969%
Volume Distribution (VD):	0.731
Pgp-substrate:	3.9895553588867188%

ADMET: Metabolism

CYP1A2-inhibitor:	0.744
CYP1A2-substrate:	0.268
CYP2C19-inhibitor:	0.944
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.896
CYP2C9-substrate:	0.928
CYP2D6-inhibitor:	0.826
CYP2D6-substrate:	0.523
CYP3A4-inhibitor:	0.373
CYP3A4-substrate:	0.142

ADMET: Excretion

Clearance (CL):	3.19
Half-life (T1/2):	0.174

ADMET: Toxicity

hERG Blockers:	0.18
Human Hepatotoxicity (H-HT):	0.892
Drug-inuced Liver Injury (DILI):	0.256
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.611
Maximum Recommended Daily Dose:	0.846
Skin Sensitization:	0.844
Carcinogencity:	0.495
Eye Corrosion:	0.003
Eye Irritation:	0.069
Respiratory Toxicity:	0.759

Download Data

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

Natural Product: NPC302762

Natural Product ID:	NPC302762
*Common Name:**	CUDNUXBRPAPDBJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CUDNUXBRPAPDBJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H24O5/c1-14(2)5-7-17-19(26)12-21-22(23(17)27)24(28)18(13-29-21)15-6-8-20-16(11-15)9-10-25(3,4)30-20/h5-6,8-13,26-27H,7H2,1-4H3
SMILES:	CC(=CCc1c(cc2c(c1O)c(=O)c(co2)c1ccc2c(C=CC(C)(C)O2)c1)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15907834
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001827] Isoflavanones [CHEMONTID:0003526] 6-prenylated isoflavanones

*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
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/S0031-9422(99)00103-X]
NPO29080	Ulex airensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858751]
NPO32756	ulex europaeus ssp. europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858751]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	root bark	n.a.	n.a.	PMID[11908991]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19969457]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21123068]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21314138]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28522265]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29641206]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29080	Ulex airensis	Species	Fabaceae	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

Activity Type	# Activity
Others	8

Activity Type	# Activity
Cell Line	4
Individual Protein	2
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	GI	=	73.0	%	PMID[28522265]
NPT660	Cell Line	SW480	Homo sapiens	GI	=	58.0	%	PMID[28522265]
NPT65	Cell Line	HepG2	Homo sapiens	GI	=	7.0	%	PMID[28522265]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	0.0	%	PMID[28522265]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	Inhibition	=	94.0	%	PMID[28522265]
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	FC	=	1.34	n.a.	PMID[28835349]
NPT2	Others	Unspecified		Inhibition	=	3.0	%	PMID[28522265]

☑ 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 NPC302762 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 NPC302762 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