NPASS Compound

Structure

NPC109816 OpenBabel06302216162D 42 46 0 0 1 0 0 0 0 0999 V2000 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 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 -3.4641 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 -1.7321 -1.0000 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 3 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 O 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 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 42 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 41 1 0 0 0 0 13 14 1 0 0 0 0 13 29 1 0 0 0 0 14 15 2 0 0 0 0 14 28 1 0 0 0 0 15 16 1 0 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 19 24 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 29 30 1 0 0 0 0 30 37 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 40 1 0 0 0 0 32 33 1 0 0 0 0 32 39 1 0 0 0 0 33 34 1 0 0 0 0 33 38 1 0 0 0 0 34 35 1 0 0 0 0 34 37 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	596.14
Volume:	535.022
LogP:	-0.94
LogD:	-0.071
LogS:	-3.029
# Rotatable Bonds:	6
TPSA:	269.43
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.142
Synthetic Accessibility Score:	4.776
Fsp3:	0.423
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.421
MDCK Permeability:	4.91016216983553e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.985
Human Intestinal Absorption (HIA):	0.92
20% Bioavailability (F20%):	0.304
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.216
Plasma Protein Binding (PPB):	71.52739715576172%
Volume Distribution (VD):	0.652
Pgp-substrate:	21.621461868286133%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.014
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.184
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.287
Half-life (T1/2):	0.42

ADMET: Toxicity

hERG Blockers:	0.092
Human Hepatotoxicity (H-HT):	0.076
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.548
Rat Oral Acute Toxicity:	0.062
Maximum Recommended Daily Dose:	0.003
Skin Sensitization:	0.034
Carcinogencity:	0.218
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.009

Download Data

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

Natural Product: NPC109816

Natural Product ID:	NPC109816
*Common Name:**	NIABBGMPPWXWOJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NIABBGMPPWXWOJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C26H28O16/c27-6-13-16(32)18(34)20(36)26(40-13)41-23-17(33)14-10(29)5-12(8-1-3-9(28)4-2-8)39-22(14)24(21(23)37)42-25-19(35)15(31)11(30)7-38-25/h1-5,11,13,15-16,18-20,25-28,30-37H,6-7H2
SMILES:	c1cc(ccc1c1cc(=O)c2c(c(c(c(c2o1)OC1C(C(C(CO1)O)O)O)O)OC1C(C(C(C(CO)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003540] Flavonoid-8-O-glycosides

*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
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[12713396]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15516765]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[16441081]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16675659]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[20022509]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20973550]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21123068]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21866899]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[22074222]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22074222]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23325115]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[23541646]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23700450]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23849114]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[23867078]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[23867078]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24310066]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24479468]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[24957203]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[25433632]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25445757]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25744461]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26841168]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[26860358]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28140583]
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]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32196343]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7381508]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Petiole	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Protoplast	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24613	Arisaema consanguineum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	Database[MetaboLights]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO15711	Radix glycyrrhizae preparata	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24613	Arisaema consanguineum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8180	Radix glycyrrhizae praeparata	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15161.1	Isodon lophanthoides var. gerardiana	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24715	Arisaema heterophyllum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24613	Arisaema consanguineum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8541	Oryza sativa	Species	Poaceae	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]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24715	Arisaema heterophyllum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1698	Glycyrrhiza inflata	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

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 NPC109816 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	496
0.1-0.2	1967
0.2-0.3	4611
0.3-0.4	10220
0.4-0.5	7811
0.5-0.6	4567
0.6-0.7	5717
0.7-0.8	4788
0.8-0.85	1442
0.85-0.9	558
0.9-0.95	408
0.95-1	112

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 NPC109816 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	426
0.1-0.2	987
0.2-0.3	2104
0.3-0.4	2728
0.4-0.5	1756
0.5-0.6	776
0.6-0.7	247
0.7-0.8	94
0.8-0.85	18
0.85-0.9	6
0.9-0.95	3
0.95-1	5

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