NPASS Compound

Structure

NPC169037 OpenBabel06302215172D 30 34 0 0 1 0 0 0 0 0999 V2000 6.1472 2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 3.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 3.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 4.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 4.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 3.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 4.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3662 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3662 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6752 0.9511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 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 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 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 11 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 11 12 1 0 0 0 0 13 5 1 1 0 0 0 13 14 1 0 0 0 0 13 27 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 30 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 6 0 0 0 22 27 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 27 25 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.12
Volume:	395.516
LogP:	2.415
LogD:	2.776
LogS:	-4.707
# Rotatable Bonds:	4
TPSA:	95.84
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.672
Synthetic Accessibility Score:	3.331
Fsp3:	0.273
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:	-5.008
MDCK Permeability:	4.265505776857026e-05
Pgp-inhibitor:	0.059
Pgp-substrate:	0.199
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	87.6517562866211%
Volume Distribution (VD):	0.716
Pgp-substrate:	8.758015632629395%

ADMET: Metabolism

CYP1A2-inhibitor:	0.334
CYP1A2-substrate:	0.976
CYP2C19-inhibitor:	0.178
CYP2C19-substrate:	0.829
CYP2C9-inhibitor:	0.066
CYP2C9-substrate:	0.77
CYP2D6-inhibitor:	0.255
CYP2D6-substrate:	0.876
CYP3A4-inhibitor:	0.525
CYP3A4-substrate:	0.36

ADMET: Excretion

Clearance (CL):	6.963
Half-life (T1/2):	0.559

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.138
Drug-inuced Liver Injury (DILI):	0.306
AMES Toxicity:	0.59
Rat Oral Acute Toxicity:	0.07
Maximum Recommended Daily Dose:	0.6
Skin Sensitization:	0.298
Carcinogencity:	0.408
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.901

Download Data

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

Natural Product: NPC169037

Natural Product ID:	NPC169037
*Common Name:**	ISCQYPPCSYRZOT-BKTGTZMESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ISCQYPPCSYRZOT-BKTGTZMESA-N
Standard InCHI:	InChI=1S/C22H20O8/c1-25-16-4-10(5-17(26-2)21(16)27-3)18-11-6-14-15(30-9-29-14)7-12(11)20(23)13-8-28-22(24)19(13)18/h4-7,13,18-19H,8-9H2,1-3H3/t13-,18+,19-/m0/s1
SMILES:	COc1cc(cc(c1OC)OC)[C@@H]1c2cc3c(cc2C(=O)[C@H]2COC(=O)[C@H]12)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	443014
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001510] Lignan lactones

*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
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16933860]
NPO26380	Tacca plantaginea	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23031596]
NPO11163	Methylobacterium organophilum	Species	Methylobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26032177]
NPO10903	Sinopodophyllum hexandrum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26359402]
NPO11163	Methylobacterium organophilum	Species	Methylobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3928379]
NPO1362	Swertia paniculata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	root	n.a.	Database[Article]
NPO26380	Tacca plantaginea	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25340	Galega officinalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26868	Diphylleia sinensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25340	Galega officinalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26380	Tacca plantaginea	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26868	Diphylleia sinensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30053	Podophyllum emodll	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26380	Tacca plantaginea	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26868	Diphylleia sinensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10903	Sinopodophyllum hexandrum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26380	Tacca plantaginea	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25340	Galega officinalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26179	Chrysosplenium tetrandrum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10903	Sinopodophyllum hexandrum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6738	Cladonia incrassata	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16081	Peltophorum dasyrhachis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4464	Senecio mexicanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23848	Podophyllum peltatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26868	Diphylleia sinensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26710	Hypotrachyna rachista	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25651	Tecoma grandiflora	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6893	Dimorphotheca sinuata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3025	Schefflera capitata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1362	Swertia paniculata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11163	Methylobacterium organophilum	Species	Methylobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11417	Gesneria cardinalis	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23767	Aspropaxillus candidus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4534	Croton nitens	Species	Euphorbiaceae	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	3

Activity Type	# Activity
Organism	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1769	Organism	Mythimna separata	Mythimna separata	mortality	=	17.2	%	PMID[511898]
NPT1769	Organism	Mythimna separata	Mythimna separata	mortality	=	3.5	%	PMID[511898]
NPT1769	Organism	Mythimna separata	Mythimna separata	mortality	=	6.7	%	PMID[511898]

☑ 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 NPC169037 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 NPC169037 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