NPASS Compound

Structure

NPC127684 OpenBabel06302215212D 34 36 0 0 1 0 0 0 0 0999 V2000 -2.5981 0.5000 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 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 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 O 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 -4.3301 -1.5000 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 -2.5981 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 1 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 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 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 -0.0000 -0.0000 0.0000 C 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 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 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 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 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 20 1 0 0 0 0 14 15 1 0 0 0 0 14 34 1 1 0 0 0 15 16 1 6 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 20 1 0 0 0 0 19 33 1 6 0 0 0 20 21 1 6 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 26 32 1 0 0 0 0 27 28 2 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	484.09
Volume:	430.778
LogP:	-0.052
LogD:	-0.123
LogS:	-1.608
# Rotatable Bonds:	7
TPSA:	243.9
# H-Bond Aceptor:	14
# H-Bond Donor:	9
# Rings:	3
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.178
Synthetic Accessibility Score:	4.102
Fsp3:	0.3
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.703
MDCK Permeability:	1.6731451978557743e-05
Pgp-inhibitor:	0.017
Pgp-substrate:	0.039
Human Intestinal Absorption (HIA):	0.959
20% Bioavailability (F20%):	0.941
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.041
Plasma Protein Binding (PPB):	89.01641082763672%
Volume Distribution (VD):	0.536
Pgp-substrate:	13.23122787475586%

ADMET: Metabolism

CYP1A2-inhibitor:	0.293
CYP1A2-substrate:	0.011
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.036
CYP2C9-inhibitor:	0.082
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.116
CYP3A4-inhibitor:	0.048
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	9.771
Half-life (T1/2):	0.963

ADMET: Toxicity

hERG Blockers:	0.184
Human Hepatotoxicity (H-HT):	0.061
Drug-inuced Liver Injury (DILI):	0.947
AMES Toxicity:	0.081
Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.002
Skin Sensitization:	0.934
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.765
Respiratory Toxicity:	0.018

Download Data

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

Natural Product: NPC127684

Natural Product ID:	NPC127684
*Common Name:**	LRRLFFLVWQTQGZ-CMJVQNDMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LRRLFFLVWQTQGZ-CMJVQNDMSA-N
Standard InCHI:	InChI=1S/C20H20O14/c21-5-12-15(28)16(33-18(29)6-1-8(22)13(26)9(23)2-6)17(20(31)32-12)34-19(30)7-3-10(24)14(27)11(25)4-7/h1-4,12,15-17,20-28,31H,5H2/t12-,15-,16+,17+,20-/m1/s1
SMILES:	c1c(cc(c(c1O)O)O)C(=O)O[C@H]1[C@@H]([C@@H](CO)O[C@H]([C@H]1OC(=O)c1cc(c(c(c1)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:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001248] Hydroxybenzoic acid derivatives [CHEMONTID:0001251] Gallic acid and derivatives [CHEMONTID:0003539] Galloyl esters

*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
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11524125]
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11524125]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22080044]
NPO25887	Turbinaria ornata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25050371]
NPO25887	Turbinaria ornata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2607351]
NPO20150	Erythrina sacleuxii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33170684]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23313	Dioscorea althaeoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25678	Albertisia papuana	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20150	Erythrina sacleuxii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25678	Albertisia papuana	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23313	Dioscorea althaeoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23854	Scilla maritima	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23313	Dioscorea althaeoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22144	Daphne lancifolia	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25372	Valeriana fedtschenkoi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21967	Astragalus asper	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25647	Taraxacum bicorne	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25678	Albertisia papuana	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25862	Lafoensia glyptocarpa	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24304	Glycyrrhiza lepidota	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24416	Artemisia tournefortiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20150	Erythrina sacleuxii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24230	Petriella sordida	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23854	Scilla maritima	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5771	Sinularia molesta	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6157	Dahlstedtia araripensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14279.1	Ficus sarmentosa var. thunbergii	Varieties	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24605	Monochaetia compta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25705	Cordia curassavica	Species	Cordiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25887	Turbinaria ornata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24446	Diotis maritima	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23313	Dioscorea althaeoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25263	Aulacomnium androgynum	Species	Aulacomniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23975	Osteophloeum platyspermum	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5064	Derris uliginosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21196	Dichotomaria marginata	Species	Galaxauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29226.1	Ficus cordata subsp. salicifolia	Subspecies	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25535	Cosmos pringlei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4074	Lonchocarpus orotinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23698	Gardneria insularis	Species	Loganiaceae	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 NPC127684 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	346
0.1-0.2	1481
0.2-0.3	3570
0.3-0.4	8145
0.4-0.5	9957
0.5-0.6	4821
0.6-0.7	6482
0.7-0.8	6817
0.8-0.85	816
0.85-0.9	181
0.9-0.95	63
0.95-1	18

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 NPC127684 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	295
0.1-0.2	849
0.2-0.3	1824
0.3-0.4	2793
0.4-0.5	1911
0.5-0.6	1028
0.6-0.7	330
0.7-0.8	108
0.8-0.85	9
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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