NPASS Compound

Structure

NPC272537 OpenBabel06302215242D 26 27 0 0 1 0 0 0 0 0999 V2000 -7.7942 1.5000 0.0000 C 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 -6.9282 0.0000 0.0000 C 0 0 0 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 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 -6.0622 -1.5000 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 -7.7942 -1.5000 0.0000 O 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 -3.4641 -0.0000 0.0000 C 0 0 1 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 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 2 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 -0.0000 2.0000 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 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 1.7321 0.0000 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 2.0000 0.0000 O 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 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 5 10 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 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 1 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	362.17
Volume:	374.286
LogP:	1.813
LogD:	2.303
LogS:	-2.691
# Rotatable Bonds:	9
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.545
Synthetic Accessibility Score:	3.112
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.668
MDCK Permeability:	4.4236676330910996e-06
Pgp-inhibitor:	0.007
Pgp-substrate:	0.548
Human Intestinal Absorption (HIA):	0.1
20% Bioavailability (F20%):	0.749
30% Bioavailability (F30%):	0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.041
Plasma Protein Binding (PPB):	94.14217376708984%
Volume Distribution (VD):	0.552
Pgp-substrate:	5.741903305053711%

ADMET: Metabolism

CYP1A2-inhibitor:	0.521
CYP1A2-substrate:	0.87
CYP2C19-inhibitor:	0.129
CYP2C19-substrate:	0.705
CYP2C9-inhibitor:	0.328
CYP2C9-substrate:	0.767
CYP2D6-inhibitor:	0.501
CYP2D6-substrate:	0.906
CYP3A4-inhibitor:	0.476
CYP3A4-substrate:	0.758

ADMET: Excretion

Clearance (CL):	13.883
Half-life (T1/2):	0.93

ADMET: Toxicity

hERG Blockers:	0.118
Human Hepatotoxicity (H-HT):	0.211
Drug-inuced Liver Injury (DILI):	0.09
AMES Toxicity:	0.095
Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.091
Skin Sensitization:	0.893
Carcinogencity:	0.154
Eye Corrosion:	0.007
Eye Irritation:	0.867
Respiratory Toxicity:	0.047

Download Data

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

Natural Product: NPC272537

Natural Product ID:	NPC272537
*Common Name:**	PUETUDUXMCLALY-IYBDPMFKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PUETUDUXMCLALY-IYBDPMFKSA-N
Standard InCHI:	InChI=1S/C20H26O6/c1-25-19-9-13(3-5-17(19)23)7-15(11-21)16(12-22)8-14-4-6-18(24)20(10-14)26-2/h3-6,9-10,15-16,21-24H,7-8,11-12H2,1-2H3/t15-,16+
SMILES:	COc1cc(ccc1O)C[C@@H](CO)[C@H](Cc1ccc(c(c1)OC)O)CO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11552274
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane lignans [CHEMONTID:0001624] Dibenzylbutanediol lignans

*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
NPO2421	Picea glauca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18636777]
NPO691	Tarchonanthus camphoratus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29244495]
NPO284	Albizia procera	Species	Fabaceae	Eukaryota	Bark	n.a.	n.a.	PMID[30520635]
NPO7770	Lactuca laciniata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO99	Artemisia porrecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5588	Bursera tonkinensis	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7155	Cypripedium calceolus	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO99	Artemisia porrecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19432	Millettia pinnata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5588	Bursera tonkinensis	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7155	Cypripedium calceolus	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7770	Lactuca laciniata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20154	Cedrus atlantica	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7155	Cypripedium calceolus	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO284	Albizia procera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4952	Pertusaria amara	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4117	Nauclea rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3415	Perymenium mendezii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19432	Millettia pinnata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15597	Calystegia pubescens	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7616	Melanargia galathea	Species	Nymphalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3263	Thea sasanqua	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29287	Alectoria ochroleuca	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO99	Artemisia porrecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO855	Elymnias thryallis	Species	Nymphalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO691	Tarchonanthus camphoratus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7770	Lactuca laciniata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7464	Uruparia lanosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5588	Bursera tonkinensis	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7155	Cypripedium calceolus	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2421	Picea glauca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1539	Artemisia giraldii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6844	Bulbophyllum protractum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4421	Penicillium cyclopium	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20154	Cedrus atlantica	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3255	Lampranthus sociorum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5981	Achlys triphylla	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2963	Diospyros glaucifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3963	Hortonia floribunda	Species	Monimiaceae	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 NPC272537 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	320
0.1-0.2	1419
0.2-0.3	4067
0.3-0.4	12216
0.4-0.5	6303
0.5-0.6	5245
0.6-0.7	8550
0.7-0.8	3314
0.8-0.85	730
0.85-0.9	407
0.9-0.95	99
0.95-1	27

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 NPC272537 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	288
0.1-0.2	879
0.2-0.3	1606
0.3-0.4	2661
0.4-0.5	1832
0.5-0.6	986
0.6-0.7	706
0.7-0.8	175
0.8-0.85	11
0.85-0.9	3
0.9-0.95	3
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