NPASS Compound

Structure

NPC50539 OpenBabel06302215502D 32 35 0 0 1 0 0 0 0 0999 V2000 0.7381 -0.6605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6577 -0.3577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8642 0.5995 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0709 1.5571 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3327 2.2176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4132 1.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2066 0.9573 0.0000 N 0 0 3 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 3.0025 1.8598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0025 2.8394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8509 3.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6992 2.8394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8509 4.3088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6992 4.7986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5475 4.3088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3959 4.7986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2442 4.3088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2442 3.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3959 2.8394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5475 3.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0926 2.8394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9409 3.3292 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.9409 4.3088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.7893 4.7986 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.6376 4.3088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.6376 3.3292 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.4860 2.8394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.3343 3.3292 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7893 2.8394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.4860 4.7986 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7893 5.7781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0926 4.7986 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 8 1 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 7 1 0 0 0 0 4 5 1 0 0 0 0 4 9 1 1 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 22 21 1 1 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 32 1 6 0 0 0 24 25 1 0 0 0 0 24 31 1 1 0 0 0 25 26 1 0 0 0 0 25 30 1 6 0 0 0 26 27 1 1 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1072.58
Volume:	1050.773
LogP:	2.73
LogD:	1.592
LogS:	-3.586
# Rotatable Bonds:	13
TPSA:	330.51
# H-Bond Aceptor:	21
# H-Bond Donor:	11
# Rings:	8
# Heavy Atoms:	21

MedChem Properties

QED Drug-Likeness Score:	0.087
Synthetic Accessibility Score:	6.858
Fsp3:	0.926
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.604
MDCK Permeability:	0.00018058430578093976
Pgp-inhibitor:	0.997
Pgp-substrate:	0.507
Human Intestinal Absorption (HIA):	0.929
20% Bioavailability (F20%):	0.088
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006
Plasma Protein Binding (PPB):	78.74293518066406%
Volume Distribution (VD):	-0.002
Pgp-substrate:	11.135597229003906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.63
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.526
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.065
CYP3A4-inhibitor:	0.019
CYP3A4-substrate:	0.012

ADMET: Excretion

Clearance (CL):	0.307
Half-life (T1/2):	0.467

ADMET: Toxicity

hERG Blockers:	0.092
Human Hepatotoxicity (H-HT):	0.243
Drug-inuced Liver Injury (DILI):	0.044
AMES Toxicity:	0.083
Rat Oral Acute Toxicity:	0.289
Maximum Recommended Daily Dose:	0.522
Skin Sensitization:	0.344
Carcinogencity:	0.006
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.944

Download Data

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

Natural Product: NPC50539

Natural Product ID:	NPC50539
*Common Name:**	VRWXOVDCMDXQDO-XSWPKGSUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VRWXOVDCMDXQDO-XSWPKGSUSA-N
Standard InCHI:	InChI=1S/C23H31NO8/c25-12-18-20(27)21(28)22(29)23(32-18)31-16-6-3-14(4-7-16)5-8-19(26)30-13-15-9-11-24-10-1-2-17(15)24/h3-8,15,17-18,20-23,25,27-29H,1-2,9-13H2/b8-5+/t15-,17-,18+,20+,21-,22+,23+/m0/s1
SMILES:	C1C[C@H]2[C@@H](CCN2C1)COC(=O)/C=C/c1ccc(cc1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19422203]
NPO22594	Solanum incanum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2380724]
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	Whole Plants	n.a.	n.a.	PMID[29412669]
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9134745]
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22594	Solanum incanum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22594	Solanum incanum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21706	Olearia paniculata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22594	Solanum incanum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18150	Agaricus pantherinus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21665.1	Mycobacterium avium subsp. paratuberculosis	Subspecies	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO22809	Gnidia involucrata	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21757	Selaginella moellendorfii	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24031	Kadsura hainanensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21206	Lobophytum cristagalli	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6007	Tetragonotheca helianthoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17485	Gordonia dassanayakei	Species	Theaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20462	Derris floribunda	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27203	Glutamicibacter nicotianae	Species	Micrococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO22709	Senecio umbellatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19164	Ustilago zeae	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19627	Oncoba glauca	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20006	Hovenia trichocarpa	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2666	Streptomyces cinnamonensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18419	Myrtillocactus eichlamii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20151	Berberis nummularia	Species	Berberidaceae	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 NPC50539 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	213
0.1-0.2	1046
0.2-0.3	3344
0.3-0.4	9994
0.4-0.5	10039
0.5-0.6	12497
0.6-0.7	5040
0.7-0.8	522
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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 NPC50539 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	139
0.1-0.2	518
0.2-0.3	1068
0.3-0.4	2582
0.4-0.5	2627
0.5-0.6	1545
0.6-0.7	650
0.7-0.8	21
0.8-0.85	0
0.85-0.9	0
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