NPASS Compound

Structure

NPC28843 OpenBabel06302216002D 32 35 0 0 1 0 0 0 0 0999 V2000 0.4492 2.7832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3475 2.7832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7967 2.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6951 2.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3475 1.2272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7967 0.4492 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4492 1.2272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.4492 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3890 -0.2246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2874 -0.2246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.8984 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7780 -1.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5560 -0.8984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5560 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3340 0.4492 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3340 -0.4492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1120 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8900 0.4492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8900 1.3475 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1120 1.7967 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5612 2.5747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3340 1.3475 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5560 1.7967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7780 1.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7780 0.4492 0.0000 C 0 0 2 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 -2.6628 2.5747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7645 2.5747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1120 3.3527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0103 3.3527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6680 1.7967 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7885 0.8677 0.0000 O 0 0 0 0 0 0 0 0 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 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 6 0 0 0 11 26 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 25 1 0 0 0 0 14 15 1 0 0 0 0 14 32 1 6 0 0 0 15 22 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 31 1 6 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 20 27 1 0 0 0 0 22 23 1 1 0 0 0 23 24 1 0 0 0 0 25 24 1 1 0 0 0 25 26 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.27
Volume:	466.222
LogP:	2.453
LogD:	2.694
LogS:	-4.246
# Rotatable Bonds:	5
TPSA:	93.06
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.39
Synthetic Accessibility Score:	6.245
Fsp3:	0.769
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:	-4.928
MDCK Permeability:	1.7692642359179445e-05
Pgp-inhibitor:	0.111
Pgp-substrate:	0.4
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.608

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.575
Plasma Protein Binding (PPB):	68.66727447509766%
Volume Distribution (VD):	1.563
Pgp-substrate:	22.010534286499023%

ADMET: Metabolism

CYP1A2-inhibitor:	0.059
CYP1A2-substrate:	0.836
CYP2C19-inhibitor:	0.396
CYP2C19-substrate:	0.754
CYP2C9-inhibitor:	0.287
CYP2C9-substrate:	0.032
CYP2D6-inhibitor:	0.145
CYP2D6-substrate:	0.092
CYP3A4-inhibitor:	0.956
CYP3A4-substrate:	0.534

ADMET: Excretion

Clearance (CL):	7.765
Half-life (T1/2):	0.179

ADMET: Toxicity

hERG Blockers:	0.103
Human Hepatotoxicity (H-HT):	0.769
Drug-inuced Liver Injury (DILI):	0.147
AMES Toxicity:	0.148
Rat Oral Acute Toxicity:	0.969
Maximum Recommended Daily Dose:	0.947
Skin Sensitization:	0.427
Carcinogencity:	0.948
Eye Corrosion:	0.034
Eye Irritation:	0.022
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC28843

Natural Product ID:	NPC28843
*Common Name:**	GRYOZIZNEBSQBX-YDICEIHXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GRYOZIZNEBSQBX-YDICEIHXSA-N
Standard InCHI:	InChI=1S/C26H38O6/c1-7-15(2)21(28)32-20-16(3)17-8-13-26(30)23(4)11-10-19(27)24(5,22(29)31-6)18(23)9-12-25(20,26)14-17/h7,17-20,27,30H,3,8-14H2,1-2,4-6H3/b15-7+/t17-,18+,19+,20+,23-,24+,25+,26-/m1/s1
SMILES:	C/C=C(C)/C(=O)O[C@H]1C(=C)[C@@H]2CC[C@]3([C@]4(C)CC[C@@H]([C@](C)([C@H]4CC[C@]13C2)C(=O)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003782] Kaurane diterpenoids

*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
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14374	Retama duriaei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11036	Piper taboganum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14581	Rubia schumanniana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13884	Microglossa pyrrhopappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10163	Oreoherzogia fallax	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11975	Antillogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1402	Adenocarpus foliolosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14173	Ipomoea reptans	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7550	Chromolaena arnottiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13484	Vidalia volubilis	Species	Tephritidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6564	Betula exilis	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29061	Anthoxanthum nitens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13183	Cereus dumortieri	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22285	Clethra macrophylla	Species	Clethraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19055	Plenodomus tracheiphilus	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10309	Ichthyothere terminalis	Species	Asteraceae	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 NPC28843 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	219
0.1-0.2	1425
0.2-0.3	4528
0.3-0.4	7979
0.4-0.5	12610
0.5-0.6	5859
0.6-0.7	6455
0.7-0.8	3132
0.8-0.85	403
0.85-0.9	84
0.9-0.95	3
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 NPC28843 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	186
0.1-0.2	1695
0.2-0.3	3806
0.3-0.4	2233
0.4-0.5	708
0.5-0.6	231
0.6-0.7	143
0.7-0.8	135
0.8-0.85	10
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