NPASS Compound

Structure

NPC125794 OpenBabel06302215402D 36 41 0 0 1 0 0 0 0 0999 V2000 6.7128 2.3690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4173 3.2784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0572 3.9890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9925 3.7902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7617 4.8984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4015 5.6090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8264 5.0972 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1866 4.3866 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.4820 3.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3160 4.7843 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5148 5.7196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3159 3.8281 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1437 3.3495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1437 2.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4869 2.3929 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6580 1.9143 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6579 0.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8290 0.4786 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9572 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8284 0.4786 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6568 0.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6568 1.9144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8284 2.3930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8283 3.3697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9144 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 2.8911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8290 2.3930 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8290 3.3495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6580 3.8281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4870 3.3495 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4870 4.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8284 -0.4980 0.0000 O 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 2.4869 1.4162 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1618 4.3164 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6054 5.4241 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 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 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 6 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 10 36 1 0 0 0 0 12 30 1 0 0 0 0 12 13 1 0 0 0 0 12 35 1 1 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 30 1 0 0 0 0 15 16 1 0 0 0 0 15 34 1 6 0 0 0 16 17 1 6 0 0 0 16 27 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 33 1 0 0 0 0 19 25 1 0 0 0 0 19 20 1 0 0 0 0 19 33 1 1 0 0 0 20 21 1 0 0 0 0 20 32 1 1 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 1 0 0 0 25 27 1 0 0 0 0 27 28 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.26
Volume:	501.281
LogP:	1.845
LogD:	1.017
LogS:	-4.288
# Rotatable Bonds:	2
TPSA:	133.66
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.386
Synthetic Accessibility Score:	5.995
Fsp3:	0.821
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.314
MDCK Permeability:	1.5708390492363833e-05
Pgp-inhibitor:	0.698
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.42
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.983
Plasma Protein Binding (PPB):	60.62004089355469%
Volume Distribution (VD):	0.557
Pgp-substrate:	21.836809158325195%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.956
CYP2C19-inhibitor:	0.062
CYP2C19-substrate:	0.789
CYP2C9-inhibitor:	0.108
CYP2C9-substrate:	0.023
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.031
CYP3A4-inhibitor:	0.66
CYP3A4-substrate:	0.936

ADMET: Excretion

Clearance (CL):	4.903
Half-life (T1/2):	0.638

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.268
Drug-inuced Liver Injury (DILI):	0.152
AMES Toxicity:	0.065
Rat Oral Acute Toxicity:	0.65
Maximum Recommended Daily Dose:	0.903
Skin Sensitization:	0.173
Carcinogencity:	0.988
Eye Corrosion:	0.006
Eye Irritation:	0.024
Respiratory Toxicity:	0.927

Download Data

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

Natural Product: NPC125794

Natural Product ID:	NPC125794
*Common Name:**	UPBUGICUKQIKTJ-KABTZXSUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UPBUGICUKQIKTJ-KABTZXSUSA-N
Standard InCHI:	InChI=1S/C28H38O8/c1-14-12-20(35-22(31)15(14)2)25(5,32)27(34)11-10-26(33)17-13-21-28(36-21)19(30)7-6-18(29)24(28,4)16(17)8-9-23(26,27)3/h6-7,16-17,19-21,30,32-34H,8-13H2,1-5H3/t16-,17+,19-,20+,21+,23-,24-,25-,26+,27-,28+/m0/s1
SMILES:	CC1=C(C)C(=O)O[C@H](C1)[C@@](C)([C@@]1(CC[C@]2([C@@H]3C[C@@H]4[C@@]5([C@H](C=CC(=O)[C@]5(C)[C@H]3CC[C@]12C)O)O4)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	73621
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001560] Withanolides and derivatives

*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
NPO28734	Physalis peruviana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28617598]
NPO28734	Physalis peruviana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30649869]
NPO28734	Physalis peruviana	Species	Solanaceae	Eukaryota	Whole Fruits	n.a.	n.a.	PMID[32159343]
NPO28734	Physalis peruviana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28734	Physalis peruviana	Species	Solanaceae	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
GI50	5
IC50	11
Others	5

Activity Type	# Activity
Cell Line	17
Individual Protein	1
NON-MOLECULAR	1
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	IC50	>	200.0	ug.mL-1	PMID[1710653]
NPT134	Cell Line	SK-BR-3	Homo sapiens	GI50	=	1700.0	nM	PMID[20438092]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	GI50	=	2100.0	nM	PMID[20438092]
NPT83	Cell Line	MCF7	Homo sapiens	GI50	=	1000.0	nM	PMID[20438092]
NPT396	Cell Line	T47D	Homo sapiens	GI50	=	2200.0	nM	PMID[20438092]
NPT71	Cell Line	HEK293	Homo sapiens	Survival	=	88.6	%	PMID[27210437]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	99.4	%	PMID[27210437]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	320.0	nM	PMID[27210437]
NPT113	Cell Line	RAW264.7	Mus musculus	Survival	=	50.1	%	PMID[27210437]
NPT369	Cell Line	ACHN	Homo sapiens	IC50	=	563.0	nM	PMID[28257574]
NPT858	Cell Line	LNCaP	Homo sapiens	IC50	=	160.0	nM	PMID[28617598]
NPT1629	Cell Line	CWR22R	Homo sapiens	IC50	=	90.0	nM	PMID[28617598]
NPT369	Cell Line	ACHN	Homo sapiens	IC50	>	2000.0	nM	PMID[28617598]
NPT387	Cell Line	M14	Homo sapiens	IC50	>	2000.0	nM	PMID[28617598]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	IC50	>	2000.0	nM	PMID[28617598]
NPT859	Cell Line	HFF	Homo sapiens	IC50	>	2000.0	nM	PMID[28617598]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	1800.0	nM	PMID[30649869]
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	=	0.9	uM	PMID[30649869]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	1100.0	nM	PMID[20438092]
NPT2	Others	Unspecified		IC50	=	40.0	nM	PMID[27210437]
NPT2	Others	Unspecified		Inhibition	=	99.5	%	PMID[27210437]

☑ 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 NPC125794 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	272
0.1-0.2	1461
0.2-0.3	4089
0.3-0.4	7165
0.4-0.5	12127
0.5-0.6	7690
0.6-0.7	6544
0.7-0.8	2894
0.8-0.85	276
0.85-0.9	121
0.9-0.95	36
0.95-1	22

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 NPC125794 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	241
0.1-0.2	1601
0.2-0.3	3660
0.3-0.4	2346
0.4-0.5	717
0.5-0.6	314
0.6-0.7	154
0.7-0.8	110
0.8-0.85	6
0.85-0.9	0
0.9-0.95	1
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