NPASS Compound

Structure

CID163365 OpenBabel06191715532D 41 48 0 0 1 0 0 0 0 0999 V2000 3.4228 -1.9761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2615 3.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 3.9158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8476 4.4054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5430 2.4473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2385 5.3839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3910 2.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3910 5.8732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7580 -1.8102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2506 -2.6890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5757 3.0699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8482 2.4475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 -1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8477 1.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7407 4.6440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6951 1.9576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5440 -1.4687 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0864 3.9169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 2.9366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2391 4.4057 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6955 2.9366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6955 3.9158 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8480 1.4688 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5325 3.2735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3911 3.9161 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8475 2.4470 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5436 4.4054 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8480 -1.4688 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8480 -0.4896 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0790 -1.0560 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4916 1.0003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2596 2.6192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6776 4.9054 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0308 -0.9970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6344 4.2464 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5440 -0.4895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 0.9792 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 0.7420 -2.4780 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 27 1 0 0 0 0 3 4 1 0 0 0 0 3 19 1 0 0 0 0 4 22 1 0 0 0 0 5 7 1 0 0 0 0 5 21 1 0 0 0 0 6 8 1 0 0 0 0 6 20 1 0 0 0 0 7 27 1 0 0 0 0 8 29 1 0 0 0 0 9 10 1 0 0 0 0 9 32 2 0 0 0 0 10 41 1 0 0 0 0 11 18 2 0 0 0 0 11 25 1 0 0 0 0 12 19 1 0 0 0 0 13 17 1 0 0 0 0 13 30 1 0 0 0 0 14 28 1 0 0 0 0 15 18 1 0 0 0 0 15 37 1 0 0 0 0 16 33 2 0 0 0 0 17 1 1 6 0 0 0 17 38 1 0 0 0 0 18 20 1 0 0 0 0 19 28 1 1 0 0 0 20 27 1 1 0 0 0 21 22 1 0 0 0 0 21 28 1 1 0 0 0 22 29 1 6 0 0 0 23 12 1 1 0 0 0 23 24 1 0 0 0 0 23 39 1 0 0 0 0 24 14 1 6 0 0 0 24 40 1 0 0 0 0 25 34 2 0 0 0 0 25 37 1 0 0 0 0 26 31 1 6 0 0 0 26 38 1 0 0 0 0 26 39 1 0 0 0 0 27 29 1 1 0 0 0 28 16 1 1 0 0 0 29 35 1 1 0 0 0 30 31 1 6 0 0 0 30 32 1 0 0 0 0 30 41 1 0 0 0 0 31 36 1 1 0 0 0 31 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	587.26
Volume:	565.562
LogP:	3.925
LogD:	3.487
LogS:	-4.356
# Rotatable Bonds:	2
TPSA:	130.95
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	8
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.345
Synthetic Accessibility Score:	6.553
Fsp3:	0.806
Lipinski Rule-of-5:	Accepted
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:	-5.338
MDCK Permeability:	1.6233156202360988e-05
Pgp-inhibitor:	0.34
Pgp-substrate:	0.663
Human Intestinal Absorption (HIA):	0.03
20% Bioavailability (F20%):	0.584
30% Bioavailability (F30%):	0.557

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.999
Plasma Protein Binding (PPB):	88.68917083740234%
Volume Distribution (VD):	1.782
Pgp-substrate:	3.147796154022217%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.806
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.35
CYP2C9-inhibitor:	0.109
CYP2C9-substrate:	0.058
CYP2D6-inhibitor:	0.026
CYP2D6-substrate:	0.16
CYP3A4-inhibitor:	0.901
CYP3A4-substrate:	0.816

ADMET: Excretion

Clearance (CL):	5.801
Half-life (T1/2):	0.156

ADMET: Toxicity

hERG Blockers:	0.437
Human Hepatotoxicity (H-HT):	0.546
Drug-inuced Liver Injury (DILI):	0.528
AMES Toxicity:	0.957
Rat Oral Acute Toxicity:	0.944
Maximum Recommended Daily Dose:	0.98
Skin Sensitization:	0.947
Carcinogencity:	0.667
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC163365

Natural Product ID:	NPC163365
*Common Name:**	Uscharin
IUPAC Name:	n.a.
Synonyms:	Uscharin
Standard InCHIKey:	DONIPVCAKBPJLH-IGACXKNBSA-N
Standard InCHI:	InChI=1S/C31H41NO8S/c1-17-13-30(32-9-10-41-30)31(36)26(38-17)39-23-12-19-3-4-22-21(28(19,16-33)14-24(23)40-31)5-7-27(2)20(6-8-29(22,27)35)18-11-25(34)37-15-18/h9,11,16-17,19-24,26,35-36H,3-8,10,12-15H2,1-2H3/t17-,19+,20-,21+,22-,23-,24-,26+,27-,28-,29+,30+,31-/m1/s1
SMILES:	C[C@@H]1C[C@]2([C@]3([C@@H](O1)O[C@@H]1C[C@@H]4CC[C@@H]5[C@H](CC[C@]6(C)[C@H](CC[C@]56O)C5=CC(=O)OC5)[C@]4(C[C@H]1O3)C=O)O)N=CCS2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL500585
PubChem CID:	11261800
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives [CHEMONTID:0001559] Cardenolide glycosides 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548837]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32649211]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31967821]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28817274]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19251412]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	root	n.a.	PMID[19052526]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	leaves	n.a.	n.a.	PMID[16933890]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16252914]
NPO8349	Uga sinensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26375	Viburnum grandifolium	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
EC50	1
IC50	10
MIC	5
Others	4

Activity Type	# Activity
Cell Line	9
CELL-LINE	3
Organism	5
Others	2
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT457	Cell Line	BT-549	Homo sapiens	IC50	=	14.6	nM	PMID[570201]
NPT402	Cell Line	Hs-578T	Homo sapiens	IC50	=	34.0	nM	PMID[570201]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	102.0	nM	PMID[570201]
NPT2	Others	Unspecified	""	Ratio IC50	=	7.0	n.a.	PMID[570201]
NPT2	Others	Unspecified	""	EC50	=	910.0	nM	PMID[570201]
NPT22491	CELL-LINE	MEB5	Mus musculus	Activity	=	36.0	%	PMID[570200]
NPT22491	CELL-LINE	MEB5	Mus musculus	Activity	=	19.5	um	PMID[570200]
NPT22491	CELL-LINE	MEB5	Mus musculus	Activity	=	20.8	%	PMID[570200]
NPT25172	SINGLE PROTEIN	Neurogenic locus notch homolog protein 1	Homo sapiens	IC50	=	400.0	nM	PMID[570200]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	275.0	nM	PMID[570199]

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☑ 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 NPC163365 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	188
0.1-0.2	1365
0.2-0.3	5944
0.3-0.4	16283
0.4-0.5	11119
0.5-0.6	5558
0.6-0.7	2002
0.7-0.8	231
0.8-0.85	1
0.85-0.9	2
0.9-0.95	1
0.95-1	3

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Similarity Score	Similarity Level	Natural Product ID
0.9329	High Similarity	NPC473208
0.8797	High Similarity	NPC473040
0.8589	High Similarity	NPC470094
0.7905	Intermediate Similarity	NPC91
0.7852	Intermediate Similarity	NPC16569

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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 NPC163365 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	134
0.1-0.2	926
0.2-0.3	4005
0.3-0.4	3070
0.4-0.5	742
0.5-0.6	236
0.6-0.7	26
0.7-0.8	10
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8986	High Similarity	NPD7625	Phase 1
0.7584	Intermediate Similarity	NPD7507	Approved
0.7434	Intermediate Similarity	NPD7319	Approved
0.702	Intermediate Similarity	NPD8294	Approved
0.702	Intermediate Similarity	NPD8377	Approved

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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