NPASS Compound

Structure

CID295110 OpenBabel06191716102D 27 31 0 0 1 0 0 0 0 0999 V2000 -0.8124 -2.4513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7161 -0.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6860 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5285 -3.4061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 -1.9466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6849 0.9728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6858 -2.9199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8425 -1.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8425 1.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0139 -1.3280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3718 -1.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1784 0.2368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5277 -0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -1.4602 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3715 -2.9194 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6855 0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8430 -1.4602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8430 -0.4867 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9651 -1.1259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6861 -1.9469 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8425 -0.4864 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2376 -3.4194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6877 -1.7765 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0667 -0.1588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 22 1 0 0 0 0 3 4 1 0 0 0 0 3 15 1 0 0 0 0 4 19 1 0 0 0 0 5 8 1 0 0 0 0 5 16 1 0 0 0 0 6 9 1 0 0 0 0 6 18 1 0 0 0 0 7 10 1 0 0 0 0 7 17 1 0 0 0 0 8 21 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 11 14 2 0 0 0 0 11 20 1 0 0 0 0 12 15 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 0 0 0 0 13 27 1 0 0 0 0 14 17 1 0 0 0 0 15 21 1 1 0 0 0 16 24 1 6 0 0 0 17 22 1 6 0 0 0 18 19 1 0 0 0 0 18 21 1 6 0 0 0 19 23 1 1 0 0 0 20 25 2 0 0 0 0 20 27 1 0 0 0 0 21 1 1 6 0 0 0 22 23 1 6 0 0 0 23 26 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.25
Volume:	393.47
LogP:	4.141
LogD:	3.715
LogS:	-4.423
# Rotatable Bonds:	1
TPSA:	73.83
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.672
Synthetic Accessibility Score:	4.646
Fsp3:	0.826
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.995
MDCK Permeability:	1.3733376363234129e-05
Pgp-inhibitor:	0.028
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.982
30% Bioavailability (F30%):	0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.361
Plasma Protein Binding (PPB):	96.69364166259766%
Volume Distribution (VD):	1.316
Pgp-substrate:	3.6784534454345703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.069
CYP1A2-substrate:	0.413
CYP2C19-inhibitor:	0.052
CYP2C19-substrate:	0.562
CYP2C9-inhibitor:	0.271
CYP2C9-substrate:	0.458
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.639
CYP3A4-inhibitor:	0.571
CYP3A4-substrate:	0.21

ADMET: Excretion

Clearance (CL):	14.228
Half-life (T1/2):	0.258

ADMET: Toxicity

hERG Blockers:	0.19
Human Hepatotoxicity (H-HT):	0.395
Drug-inuced Liver Injury (DILI):	0.038
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.907
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.91
Carcinogencity:	0.398
Eye Corrosion:	0.009
Eye Irritation:	0.036
Respiratory Toxicity:	0.958

Download Data

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

Natural Product: NPC295110

Natural Product ID:	NPC295110
*Common Name:**	Digitoxigenin
IUPAC Name:	3-[(3S,5R,8R,9S,10S,13R,14S,17R)-3,14-dihydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one
Synonyms:	Digitoxigenin; Digoxigenin; Uzarigenin
Standard InCHIKey:	XZTUSOXSLKTKJQ-CESUGQOBSA-N
Standard InCHI:	InChI=1S/C23H34O4/c1-21-8-5-16(24)12-15(21)3-4-19-18(21)6-9-22(2)17(7-10-23(19,22)26)14-11-20(25)27-13-14/h11,15-19,24,26H,3-10,12-13H2,1-2H3/t15-,16+,17-,18+,19-,21+,22-,23+/m1/s1
SMILES:	C[C@]12CC[C@@H](C[C@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@H](CC[C@]12O)C1=CC(=O)OC1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1453
PubChem CID:	4369270
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

*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
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834166]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548837]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	Leaves; Stems	n.a.	n.a.	PMID[9214727]
NPO32604	asclepias fructicosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3981544]
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]
NPO32958	Streptocaulon juventas	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31120251]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29693393]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28817274]
NPO3447	Beaumontia murtonii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28598616]

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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
AC50	3
EC50	4
GI50	59
IC50	58
Ki	2
Others	53
Potency	28

Activity Type	# Activity
Cell Line	89
Individual Protein	22
NON-MOLECULAR	4
Organism	21
Others	62
Protein Complex	7
SINGLE PROTEIN	1
Tissue	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.17	%	PMID[468209]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	2.594	%	PMID[468208]
NPT189	Cell Line	Vero	Chlorocebus aethiops	CC50	=	27540.0	nM	PMID[468207]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	1680.0	nM	PMID[468207]
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	=	2480.0	nM	PMID[468207]
NPT858	Cell Line	LNCaP	Homo sapiens	IC50	=	3700.0	nM	PMID[468207]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	2410.0	nM	PMID[468207]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	920.0	nM	PMID[468207]
NPT171	Cell Line	MRC5	Homo sapiens	IC50	=	1160.0	nM	PMID[468207]
NPT190	Organism	Human herpesvirus 1	Human herpesvirus 1	IC50	=	1090.0	nM	PMID[468207]

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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 NPC295110 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	193
0.1-0.2	1348
0.2-0.3	4612
0.3-0.4	11318
0.4-0.5	10345
0.5-0.6	5935
0.6-0.7	5872
0.7-0.8	2714
0.8-0.85	260
0.85-0.9	76
0.9-0.95	7
0.95-1	17

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC268829
1.0	High Similarity	NPC25177
1.0	High Similarity	NPC222875
1.0	High Similarity	NPC247701
0.9789	High Similarity	NPC196471

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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 NPC295110 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	160
0.1-0.2	1470
0.2-0.3	4047
0.3-0.4	2392
0.4-0.5	583
0.5-0.6	205
0.6-0.7	185
0.7-0.8	92
0.8-0.85	12
0.85-0.9	1
0.9-0.95	3
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9167	High Similarity	NPD7638	Approved
0.9072	High Similarity	NPD7640	Approved
0.9072	High Similarity	NPD7639	Approved
0.8611	High Similarity	NPD7328	Approved
0.8611	High Similarity	NPD7327	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