NPASS Compound

Structure

CID278681 OpenBabel06191716082D 30 35 0 0 1 0 0 0 0 0999 V2000 -2.5091 2.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7053 2.6791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6213 1.8695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8111 1.4020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6398 2.6791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6217 4.6748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8080 3.2730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6183 2.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8117 4.2078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4316 3.2719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7053 1.0606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0021 3.7406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2381 1.8699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6216 2.8049 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4316 4.2069 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0014 2.8054 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0011 1.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1070 1.8699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4288 1.4026 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4286 0.4682 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6191 0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6186 1.8701 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8117 3.2729 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8091 1.4024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2865 4.6299 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2977 4.7067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0415 1.8699 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2947 -0.0317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6398 1.0606 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 1 22 1 0 0 0 0 2 5 2 0 0 0 0 2 13 1 0 0 0 0 3 4 1 0 0 0 0 3 14 1 0 0 0 0 4 17 1 0 0 0 0 5 18 1 0 0 0 0 6 9 1 0 0 0 0 6 15 1 0 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 22 1 0 0 0 0 9 23 1 0 0 0 0 10 14 1 0 0 0 0 10 15 1 0 0 0 0 11 13 2 0 0 0 0 11 29 1 0 0 0 0 12 25 1 0 0 0 0 13 19 1 0 0 0 0 14 23 1 1 0 0 0 15 26 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 6 0 0 0 17 24 1 1 0 0 0 18 27 2 0 0 0 0 18 29 1 0 0 0 0 19 20 1 0 0 0 0 19 22 1 6 0 0 0 20 21 1 0 0 0 0 20 28 1 6 0 0 0 21 24 1 1 0 0 0 21 30 1 0 0 0 0 22 24 1 6 0 0 0 23 12 1 6 0 0 0 24 30 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.22
Volume:	417.153
LogP:	2.008
LogD:	2.245
LogS:	-3.596
# Rotatable Bonds:	2
TPSA:	103.43
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.639
Synthetic Accessibility Score:	5.401
Fsp3:	0.792
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:	-5.346
MDCK Permeability:	2.546954056015238e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.117
20% Bioavailability (F20%):	0.994
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.296
Plasma Protein Binding (PPB):	91.03826141357422%
Volume Distribution (VD):	1.268
Pgp-substrate:	7.121382713317871%

ADMET: Metabolism

CYP1A2-inhibitor:	0.039
CYP1A2-substrate:	0.579
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.505
CYP2C9-inhibitor:	0.067
CYP2C9-substrate:	0.037
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.275
CYP3A4-inhibitor:	0.597
CYP3A4-substrate:	0.179

ADMET: Excretion

Clearance (CL):	9.625
Half-life (T1/2):	0.514

ADMET: Toxicity

hERG Blockers:	0.404
Human Hepatotoxicity (H-HT):	0.844
Drug-inuced Liver Injury (DILI):	0.232
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.879
Maximum Recommended Daily Dose:	0.918
Skin Sensitization:	0.352
Carcinogencity:	0.385
Eye Corrosion:	0.011
Eye Irritation:	0.093
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC278681

Natural Product ID:	NPC278681
*Common Name:**	XDCJWJYMHNAEQH-DFJCLZAPSA-N
IUPAC Name:	n.a.
Synonyms:	19-Hydroxydesacetylcinobufagin
Standard InCHIKey:	XDCJWJYMHNAEQH-DFJCLZAPSA-N
Standard InCHI:	InChI=1S/C24H32O6/c1-22-8-7-16-17(4-3-14-10-15(26)6-9-23(14,16)12-25)24(22)21(30-24)20(28)19(22)13-2-5-18(27)29-11-13/h2,5,11,14-17,19-21,25-26,28H,3-4,6-10,12H2,1H3/t14-,15+,16+,17-,19+,20-,21-,22-,23-,24-/m1/s1
SMILES:	C[C@@]12CC[C@H]3[C@@H](CC[C@@H]4C[C@H](CC[C@]34CO)O)[C@]32[C@@H]([C@@H]([C@@H]1c1ccc(=O)oc1)O)O3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL518554
PubChem CID:	15513543
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001557] Bufanolides 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
NPO18636	Cupressus macrocarpa	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223924]
NPO11981	Bufo gargarizans	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28256122]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26722868]
NPO11981	Bufo gargarizans	Species	Bufonidae	Eukaryota	venom	n.a.	n.a.	PMID[24050254]
NPO10672	Vitex megapotamica	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22708620]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21954912]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	n.a.	twig	n.a.	PMID[21954912]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	twigs and leaves	Yunnan Province, China	2008-OCT	PMID[21954912]
NPO9576	Bufo bufo	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21185919]
NPO664	Potentilla multifida	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17504571]

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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
IC50	3

Activity Type	# Activity
Cell Line	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	3.9	ug.mL-1	PMID[512516]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	0.49	ug.mL-1	PMID[512516]
NPT1366	Cell Line	MH60	Mus musculus	IC50	>	25.0	ug.mL-1	PMID[512516]

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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 NPC278681 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	391
0.1-0.2	1419
0.2-0.3	2930
0.3-0.4	5428
0.4-0.5	10162
0.5-0.6	10121
0.6-0.7	9764
0.7-0.8	2117
0.8-0.85	282
0.85-0.9	37
0.9-0.95	30
0.95-1	16

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Similarity Score	Similarity Level	Natural Product ID
0.9909	High Similarity	NPC112936
0.9908	High Similarity	NPC16701
0.9818	High Similarity	NPC35171
0.9818	High Similarity	NPC213761
0.9817	High Similarity	NPC157380

Showing 1 to 5 of 200 entries

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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 NPC278681 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	331
0.1-0.2	855
0.2-0.3	1770
0.3-0.4	2662
0.4-0.5	2137
0.5-0.6	1018
0.6-0.7	346
0.7-0.8	26
0.8-0.85	4
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
0.8644	High Similarity	NPD7503	Approved
0.8182	Intermediate Similarity	NPD8033	Approved
0.8083	Intermediate Similarity	NPD7327	Approved
0.8083	Intermediate Similarity	NPD7328	Approved
0.8017	Intermediate Similarity	NPD7516	Approved

Showing 1 to 5 of 200 entries

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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