NPASS Compound

Structure

CID230968 OpenBabel06191716022D 26 30 0 0 1 0 0 0 0 0999 V2000 1.2321 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7248 2.9074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9328 3.8855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2601 1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4190 2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4345 5.6215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2851 5.0035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4680 2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8838 4.1945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 4.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6270 3.5254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5878 -0.8090 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 2.8412 4.7080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2905 5.1081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4400 5.5170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4930 4.0254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 12 1 0 0 0 0 2 4 2 0 0 0 0 2 13 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 6 15 2 0 0 0 0 7 12 2 0 0 0 0 7 18 1 0 0 0 0 8 13 2 0 0 0 0 8 19 1 0 0 0 0 9 14 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 10 25 1 0 0 0 0 11 24 1 0 0 0 0 11 26 1 0 0 0 0 14 5 1 1 0 0 0 14 15 1 0 0 0 0 15 20 1 0 0 0 0 16 18 2 0 0 0 0 16 23 1 0 0 0 0 17 19 2 0 0 0 0 17 24 1 0 0 0 0 18 25 1 0 0 0 0 19 26 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	352.09
Volume:	343.344
LogP:	3.931
LogD:	3.791
LogS:	-6.115
# Rotatable Bonds:	3
TPSA:	63.22
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.625
Synthetic Accessibility Score:	3.098
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.046
MDCK Permeability:	2.9305811040103436e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.023
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	99.70003509521484%
Volume Distribution (VD):	0.577
Pgp-substrate:	1.5363420248031616%

ADMET: Metabolism

CYP1A2-inhibitor:	0.989
CYP1A2-substrate:	0.143
CYP2C19-inhibitor:	0.983
CYP2C19-substrate:	0.083
CYP2C9-inhibitor:	0.913
CYP2C9-substrate:	0.775
CYP2D6-inhibitor:	0.987
CYP2D6-substrate:	0.852
CYP3A4-inhibitor:	0.976
CYP3A4-substrate:	0.223

ADMET: Excretion

Clearance (CL):	16.499
Half-life (T1/2):	0.192

ADMET: Toxicity

hERG Blockers:	0.103
Human Hepatotoxicity (H-HT):	0.166
Drug-inuced Liver Injury (DILI):	0.858
AMES Toxicity:	0.766
Rat Oral Acute Toxicity:	0.083
Maximum Recommended Daily Dose:	0.87
Skin Sensitization:	0.758
Carcinogencity:	0.876
Eye Corrosion:	0.003
Eye Irritation:	0.407
Respiratory Toxicity:	0.417

Download Data

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

Natural Product: NPC230968

Natural Product ID:	NPC230968
*Common Name:**	Savinin
IUPAC Name:	(3E,4R)-4-(1,3-benzodioxol-5-ylmethyl)-3-(1,3-benzodioxol-5-ylmethylidene)oxolan-2-one
Synonyms:	Savinin
Standard InCHIKey:	CMJGAYUQSLJSCR-ULIPXBITSA-N
Standard InCHI:	InChI=1S/C20H16O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,6-8,14H,5,9-11H2/b15-6+/t14-/m0/s1
SMILES:	O=C1OC[C@@H](/C/1=Cc1ccc2c(c1)OCO2)Cc1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL395263
PubChem CID:	5281867
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

*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
NPO8725	Aristolochia indica	Species	Aristolochiaceae	Eukaryota	roots	n.a.	n.a.	PMID[6539809]
NPO8500	Acanthopanax gracilistylus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32319765]
NPO18983	Cleidion brevipetiolatum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31419126]
NPO16966	Leptospermum scoparium	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26731565]
NPO16653	Matteuccia struthiopteris	Species	Onocleaceae	Eukaryota	rhizomes	Liaoning province, China	2011-SEP	PMID[25927664]
NPO9604	Amycolatopsis lurida	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25323720]
NPO1338	Arcangelisia gusanlung	Species	Menispermaceae	Eukaryota	n.a.	stem	n.a.	PMID[21500777]
NPO15275	Briareum asbestinum	Species	Briareidae	Eukaryota	n.a.	Caribbean	n.a.	PMID[1686898]
NPO21302	Cladosporium herbarum	Species	Cladosporiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16038560]
NPO8520	Mucor spinosus	Species	Mucoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844967]

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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	4
EC50	1
ED50	1
IC50	1
Ki	1
Others	4
Potency	13

Activity Type	# Activity
Cell Line	1
Individual Protein	11
NON-MOLECULAR	1
Organism	3
Others	9

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	16360.1	nM	PMID[537094]
NPT478	Individual Protein	Ataxin-2	Homo sapiens	Potency	n.a.	33587.5	nM	PMID[537094]
NPT101	Individual Protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency	n.a.	31622.8	nM	PMID[537094]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	8199.5	nM	PMID[537094]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	5804.8	nM	PMID[537094]
NPT160	Individual Protein	TAR DNA-binding protein 43	Homo sapiens	Potency	n.a.	22387.2	nM	PMID[537094]
NPT535	Individual Protein	Parathyroid hormone receptor	Homo sapiens	Potency	n.a.	63095.7	nM	PMID[537094]
NPT11	Individual Protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency	n.a.	35481.3	nM	PMID[537094]
NPT8	Individual Protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	28183.8	nM	PMID[537094]
NPT84	Individual Protein	Dual specificity tyrosine-phosphorylation-regulated kinase 1A	Rattus norvegicus	AC50	=	243.0	nM	PMID[537094]

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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 NPC230968 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	353
0.1-0.2	1432
0.2-0.3	3315
0.3-0.4	8841
0.4-0.5	10221
0.5-0.6	4901
0.6-0.7	11202
0.7-0.8	2192
0.8-0.85	182
0.85-0.9	44
0.9-0.95	10
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC102260
0.9692	High Similarity	NPC110958
0.9692	High Similarity	NPC19890
0.9466	High Similarity	NPC205915
0.9265	High Similarity	NPC218092

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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 NPC230968 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	291
0.1-0.2	873
0.2-0.3	1469
0.3-0.4	2628
0.4-0.5	2071
0.5-0.6	1214
0.6-0.7	528
0.7-0.8	74
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8472	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.8176	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.803	Intermediate Similarity	NPD5536	Phase 2
0.7987	Intermediate Similarity	NPD4967	Phase 2
0.7987	Intermediate Similarity	NPD4966	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