NPASS Compound

Structure

CID117596 OpenBabel06191715472D 29 30 0 0 1 0 0 0 0 0999 V2000 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 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 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 4 2 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 5 12 1 0 0 0 0 6 19 1 0 0 0 0 7 10 2 0 0 0 0 7 27 1 0 0 0 0 8 4 1 6 0 0 0 8 9 1 0 0 0 0 8 17 1 0 0 0 0 9 5 1 6 0 0 0 9 10 1 0 0 0 0 10 16 1 0 0 0 0 11 6 1 1 0 0 0 11 13 1 0 0 0 0 11 28 1 0 0 0 0 12 20 2 0 0 0 0 12 25 1 0 0 0 0 13 14 1 0 0 0 0 13 21 1 6 0 0 0 14 15 1 0 0 0 0 14 22 1 1 0 0 0 15 18 1 0 0 0 0 15 23 1 6 0 0 0 16 24 2 0 0 0 0 16 26 1 0 0 0 0 17 27 1 0 0 0 0 17 29 1 1 0 0 0 18 28 1 0 0 0 0 18 29 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	418.15
Volume:	388.918
LogP:	0.169
LogD:	0.088
LogS:	-1.024
# Rotatable Bonds:	9
TPSA:	161.21
# H-Bond Aceptor:	11
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.273
Synthetic Accessibility Score:	4.562
Fsp3:	0.667
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:	-5.859
MDCK Permeability:	0.00012338200758676976
Pgp-inhibitor:	0.001
Pgp-substrate:	0.211
Human Intestinal Absorption (HIA):	0.958
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.448
Plasma Protein Binding (PPB):	25.40500831604004%
Volume Distribution (VD):	0.377
Pgp-substrate:	55.31619644165039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.315
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.349
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.033
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.022
CYP3A4-substrate:	0.173

ADMET: Excretion

Clearance (CL):	1.965
Half-life (T1/2):	0.938

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.418
Drug-inuced Liver Injury (DILI):	0.508
AMES Toxicity:	0.075
Rat Oral Acute Toxicity:	0.27
Maximum Recommended Daily Dose:	0.098
Skin Sensitization:	0.092
Carcinogencity:	0.887
Eye Corrosion:	0.003
Eye Irritation:	0.029
Respiratory Toxicity:	0.795

Download Data

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

Natural Product: NPC117596

Natural Product ID:	NPC117596
*Common Name:**	Dimethyl Secoxyloganoside
IUPAC Name:	methyl (2S,3R,4S)-3-ethenyl-4-(2-methoxy-2-oxoethyl)-2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3,4-dihydro-2H-pyran-5-carboxylate
Synonyms:
Standard InCHIKey:	MPCHHOVJEMEKKG-VPNMNMBESA-N
Standard InCHI:	InChI=1S/C18H26O11/c1-4-8-9(5-12(20)25-2)10(16(24)26-3)7-27-17(8)29-18-15(23)14(22)13(21)11(6-19)28-18/h4,7-9,11,13-15,17-19,21-23H,1,5-6H2,2-3H3/t8-,9+,11-,13-,14+,15-,17+,18+/m1/s1
SMILES:	C=C[C@@H]1[C@H](CC(=O)OC)C(=CO[C@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3092673
PubChem CID:	14105070
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO9096	Scutellaria lateriflora	Species	Lamiaceae	Eukaryota	aerial part	n.a.	n.a.	PMID[25442304]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[24279769]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23265495]
NPO17072	Lonicera macranthoides	Species	Caprifoliaceae	Eukaryota	n.a.	flower bud	n.a.	PMID[22822669]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower bud	n.a.	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	flower buds	Henan province, China	2005-MAY	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower	n.a.	PMID[21804227]
NPO9096	Scutellaria lateriflora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19555121]
NPO9096	Scutellaria lateriflora	Species	Lamiaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[19555121]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[18321056]

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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
Others	1

Activity Type	# Activity
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	<	30.0	%	PMID[485134]

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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 NPC117596 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	200
0.1-0.2	1592
0.2-0.3	5449
0.3-0.4	12092
0.4-0.5	13267
0.5-0.6	8106
0.6-0.7	1722
0.7-0.8	221
0.8-0.85	9
0.85-0.9	29
0.9-0.95	8
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9651	High Similarity	NPC472125
0.9651	High Similarity	NPC472126
0.9651	High Similarity	NPC472124
0.954	High Similarity	NPC61201
0.9535	High Similarity	NPC307699

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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 NPC117596 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	180
0.1-0.2	2102
0.2-0.3	3900
0.3-0.4	2008
0.4-0.5	739
0.5-0.6	195
0.6-0.7	23
0.7-0.8	3
0.8-0.85	0
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
0.7264	Intermediate Similarity	NPD6686	Approved
0.7157	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD46	Approved
0.7143	Intermediate Similarity	NPD6698	Approved
0.681	Remote Similarity	NPD8513	Phase 3

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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