NPASS Compound

Structure

NPC471667 OpenBabel07101719252D 37 40 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4128 0.0296 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 6.9128 -4.3005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4128 -3.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 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 5.9128 -4.3005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9128 -2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4128 -1.7024 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 3.6915 -2.1637 0.0000 C 0 0 0 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 6.9128 -2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4128 -1.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4347 -1.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9128 -0.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9128 -0.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.4128 -5.1665 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7405 -1.8546 0.0000 O 0 0 0 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 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4128 0.0296 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 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2437 -0.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 32 1 0 0 0 0 3 33 1 0 0 0 0 4 34 1 0 0 0 0 5 6 1 0 0 0 0 5 9 1 0 0 0 0 6 15 1 0 0 0 0 7 8 2 0 0 0 0 7 16 1 0 0 0 0 8 19 1 0 0 0 0 9 28 1 0 0 0 0 10 15 2 0 0 0 0 10 17 1 0 0 0 0 11 15 1 0 0 0 0 11 21 2 0 0 0 0 12 16 2 0 0 0 0 12 20 1 0 0 0 0 13 29 1 0 0 0 0 14 1 1 1 0 0 0 14 22 1 0 0 0 0 14 35 1 0 0 0 0 17 18 1 0 0 0 0 17 25 2 0 0 0 0 18 13 1 1 0 0 0 18 24 1 0 0 0 0 19 20 2 0 0 0 0 19 36 1 0 0 0 0 20 32 1 0 0 0 0 21 25 1 0 0 0 0 21 33 1 0 0 0 0 22 26 1 0 0 0 0 22 30 1 6 0 0 0 23 26 1 0 0 0 0 23 27 1 0 0 0 0 23 31 1 1 0 0 0 24 16 1 6 0 0 0 24 37 1 0 0 0 0 25 37 1 0 0 0 0 26 34 1 1 0 0 0 27 35 1 0 0 0 0 27 36 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	520.23
Volume:	513.406
LogP:	1.753
LogD:	2.023
LogS:	-4.314
# Rotatable Bonds:	10
TPSA:	136.3
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.366
Synthetic Accessibility Score:	4.329
Fsp3:	0.556
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.441
MDCK Permeability:	5.0546546844998375e-05
Pgp-inhibitor:	0.791
Pgp-substrate:	0.894
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.281
Plasma Protein Binding (PPB):	60.45708465576172%
Volume Distribution (VD):	0.464
Pgp-substrate:	19.836870193481445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.745
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.854
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.373
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.473
CYP3A4-inhibitor:	0.3
CYP3A4-substrate:	0.714

ADMET: Excretion

Clearance (CL):	7.539
Half-life (T1/2):	0.374

ADMET: Toxicity

hERG Blockers:	0.245
Human Hepatotoxicity (H-HT):	0.351
Drug-inuced Liver Injury (DILI):	0.363
AMES Toxicity:	0.288
Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.124
Skin Sensitization:	0.71
Carcinogencity:	0.062
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC471667

Natural Product ID:	NPC471667
*Common Name:**	Juniperigiside
IUPAC Name:	(2S,3R,4R,5S,6S)-2-[4-[(2R,3S)-3-(hydroxymethyl)-5-(3-hydroxypropyl)-7-methoxy-2,3-dihydro-1-benzofuran-2-yl]-2-methoxyphenoxy]-4-methoxy-6-methyloxane-3,5-diol
Synonyms:
Standard InCHIKey:	HGJHDZJWZDHNTJ-YGDJOXSMSA-N
Standard InCHI:	InChI=1S/C27H36O10/c1-14-22(30)26(34-4)23(31)27(35-14)36-19-8-7-16(12-20(19)32-2)24-18(13-29)17-10-15(6-5-9-28)11-21(33-3)25(17)37-24/h7-8,10-12,14,18,22-24,26-31H,5-6,9,13H2,1-4H3/t14-,18+,22-,23+,24-,26+,27-/m0/s1
SMILES:	OCCCc1cc2[C@@H](CO)[C@@H](Oc2c(c1)OC)c1ccc(c(c1)OC)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3088136
PubChem CID:	75202314
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO29383	Abies holophylla	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30063340]
NPO29383	Abies holophylla	Species	Pinaceae	Eukaryota	Trunk	n.a.	n.a.	PMID[26812172]
NPO29383	Abies holophylla	Species	Pinaceae	Eukaryota	trunk	n.a.	n.a.	PMID[24224862]
NPO29383	Abies holophylla	Species	Pinaceae	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
Others	1

Activity Type	# Activity
Cell Line	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	159.0	%	PMID[555982]

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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 NPC471667 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	407
0.1-0.2	1436
0.2-0.3	3609
0.3-0.4	9240
0.4-0.5	9318
0.5-0.6	4882
0.6-0.7	8546
0.7-0.8	4147
0.8-0.85	798
0.85-0.9	255
0.9-0.95	43
0.95-1	16

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC217635
1.0	High Similarity	NPC79429
0.9927	High Similarity	NPC476301
0.9927	High Similarity	NPC43508
0.9784	High Similarity	NPC114505

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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 NPC471667 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	332
0.1-0.2	809
0.2-0.3	1701
0.3-0.4	2780
0.4-0.5	1805
0.5-0.6	998
0.6-0.7	608
0.7-0.8	110
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8944	High Similarity	NPD6674	Discontinued
0.8252	Intermediate Similarity	NPD1613	Approved
0.8252	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.8133	Intermediate Similarity	NPD5058	Phase 3
0.8129	Intermediate Similarity	NPD37	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