NPASS Compound

Structure

CID13171 OpenBabel06191715342D 28 30 0 0 1 0 0 0 0 0999 V2000 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 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 -1.8549 2.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 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 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 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 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 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 -2.8060 2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1118 2.1180 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 2.5981 1.5000 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 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.4563 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 -0.0000 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 1 25 1 0 0 0 0 2 3 2 0 0 0 0 3 17 1 0 0 0 0 4 18 1 0 0 0 0 5 8 2 0 0 0 0 5 26 1 0 0 0 0 6 17 1 0 0 0 0 6 19 1 0 0 0 0 7 2 1 1 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 14 1 0 0 0 0 9 4 1 1 0 0 0 9 11 1 0 0 0 0 9 27 1 0 0 0 0 10 15 1 0 0 0 0 10 17 1 1 0 0 0 11 12 1 0 0 0 0 11 20 1 6 0 0 0 12 13 1 0 0 0 0 12 21 1 1 0 0 0 13 16 1 0 0 0 0 13 22 1 6 0 0 0 14 23 2 0 0 0 0 14 25 1 0 0 0 0 15 26 1 0 0 0 0 15 28 1 6 0 0 0 16 27 1 0 0 0 0 16 28 1 1 0 0 0 17 24 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	404.13
Volume:	365.702
LogP:	-0.603
LogD:	-0.579
LogS:	-0.934
# Rotatable Bonds:	6
TPSA:	175.37
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	4.928
Fsp3:	0.706
Lipinski Rule-of-5:	Rejected
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:	-5.941
MDCK Permeability:	0.0001482335792388767
Pgp-inhibitor:	0.0
Pgp-substrate:	0.151
Human Intestinal Absorption (HIA):	0.138
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.212
Plasma Protein Binding (PPB):	18.666656494140625%
Volume Distribution (VD):	0.326
Pgp-substrate:	54.98667907714844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.401
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.09
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.024
CYP3A4-substrate:	0.082

ADMET: Excretion

Clearance (CL):	1.443
Half-life (T1/2):	0.849

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.149
Drug-inuced Liver Injury (DILI):	0.362
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.15
Carcinogencity:	0.931
Eye Corrosion:	0.003
Eye Irritation:	0.06
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC13171

Natural Product ID:	NPC13171
*Common Name:**	Gardenoside
IUPAC Name:	methyl (1S,4aS,7S,7aS)-7-hydroxy-7-(hydroxymethyl)-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4a,7a-dihydro-1H-cyclopenta[c]pyran-4-carboxylate
Synonyms:	Gardenoside
Standard InCHIKey:	XJMPAUZQVRGFRE-AYDWLWLASA-N
Standard InCHI:	InChI=1S/C17H24O11/c1-25-14(23)8-5-26-15(10-7(8)2-3-17(10,24)6-19)28-16-13(22)12(21)11(20)9(4-18)27-16/h2-3,5,7,9-13,15-16,18-22,24H,4,6H2,1H3/t7-,9-,10-,11-,12+,13-,15+,16+,17-/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@@H]3[C@H]2[C@](O)(CO)C=C3)C(=O)OC)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1079679
PubChem CID:	442423
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-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
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141747]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23305920]
NPO23142	Lamium album	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19904996]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[19650637]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[18505286]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1667413]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	Seoul, Korea	2000-Jun	PMID[16643034]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[16309325]
NPO8164	Haliclona vansoesti	Species	Chalinidae	Eukaryota	n.a.	caribbean	n.a.	PMID[10924178]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10425120]

Showing 1 to 10 of 25 entries

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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	7

Activity Type	# Activity
Cell Line	1
Organism	2
Others	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	Inhibition	=	-3.4	%	PMID[449643]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	Inhibition	=	21.1	%	PMID[449643]
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	80.0	%	PMID[449642]
NPT2	Others	Unspecified	""	Inhibition	=	92.6	%	PMID[449642]
NPT2	Others	Unspecified	""	Inhibition	=	100.0	%	PMID[449642]

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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 NPC13171 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	211
0.1-0.2	1282
0.2-0.3	4438
0.3-0.4	8022
0.4-0.5	14653
0.5-0.6	9132
0.6-0.7	4389
0.7-0.8	494
0.8-0.85	46
0.85-0.9	10
0.9-0.95	15
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC195510
0.9394	High Similarity	NPC254538
0.9394	High Similarity	NPC474285
0.9375	High Similarity	NPC255677
0.9375	High Similarity	NPC22149

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 NPC13171 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	1609
0.2-0.3	3807
0.3-0.4	2346
0.4-0.5	858
0.5-0.6	284
0.6-0.7	70
0.7-0.8	4
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
0.7706	Intermediate Similarity	NPD6686	Approved
0.7521	Intermediate Similarity	NPD8513	Phase 3
0.75	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7453	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7373	Intermediate Similarity	NPD8515	Approved

Showing 1 to 5 of 179 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