NPASS Compound

Structure

CID139966 OpenBabel06191715502D 27 29 0 0 1 0 0 0 0 0999 V2000 -6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.0000 0.0000 C 0 0 0 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 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 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 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 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 -2.5981 -1.5000 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 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 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 0.8660 -1.5000 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 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 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 2.5981 0.5000 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 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 -3.4641 -3.0000 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 1 6 1 0 0 0 0 2 6 1 0 0 0 0 3 7 1 0 0 0 0 3 9 2 0 0 0 0 4 8 2 0 0 0 0 4 10 1 0 0 0 0 5 19 1 0 0 0 0 6 9 1 0 0 0 0 7 12 1 0 0 0 0 7 20 2 0 0 0 0 8 13 1 0 0 0 0 8 21 1 0 0 0 0 9 26 1 0 0 0 0 10 12 2 0 0 0 0 10 26 1 0 0 0 0 11 5 1 6 0 0 0 11 14 1 0 0 0 0 11 27 1 0 0 0 0 12 15 1 0 0 0 0 13 15 2 0 0 0 0 14 16 1 0 0 0 0 14 22 1 1 0 0 0 15 23 1 0 0 0 0 16 17 1 0 0 0 0 16 24 1 6 0 0 0 17 18 1 0 0 0 0 17 25 1 1 0 0 0 18 13 1 6 0 0 0 18 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	382.13
Volume:	360.145
LogP:	0.632
LogD:	0.024
LogS:	-2.355
# Rotatable Bonds:	3
TPSA:	160.82
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.424
Synthetic Accessibility Score:	4.104
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.881
MDCK Permeability:	6.163566922623431e-06
Pgp-inhibitor:	0.01
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.784
20% Bioavailability (F20%):	0.056
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	84.58177947998047%
Volume Distribution (VD):	1.061
Pgp-substrate:	14.938312530517578%

ADMET: Metabolism

CYP1A2-inhibitor:	0.086
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.342
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.686
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.168
CYP3A4-inhibitor:	0.017
CYP3A4-substrate:	0.034

ADMET: Excretion

Clearance (CL):	1.725
Half-life (T1/2):	0.805

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.176
Drug-inuced Liver Injury (DILI):	0.873
AMES Toxicity:	0.647
Rat Oral Acute Toxicity:	0.041
Maximum Recommended Daily Dose:	0.027
Skin Sensitization:	0.51
Carcinogencity:	0.034
Eye Corrosion:	0.003
Eye Irritation:	0.093
Respiratory Toxicity:	0.107

Download Data

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

Natural Product: NPC139966

Natural Product ID:	NPC139966
*Common Name:**	6-Beta-C-Glucopyranosyl-5,7-Dihydroxy-2-Isopropylchromone
IUPAC Name:	5,7-dihydroxy-2-propan-2-yl-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one
Synonyms:
Standard InCHIKey:	NSNHBTNFVNVELM-PWUYNPNPSA-N
Standard InCHI:	InChI=1S/C18H22O9/c1-6(2)9-3-7(20)12-10(26-9)4-8(21)13(15(12)23)18-17(25)16(24)14(22)11(5-19)27-18/h3-4,6,11,14,16-19,21-25H,5H2,1-2H3/t11-,14-,16+,17-,18+/m1/s1
SMILES:	CC(C)c1cc(=O)c2c(cc(c(c2O)[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)o1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL465160
PubChem CID:	5317687
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO11277	Baeckea frutescens	Species	Myrtaceae	Eukaryota	aerial parts	Nanning, Guangxi Province, China	2014-OCT	PMID[28753309]
NPO22637	Kunzea ambigua	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043420]
NPO11277	Baeckea frutescens	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932146]
NPO11277	Baeckea frutescens	Species	Myrtaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(98)00534-2]
NPO11277	Baeckea frutescens	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22637	Kunzea ambigua	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11277	Baeckea frutescens	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

Showing 1 to 7 of 7 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	8

Activity Type	# Activity
Cell Line	4
Others	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	70.0	%	PMID[526594]
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	80.0	%	PMID[526594]
NPT2	Others	Unspecified	""	Inhibition	=	4.6	%	PMID[526594]
NPT2	Others	Unspecified	""	Inhibition	=	23.7	%	PMID[526594]
NPT2	Others	Unspecified	""	Inhibition	=	65.0	%	PMID[526594]
NPT2	Others	Unspecified	""	Inhibition	=	91.0	%	PMID[526594]

Showing 1 to 6 of 6 entries

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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 NPC139966 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	389
0.1-0.2	1452
0.2-0.3	3290
0.3-0.4	8468
0.4-0.5	10542
0.5-0.6	3946
0.6-0.7	5587
0.7-0.8	4798
0.8-0.85	2688
0.85-0.9	1398
0.9-0.95	133
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC307052
0.993	High Similarity	NPC10097
0.972	High Similarity	NPC470670
0.972	High Similarity	NPC47388
0.972	High Similarity	NPC473133

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 NPC139966 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	335
0.1-0.2	854
0.2-0.3	1704
0.3-0.4	2597
0.4-0.5	2009
0.5-0.6	1075
0.6-0.7	391
0.7-0.8	132
0.8-0.85	39
0.85-0.9	13
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9388	High Similarity	NPD4380	Phase 2
0.9073	High Similarity	NPD2393	Clinical (unspecified phase)
0.9048	High Similarity	NPD4378	Clinical (unspecified phase)
0.902	High Similarity	NPD7075	Discontinued
0.902	High Similarity	NPD4381	Clinical (unspecified phase)

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