NPASS Compound

Structure

CID45400 OpenBabel06191715382D 32 35 0 0 1 0 0 0 0 0999 V2000 6.9282 1.0000 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 7.7942 1.5000 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 7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -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 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 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 8.6603 1.0000 0.0000 C 0 0 0 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 8.6603 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -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 2 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 3.4641 0.0000 0.0000 C 0 0 0 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 4.3301 -0.5000 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 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 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 9.5263 -0.5000 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 3.4641 1.0000 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 5.1962 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 8 1 0 0 0 0 2 4 2 0 0 0 0 2 9 1 0 0 0 0 3 10 1 0 0 0 0 4 13 1 0 0 0 0 5 8 2 0 0 0 0 5 12 1 0 0 0 0 6 11 1 0 0 0 0 6 14 1 0 0 0 0 7 22 1 0 0 0 0 9 11 1 0 0 0 0 9 20 2 0 0 0 0 10 12 2 0 0 0 0 10 23 1 0 0 0 0 11 24 2 0 0 0 0 12 25 1 0 0 0 0 13 17 2 0 0 0 0 13 31 1 0 0 0 0 14 8 1 6 0 0 0 14 30 1 0 0 0 0 15 7 1 1 0 0 0 15 16 1 0 0 0 0 15 32 1 0 0 0 0 16 18 1 0 0 0 0 16 26 1 6 0 0 0 17 20 1 0 0 0 0 17 27 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 1 0 0 0 19 21 1 0 0 0 0 19 29 1 6 0 0 0 20 30 1 0 0 0 0 21 31 1 1 0 0 0 21 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.12
Volume:	415.784
LogP:	-0.144
LogD:	-0.19
LogS:	-3.959
# Rotatable Bonds:	4
TPSA:	186.37
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.303
Synthetic Accessibility Score:	4.177
Fsp3:	0.381
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.274
MDCK Permeability:	1.3695655979972798e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.534
Human Intestinal Absorption (HIA):	0.131
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.097
Plasma Protein Binding (PPB):	87.0485610961914%
Volume Distribution (VD):	0.541
Pgp-substrate:	21.23603630065918%

ADMET: Metabolism

CYP1A2-inhibitor:	0.041
CYP1A2-substrate:	0.034
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.027
CYP2C9-substrate:	0.264
CYP2D6-inhibitor:	0.071
CYP2D6-substrate:	0.194
CYP3A4-inhibitor:	0.047
CYP3A4-substrate:	0.067

ADMET: Excretion

Clearance (CL):	6.94
Half-life (T1/2):	0.866

ADMET: Toxicity

hERG Blockers:	0.184
Human Hepatotoxicity (H-HT):	0.201
Drug-inuced Liver Injury (DILI):	0.948
AMES Toxicity:	0.633
Rat Oral Acute Toxicity:	0.499
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.935
Carcinogencity:	0.588
Eye Corrosion:	0.003
Eye Irritation:	0.3
Respiratory Toxicity:	0.072

Download Data

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

Natural Product: NPC45400

Natural Product ID:	NPC45400
*Common Name:**	Flavanomarein
IUPAC Name:	(2S)-2-(3,4-dihydroxyphenyl)-8-hydroxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,3-dihydrochromen-4-one
Synonyms:	Flavanomarein
Standard InCHIKey:	DGGOLFCPSUVVHX-RTHJTPBESA-N
Standard InCHI:	InChI=1S/C21H22O11/c22-7-15-16(26)18(28)19(29)21(32-15)31-13-4-2-9-11(24)6-14(30-20(9)17(13)27)8-1-3-10(23)12(25)5-8/h1-5,14-16,18-19,21-23,25-29H,6-7H2/t14-,15+,16+,18-,19+,21+/m0/s1
SMILES:	c1cc(c(cc1[C@@H]1CC(=O)c2ccc(c(c2O1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1405715
PubChem CID:	101781
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-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
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[25282892]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21625	Bidens tripartita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21625	Bidens tripartita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21625	Bidens tripartita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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	4
Potency	3

Activity Type	# Activity
CELL-LINE	1
Individual Protein	4
Organism	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT22036	CELL-LINE	HL	Homo sapiens	Activity	=	82.6	%	PMID[524814]
NPT5310	Organism	Chlamydophila pneumoniae	Chlamydophila pneumoniae	Inhibition	=	22.1	%	PMID[524814]
NPT66	Individual Protein	Acetylcholinesterase	Electrophorus electricus	Inhibition	=	8.08	%	PMID[524813]
NPT67	Individual Protein	Cholinesterase	Equus caballus	Inhibition	=	3.1	%	PMID[524813]
NPT199	Individual Protein	DNA polymerase kappa	Homo sapiens	Potency	n.a.	2667.9	nM	PMID[524812]
NPT49	Individual Protein	DNA-(apurinic or apyrimidinic site) lyase	Homo sapiens	Potency	n.a.	7943.3	nM	PMID[524812]
NPT2	Others	Unspecified		Potency	n.a.	31622.8	nM	PMID[524812]

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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 NPC45400 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	427
0.1-0.2	1733
0.2-0.3	3984
0.3-0.4	9426
0.4-0.5	8648
0.5-0.6	3980
0.6-0.7	4902
0.7-0.8	5721
0.8-0.85	2363
0.85-0.9	1060
0.9-0.95	408
0.95-1	45

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Similarity Score	Similarity Level	Natural Product ID
0.9937	High Similarity	NPC229687
0.9874	High Similarity	NPC471416
0.9874	High Similarity	NPC34287
0.9873	High Similarity	NPC165720
0.9811	High Similarity	NPC471457

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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 NPC45400 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	389
0.1-0.2	908
0.2-0.3	1894
0.3-0.4	2680
0.4-0.5	1810
0.5-0.6	923
0.6-0.7	369
0.7-0.8	131
0.8-0.85	25
0.85-0.9	13
0.9-0.95	8
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9627	High Similarity	NPD7074	Phase 3
0.9625	High Similarity	NPD3818	Discontinued
0.9565	High Similarity	NPD7054	Approved
0.9506	High Similarity	NPD7472	Approved
0.9367	High Similarity	NPD4381	Clinical (unspecified phase)

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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