NPASS Compound

Structure

CID278476 OpenBabel06191716082D 31 33 0 0 1 0 0 0 0 0999 V2000 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 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 3.4641 -3.0000 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 2.5981 -1.5000 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 -2.5981 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 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 -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 -3.4641 -4.0000 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 -2.5981 -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 1.7321 -0.0000 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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 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 0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 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 0.5000 0.0000 C 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 3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 4 14 1 0 0 0 0 5 7 1 0 0 0 0 5 13 2 0 0 0 0 6 9 1 0 0 0 0 6 14 2 0 0 0 0 7 15 1 0 0 0 0 8 10 1 0 0 0 0 8 16 2 0 0 0 0 9 17 1 0 0 0 0 10 18 2 0 0 0 0 11 15 2 0 0 0 0 11 16 1 0 0 0 0 12 19 2 0 0 0 0 12 20 1 0 0 0 0 15 18 1 0 0 0 0 17 19 1 0 0 0 0 17 25 2 0 0 0 0 18 26 1 0 0 0 0 19 27 1 0 0 0 0 20 21 2 0 0 0 0 20 28 1 0 0 0 0 21 22 1 0 0 0 0 21 25 1 0 0 0 0 22 23 1 0 0 0 0 22 29 2 0 0 0 0 23 24 1 0 0 0 0 23 30 1 1 0 0 0 24 16 1 6 0 0 0 24 31 1 0 0 0 0 25 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	424.19
Volume:	444.3
LogP:	5.688
LogD:	3.674
LogS:	-2.72
# Rotatable Bonds:	5
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.527
Synthetic Accessibility Score:	3.863
Fsp3:	0.32
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.937
MDCK Permeability:	1.313045959250303e-05
Pgp-inhibitor:	0.631
Pgp-substrate:	0.118
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.939
30% Bioavailability (F30%):	0.165

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008
Plasma Protein Binding (PPB):	95.67901611328125%
Volume Distribution (VD):	0.691
Pgp-substrate:	4.549530982971191%

ADMET: Metabolism

CYP1A2-inhibitor:	0.193
CYP1A2-substrate:	0.169
CYP2C19-inhibitor:	0.684
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.862
CYP2C9-substrate:	0.901
CYP2D6-inhibitor:	0.934
CYP2D6-substrate:	0.27
CYP3A4-inhibitor:	0.389
CYP3A4-substrate:	0.162

ADMET: Excretion

Clearance (CL):	10.453
Half-life (T1/2):	0.16

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.423
Drug-inuced Liver Injury (DILI):	0.859
AMES Toxicity:	0.058
Rat Oral Acute Toxicity:	0.269
Maximum Recommended Daily Dose:	0.087
Skin Sensitization:	0.83
Carcinogencity:	0.056
Eye Corrosion:	0.003
Eye Irritation:	0.416
Respiratory Toxicity:	0.112

Download Data

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

Natural Product: NPC278476

Natural Product ID:	NPC278476
*Common Name:**	(2R,3R)-Lespedezaflavanone C
IUPAC Name:	(2R,3R)-3,5,7-trihydroxy-2-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]-8-(3-methylbut-2-enyl)-2,3-dihydrochromen-4-one
Synonyms:	(2R,3R)-Lespedezaflavanone C
Standard InCHIKey:	WFHBGCVPESHDKZ-BJKOFHAPSA-N
Standard InCHI:	InChI=1S/C25H28O6/c1-13(2)5-7-15-11-16(8-10-18(15)26)24-23(30)22(29)21-20(28)12-19(27)17(25(21)31-24)9-6-14(3)4/h5-6,8,10-12,23-24,26-28,30H,7,9H2,1-4H3/t23-,24+/m0/s1
SMILES:	CC(=CCc1cc(ccc1O)[C@@H]1[C@H](C(=O)c2c(cc(c(CC=C(C)C)c2O1)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL463256
PubChem CID:	14542252
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans [CHEMONTID:0003508] 8-prenylated flavanones

*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
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9358644]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	formosan	n.a.	PMID[8864236]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	Fruits	n.a.	n.a.	PMID[19296617]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	leaves	Kaohsiung, Taiwan	2006-SEP	PMID[18986201]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12419367]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	whole plants	n.a.	n.a.	PMID[11678652]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	whole plants	Shawnee National Forest, Harrisburg, IL, US	n.a.	PMID[11678652]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[11395279]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5495	Broussonetia papyrifera	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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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
IC50	1

Activity Type	# Activity
Individual Protein	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	IC50	>	40.0	ug.mL-1	PMID[571185]

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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 NPC278476 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	380
0.1-0.2	1405
0.2-0.3	3588
0.3-0.4	8679
0.4-0.5	9761
0.5-0.6	3646
0.6-0.7	5131
0.7-0.8	5287
0.8-0.85	2754
0.85-0.9	1422
0.9-0.95	552
0.95-1	92

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC254412
1.0	High Similarity	NPC262039
1.0	High Similarity	NPC319910
1.0	High Similarity	NPC262038
0.9931	High Similarity	NPC105136

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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 NPC278476 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	861
0.2-0.3	1656
0.3-0.4	2577
0.4-0.5	1892
0.5-0.6	1107
0.6-0.7	495
0.7-0.8	171
0.8-0.85	36
0.85-0.9	12
0.9-0.95	11
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9448	High Similarity	NPD4378	Clinical (unspecified phase)
0.9404	High Similarity	NPD7075	Discontinued
0.9392	High Similarity	NPD4380	Phase 2
0.9333	High Similarity	NPD7096	Clinical (unspecified phase)
0.9333	High Similarity	NPD2393	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