NPASS Compound

Structure

CID48624 OpenBabel06191715382D 30 32 0 0 0 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 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 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 -4.3301 -0.5000 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 -3.4641 0.0000 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 -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 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 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 2.5981 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 0.8660 -0.5000 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 -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 -0.8660 -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 0.0000 0.0000 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 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 O 0 0 0 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 14 1 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 4 15 1 0 0 0 0 5 7 1 0 0 0 0 5 14 2 0 0 0 0 6 9 1 0 0 0 0 6 15 2 0 0 0 0 7 17 1 0 0 0 0 8 10 2 0 0 0 0 8 16 1 0 0 0 0 9 18 1 0 0 0 0 10 20 1 0 0 0 0 11 16 2 0 0 0 0 11 17 1 0 0 0 0 12 21 2 0 0 0 0 12 22 1 0 0 0 0 13 19 2 0 0 0 0 13 30 1 0 0 0 0 16 19 1 0 0 0 0 17 20 2 0 0 0 0 18 21 1 0 0 0 0 18 24 2 0 0 0 0 19 25 1 0 0 0 0 20 26 1 0 0 0 0 21 27 1 0 0 0 0 22 23 2 0 0 0 0 22 30 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 24 28 1 0 0 0 0 25 29 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	406.18
Volume:	432.873
LogP:	6.395
LogD:	3.379
LogS:	-2.699
# Rotatable Bonds:	5
TPSA:	90.9
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.48
Synthetic Accessibility Score:	3.01
Fsp3:	0.24
Lipinski Rule-of-5:	Accepted
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:	-4.792
MDCK Permeability:	1.2414256161719095e-05
Pgp-inhibitor:	0.865
Pgp-substrate:	0.492
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.987
30% Bioavailability (F30%):	0.945

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	92.18101501464844%
Volume Distribution (VD):	1.034
Pgp-substrate:	8.261439323425293%

ADMET: Metabolism

CYP1A2-inhibitor:	0.787
CYP1A2-substrate:	0.176
CYP2C19-inhibitor:	0.926
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.851
CYP2C9-substrate:	0.892
CYP2D6-inhibitor:	0.691
CYP2D6-substrate:	0.379
CYP3A4-inhibitor:	0.172
CYP3A4-substrate:	0.086

ADMET: Excretion

Clearance (CL):	8.048
Half-life (T1/2):	0.36

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.734
Drug-inuced Liver Injury (DILI):	0.414
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.522
Maximum Recommended Daily Dose:	0.173
Skin Sensitization:	0.934
Carcinogencity:	0.078
Eye Corrosion:	0.003
Eye Irritation:	0.805
Respiratory Toxicity:	0.165

Download Data

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

Natural Product: NPC48624

Natural Product ID:	NPC48624
*Common Name:**	Lupalbigenin
IUPAC Name:	5,7-dihydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]-6-(3-methylbut-2-enyl)chromen-4-one
Synonyms:	Lupalbigenin
Standard InCHIKey:	HTAZIHDXIUPDQP-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H26O5/c1-14(2)5-7-17-11-16(8-10-20(17)26)19-13-30-22-12-21(27)18(9-6-15(3)4)24(28)23(22)25(19)29/h5-6,8,10-13,26-28H,7,9H2,1-4H3
SMILES:	CC(=CCc1cc(ccc1O)c1coc2c(c1=O)c(O)c(c(c2)O)CC=C(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL463936
PubChem CID:	10001388
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001827] Isoflavanones [CHEMONTID:0003526] 6-prenylated isoflavanones

*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
NPO19231	Sophora flavescens	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[9868163]
NPO19231	Sophora flavescens	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30298740]
NPO19231	Sophora flavescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27575476]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24459770]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24333010]
NPO19231	Sophora flavescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295087]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	bark	n.a.	PMID[21553897]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21314138]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19969457]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19407970]

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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	30

Activity Type	# Activity
Organism	30

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	62.7	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	32.8	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	9.5	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	9.1	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	mortality	=	26.4	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	mortality	=	32.2	%	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	612.0	mg	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	Activity	=	587.0	mg	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	TIME	=	273.6	hr	PMID[545391]
NPT2747	Organism	Achaea janata	Achaea janata	TIME	=	309.6	hr	PMID[545391]

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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 NPC48624 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	391
0.1-0.2	1579
0.2-0.3	3841
0.3-0.4	10204
0.4-0.5	8329
0.5-0.6	3741
0.6-0.7	5714
0.7-0.8	4735
0.8-0.85	2004
0.85-0.9	1464
0.9-0.95	577
0.95-1	118

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC80962
1.0	High Similarity	NPC219917
1.0	High Similarity	NPC172250
1.0	High Similarity	NPC259166
1.0	High Similarity	NPC215311

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 NPC48624 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	350
0.1-0.2	955
0.2-0.3	1474
0.3-0.4	2603
0.4-0.5	1967
0.5-0.6	1188
0.6-0.7	412
0.7-0.8	126
0.8-0.85	46
0.85-0.9	24
0.9-0.95	4
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9627	High Similarity	NPD1510	Phase 2
0.9429	High Similarity	NPD4378	Clinical (unspecified phase)
0.9328	High Similarity	NPD1240	Approved
0.9236	High Similarity	NPD4380	Phase 2
0.9191	High Similarity	NPD1607	Approved

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