NPASS Compound

Structure

CID62840 OpenBabel06191715402D 31 34 0 0 0 0 0 0 0 0999 V2000 6.9282 -3.0000 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 -0.5000 1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 1.0000 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 6.9282 0.0000 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 6.0622 -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 0.8660 1.5000 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 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 4.3301 -1.5000 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 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 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 -2.0000 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 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 -3.0000 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 3.4641 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 13 1 0 0 0 0 2 13 1 0 0 0 0 3 25 1 0 0 0 0 4 25 1 0 0 0 0 5 7 1 0 0 0 0 5 13 2 0 0 0 0 6 8 2 0 0 0 0 6 14 1 0 0 0 0 7 17 1 0 0 0 0 8 15 1 0 0 0 0 9 10 2 0 0 0 0 9 16 1 0 0 0 0 10 25 1 0 0 0 0 11 14 2 0 0 0 0 11 18 1 0 0 0 0 12 19 2 0 0 0 0 12 20 1 0 0 0 0 14 26 1 0 0 0 0 15 18 2 0 0 0 0 15 23 1 0 0 0 0 16 20 2 0 0 0 0 16 24 1 0 0 0 0 17 22 1 0 0 0 0 17 23 2 0 0 0 0 18 27 1 0 0 0 0 19 21 1 0 0 0 0 19 28 1 0 0 0 0 20 31 1 0 0 0 0 21 22 1 0 0 0 0 21 24 2 0 0 0 0 22 29 2 0 0 0 0 23 30 1 0 0 0 0 24 30 1 0 0 0 0 25 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	420.16
Volume:	433.107
LogP:	5.973
LogD:	4.02
LogS:	-2.713
# Rotatable Bonds:	3
TPSA:	100.13
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.499
Synthetic Accessibility Score:	3.284
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:	-4.874
MDCK Permeability:	1.5354929928435013e-05
Pgp-inhibitor:	0.249
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.051
20% Bioavailability (F20%):	0.027
30% Bioavailability (F30%):	0.223

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	97.67343139648438%
Volume Distribution (VD):	0.564
Pgp-substrate:	3.7040040493011475%

ADMET: Metabolism

CYP1A2-inhibitor:	0.858
CYP1A2-substrate:	0.189
CYP2C19-inhibitor:	0.906
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.882
CYP2C9-substrate:	0.94
CYP2D6-inhibitor:	0.896
CYP2D6-substrate:	0.271
CYP3A4-inhibitor:	0.516
CYP3A4-substrate:	0.105

ADMET: Excretion

Clearance (CL):	4.881
Half-life (T1/2):	0.31

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.952
Drug-inuced Liver Injury (DILI):	0.981
AMES Toxicity:	0.645
Rat Oral Acute Toxicity:	0.519
Maximum Recommended Daily Dose:	0.861
Skin Sensitization:	0.419
Carcinogencity:	0.855
Eye Corrosion:	0.003
Eye Irritation:	0.287
Respiratory Toxicity:	0.554

Download Data

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

Natural Product: NPC62840

Natural Product ID:	NPC62840
*Common Name:**	Morusin
IUPAC Name:	2-(2,4-dihydroxyphenyl)-5-hydroxy-8,8-dimethyl-3-(3-methylbut-2-enyl)pyrano[2,3-h]chromen-4-one
Synonyms:	TCMDC-124149
Standard InCHIKey:	XFFOMNJIDRDDLQ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H24O6/c1-13(2)5-7-17-22(29)21-19(28)12-20-16(9-10-25(3,4)31-20)24(21)30-23(17)15-8-6-14(26)11-18(15)27/h5-6,8-12,26-28H,7H2,1-4H3
SMILES:	CC(=CCc1c(oc2c(c1=O)c(O)cc1c2C=CC(O1)(C)C)c1ccc(cc1O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464006
PubChem CID:	5281671
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0003501] 3-prenylated flavones

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11796	Morus australis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9358644]
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]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[29140705]
NPO11796	Morus australis	Species	Moraceae	Eukaryota	Root Bark	n.a.	n.a.	PMID[27908762]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO9090	Patrinia villosa	Species	Caprifoliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[27019553]
NPO33150	Artocarpus communis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26178912]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]

Showing 1 to 10 of 76 entries

Previous1 2 3 4 5…8Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
EC50	4
IC50	29
Ki	2
Others	44
Potency	19

Activity Type	# Activity
Cell Line	14
CELL-LINE	4
Individual Protein	36
NON-MOLECULAR	21
Organism	11
Others	9
SINGLE PROTEIN	3

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT5536	Individual Protein	Sarcoplasmic/endoplasmic reticulum calcium ATP-ase	Oryctolagus cuniculus	IC50	=	43570.0	nM	PMID[482610]
NPT6571	Individual Protein	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	Rattus norvegicus	IC50	=	28650.0	nM	PMID[482610]
NPT1872	Cell Line	Bcap37	Homo sapiens	IC50	=	33100.0	nM	PMID[482609]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	11510.0	nM	PMID[482609]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	9300.0	nM	PMID[482609]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	24090.0	nM	PMID[482609]
NPT380	Cell Line	U-251	Homo sapiens	IC50	=	17950.0	nM	PMID[482609]
NPT3997	Individual Protein	Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP	Homo sapiens	IC50	=	14970.0	nM	PMID[482608]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	10320.0	nM	PMID[482608]
NPT3985	Individual Protein	Probable low molecular weight protein-tyrosine-phosphatase	Mycobacterium tuberculosis	IC50	=	4650.0	nM	PMID[482608]

Showing 1 to 10 of 89 entries

Previous1 2 3 4 5…9Next

☑ 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 NPC62840 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	408
0.1-0.2	1667
0.2-0.3	4321
0.3-0.4	11386
0.4-0.5	6799
0.5-0.6	4076
0.6-0.7	5959
0.7-0.8	4200
0.8-0.85	1910
0.85-0.9	1331
0.9-0.95	569
0.95-1	71

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC299080
1.0	High Similarity	NPC59739
1.0	High Similarity	NPC293852
1.0	High Similarity	NPC214236
1.0	High Similarity	NPC217083

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC62840 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	367
0.1-0.2	957
0.2-0.3	1471
0.3-0.4	2678
0.4-0.5	1959
0.5-0.6	1167
0.6-0.7	364
0.7-0.8	123
0.8-0.85	39
0.85-0.9	22
0.9-0.95	3
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9571	High Similarity	NPD7410	Clinical (unspecified phase)
0.9433	High Similarity	NPD4378	Clinical (unspecified phase)
0.9071	High Similarity	NPD1550	Clinical (unspecified phase)
0.9071	High Similarity	NPD1552	Clinical (unspecified phase)
0.9007	High Similarity	NPD1549	Phase 2

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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