NPASS Compound

Structure

NPC475144 OpenBabel07101718302D 50 53 0 0 0 0 0 0 0 0999 V2000 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 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 -3.4641 0.0000 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -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 0.0000 5.0000 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 6.9282 -1.0000 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 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 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 3.4641 2.0000 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 -1.7321 2.0000 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 -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 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 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 3.4641 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 -2.5981 1.5000 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 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 4.3301 0.5000 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 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 -1.5000 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 0.0000 3.0000 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 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 4.3301 1.5000 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 -1.7321 -3.0000 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 0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 5 27 1 0 0 0 0 6 27 1 0 0 0 0 7 45 1 0 0 0 0 8 46 1 0 0 0 0 9 47 1 0 0 0 0 10 48 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 12 14 1 0 0 0 0 13 15 2 0 0 0 0 14 28 2 0 0 0 0 15 28 1 0 0 0 0 16 19 1 0 0 0 0 16 25 2 0 0 0 0 17 20 1 0 0 0 0 17 26 2 0 0 0 0 18 21 1 0 0 0 0 18 27 2 0 0 0 0 19 29 1 0 0 0 0 20 30 1 0 0 0 0 21 31 1 0 0 0 0 22 29 2 0 0 0 0 22 35 1 0 0 0 0 23 33 2 0 0 0 0 23 34 1 0 0 0 0 24 32 1 0 0 0 0 24 49 1 0 0 0 0 28 32 1 0 0 0 0 29 36 1 0 0 0 0 30 33 1 0 0 0 0 30 40 2 0 0 0 0 31 36 2 0 0 0 0 31 39 1 0 0 0 0 32 43 2 0 0 0 0 33 45 1 0 0 0 0 34 37 2 0 0 0 0 34 46 1 0 0 0 0 35 39 2 0 0 0 0 35 47 1 0 0 0 0 36 41 1 0 0 0 0 37 38 1 0 0 0 0 37 40 1 0 0 0 0 38 42 1 0 0 0 0 38 44 2 0 0 0 0 39 48 1 0 0 0 0 40 50 1 0 0 0 0 41 42 2 0 0 0 0 41 50 1 0 0 0 0 42 49 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	680.33
Volume:	731.537
LogP:	8.842
LogD:	4.813
LogS:	-4.932
# Rotatable Bonds:	15
TPSA:	93.43
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.091
Synthetic Accessibility Score:	3.489
Fsp3:	0.333
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.838
MDCK Permeability:	1.3124910765327513e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.085
Human Intestinal Absorption (HIA):	0.032
20% Bioavailability (F20%):	0.043
30% Bioavailability (F30%):	0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	66.56458282470703%
Volume Distribution (VD):	0.847
Pgp-substrate:	36.16849899291992%

ADMET: Metabolism

CYP1A2-inhibitor:	0.049
CYP1A2-substrate:	0.718
CYP2C19-inhibitor:	0.82
CYP2C19-substrate:	0.277
CYP2C9-inhibitor:	0.964
CYP2C9-substrate:	0.93
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.449
CYP3A4-inhibitor:	0.548
CYP3A4-substrate:	0.199

ADMET: Excretion

Clearance (CL):	8.794
Half-life (T1/2):	0.035

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.981
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.059
Rat Oral Acute Toxicity:	0.035
Maximum Recommended Daily Dose:	0.022
Skin Sensitization:	0.179
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.368

Download Data

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

Natural Product: NPC475144

Natural Product ID:	NPC475144
*Common Name:**	2-[3,4-Dimethoxy-2,6-Bis(3-Methylbut-2-Enyl)Phenyl]-5,7-Dimethoxy-8-(3-Methylbut-2-Enyl)-3-Phenacyloxychromen-4-One
IUPAC Name:	2-[3,4-dimethoxy-2,6-bis(3-methylbut-2-enyl)phenyl]-5,7-dimethoxy-8-(3-methylbut-2-enyl)-3-phenacyloxychromen-4-one
Synonyms:
Standard InCHIKey:	PIXAPMGONJHYEX-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C42H48O8/c1-25(2)16-19-29-22-35(47-9)39(48-10)31(21-18-27(5)6)36(29)41-42(49-24-32(43)28-14-12-11-13-15-28)38(44)37-34(46-8)23-33(45-7)30(40(37)50-41)20-17-26(3)4/h11-18,22-23H,19-21,24H2,1-10H3
SMILES:	CC(=CCC1=CC(=C(C(=C1C2=C(C(=O)C3=C(C=C(C(=C3O2)CC=C(C)C)OC)OC)OCC(=O)C4=CC=CC=C4)CC=C(C)C)OC)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL499297
PubChem CID:	44584423
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0003587] 2'-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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27127	Petalostemum purpureum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[8289060]
NPO27127	Petalostemum purpureum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 2 of 2 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
MIC	6

Activity Type	# Activity
Organism	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	5.0	ug.mL-1	PMID[476354]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	MIC	=	5.0	ug.mL-1	PMID[476354]
NPT86	Organism	Mycobacterium intracellulare	Mycobacterium intracellulare	MIC	=	5.0	ug.mL-1	PMID[476354]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	5.0	ug.mL-1	PMID[476354]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	5.0	ug.mL-1	PMID[476354]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	5.0	ug.mL-1	PMID[476354]

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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 NPC475144 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	542
0.1-0.2	1839
0.2-0.3	4527
0.3-0.4	10833
0.4-0.5	7233
0.5-0.6	3785
0.6-0.7	5824
0.7-0.8	5028
0.8-0.85	2231
0.85-0.9	793
0.9-0.95	60
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9542	High Similarity	NPC473664
0.915	High Similarity	NPC299923
0.9103	High Similarity	NPC40033
0.9097	High Similarity	NPC5840
0.9097	High Similarity	NPC189270

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 NPC475144 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	452
0.1-0.2	1010
0.2-0.3	1750
0.3-0.4	2683
0.4-0.5	1844
0.5-0.6	877
0.6-0.7	368
0.7-0.8	122
0.8-0.85	36
0.85-0.9	8
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8868	High Similarity	NPD3817	Phase 2
0.8765	High Similarity	NPD5494	Approved
0.8688	High Similarity	NPD7819	Suspended
0.8667	High Similarity	NPD6166	Phase 2
0.8667	High Similarity	NPD6168	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