NPASS Compound

Structure

CID235448 OpenBabel06191716032D 29 31 0 0 0 0 0 0 0 0999 V2000 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9641 2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9641 2.8660 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 2.5981 3.5000 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 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 2.5981 4.5000 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 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 -0.8660 0.5000 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 -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 -0.0000 2.0000 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 -3.4641 2.0000 0.0000 C 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 3.4641 0.0000 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 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 2 11 1 0 0 0 0 3 11 1 0 0 0 0 4 23 1 0 0 0 0 5 23 1 0 0 0 0 6 23 1 0 0 0 0 7 8 1 0 0 0 0 7 11 2 0 0 0 0 8 12 1 0 0 0 0 9 12 2 0 0 0 0 9 14 1 0 0 0 0 10 13 2 0 0 0 0 10 15 1 0 0 0 0 12 16 1 0 0 0 0 13 18 1 0 0 0 0 13 24 1 0 0 0 0 14 19 2 0 0 0 0 14 25 1 0 0 0 0 15 17 2 0 0 0 0 15 29 1 0 0 0 0 16 20 1 0 0 0 0 16 22 2 0 0 0 0 17 20 1 0 0 0 0 17 21 1 0 0 0 0 18 21 2 0 0 0 0 18 23 1 0 0 0 0 19 22 1 0 0 0 0 19 26 1 0 0 0 0 20 27 2 0 0 0 0 21 28 1 0 0 0 0 22 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	396.16
Volume:	409.708
LogP:	5.502
LogD:	2.757
LogS:	-3.31
# Rotatable Bonds:	4
TPSA:	111.13
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.288
Synthetic Accessibility Score:	3.492
Fsp3:	0.261
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.89
MDCK Permeability:	1.2857883120886981e-05
Pgp-inhibitor:	0.9
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.265
20% Bioavailability (F20%):	0.918
30% Bioavailability (F30%):	0.519

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006
Plasma Protein Binding (PPB):	92.5338134765625%
Volume Distribution (VD):	0.921
Pgp-substrate:	11.743237495422363%

ADMET: Metabolism

CYP1A2-inhibitor:	0.79
CYP1A2-substrate:	0.222
CYP2C19-inhibitor:	0.473
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.765
CYP2C9-substrate:	0.742
CYP2D6-inhibitor:	0.531
CYP2D6-substrate:	0.181
CYP3A4-inhibitor:	0.162
CYP3A4-substrate:	0.071

ADMET: Excretion

Clearance (CL):	1.266
Half-life (T1/2):	0.6

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.187
Drug-inuced Liver Injury (DILI):	0.944
AMES Toxicity:	0.539
Rat Oral Acute Toxicity:	0.116
Maximum Recommended Daily Dose:	0.408
Skin Sensitization:	0.898
Carcinogencity:	0.237
Eye Corrosion:	0.005
Eye Irritation:	0.907
Respiratory Toxicity:	0.238

Download Data

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

Natural Product: NPC235448

Natural Product ID:	NPC235448
*Common Name:**	Alvaxanthone
IUPAC Name:	1,3,5,6-tetrahydroxy-2-(2-methylbut-3-en-2-yl)-8-(3-methylbut-2-enyl)xanthen-9-one
Synonyms:	Alvaxanthone
Standard InCHIKey:	IXUNODGMZUQIQP-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H24O6/c1-6-23(4,5)18-13(24)10-15-17(21(18)28)20(27)16-12(8-7-11(2)3)9-14(25)19(26)22(16)29-15/h6-7,9-10,24-26,28H,1,8H2,2-5H3
SMILES:	C=CC(C)(C)c1c(cc2c(c(=O)c3c(CC=C(C)C)cc(c(c3o2)O)O)c1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL478937
PubChem CID:	12305823
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003519] 8-prenylated xanthones

*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
NPO25837	Euphorbia micractina	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[23691978]
NPO25837	Euphorbia micractina	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[21534583]
NPO25837	Euphorbia micractina	Species	Euphorbiaceae	Eukaryota	Roots	Zhang County, Gansu Province, China	2002-Sep	PMID[19702283]
NPO29752	Cudrania cochinchinensis	n.a.	n.a.	n.a.	roots	n.a.	n.a.	PMID[12932139]
NPO29752	Cudrania cochinchinensis	n.a.	n.a.	n.a.	roots	n.a.	n.a.	PMID[11170668]
NPO24502	Rosa roxburghii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19038	Zanha golungensis	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25806	Streptomyces violaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO25837	Euphorbia micractina	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26671	Hapalosiphon welwitschii	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 17 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
Others	3

Activity Type	# Activity
Cell Line	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT924	Cell Line	HSC-2	Homo sapiens	CC50	=	22000.0	nM	PMID[571546]
NPT924	Cell Line	HSC-2	Homo sapiens	Ratio	=	1.1	n.a.	PMID[571546]
NPT27	Others	Unspecified	""	CC50	=	25000.0	nM	PMID[571546]

Showing 1 to 3 of 3 entries

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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 NPC235448 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	458
0.1-0.2	1881
0.2-0.3	4271
0.3-0.4	10734
0.4-0.5	7325
0.5-0.6	3635
0.6-0.7	5201
0.7-0.8	5218
0.8-0.85	2479
0.85-0.9	1021
0.9-0.95	436
0.95-1	38

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Similarity Score	Similarity Level	Natural Product ID
0.9801	High Similarity	NPC136674
0.9801	High Similarity	NPC161960
0.9801	High Similarity	NPC304008
0.9801	High Similarity	NPC187745
0.974	High Similarity	NPC220313

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 NPC235448 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	410
0.1-0.2	1011
0.2-0.3	1708
0.3-0.4	2745
0.4-0.5	1758
0.5-0.6	951
0.6-0.7	398
0.7-0.8	124
0.8-0.85	29
0.85-0.9	12
0.9-0.95	4
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9221	High Similarity	NPD2393	Clinical (unspecified phase)
0.9156	High Similarity	NPD1934	Approved
0.9097	High Similarity	NPD2801	Approved
0.8882	High Similarity	NPD1511	Approved
0.8861	High Similarity	NPD3882	Suspended

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