NPASS Compound

Structure

NPC79810 OpenBabel06302215502D 29 30 0 0 0 0 0 0 0 0999 V2000 -4.1904 -2.4194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0285 -1.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0285 -0.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1904 -0.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1904 0.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0285 0.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0285 1.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1904 2.4194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3524 1.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5143 2.4194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5143 3.3871 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3524 0.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6762 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6762 -0.9677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8381 0.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8381 1.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8381 1.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6762 1.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8381 0.4839 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 0.0000 -0.9677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8381 -1.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6762 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.9032 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -1.6762 1.9355 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1904 3.3871 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8666 0.4839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8666 -2.4194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 29 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 12 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 28 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 27 1 0 0 0 0 9 10 1 0 0 0 0 9 12 1 0 0 0 0 10 11 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 21 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 26 1 0 0 0 0 17 18 1 0 0 0 0 17 25 1 0 0 0 0 18 19 1 0 0 0 0 18 20 2 0 0 0 0 20 21 1 0 0 0 0 20 24 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.06
Volume:	414.095
LogP:	6.034
LogD:	3.68
LogS:	-5.05
# Rotatable Bonds:	6
TPSA:	104.06
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.425
Synthetic Accessibility Score:	3.375
Fsp3:	0.238
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:	-5.02
MDCK Permeability:	1.6910133126657456e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.043
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.011
Plasma Protein Binding (PPB):	101.63964080810547%
Volume Distribution (VD):	0.187
Pgp-substrate:	0.8460018038749695%

ADMET: Metabolism

CYP1A2-inhibitor:	0.783
CYP1A2-substrate:	0.851
CYP2C19-inhibitor:	0.239
CYP2C19-substrate:	0.124
CYP2C9-inhibitor:	0.899
CYP2C9-substrate:	0.899
CYP2D6-inhibitor:	0.486
CYP2D6-substrate:	0.205
CYP3A4-inhibitor:	0.228
CYP3A4-substrate:	0.178

ADMET: Excretion

Clearance (CL):	5.124
Half-life (T1/2):	0.095

ADMET: Toxicity

hERG Blockers:	0.018
Human Hepatotoxicity (H-HT):	0.287
Drug-inuced Liver Injury (DILI):	0.94
AMES Toxicity:	0.498
Rat Oral Acute Toxicity:	0.111
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.573
Carcinogencity:	0.683
Eye Corrosion:	0.006
Eye Irritation:	0.946
Respiratory Toxicity:	0.358

Download Data

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

Natural Product: NPC79810

Natural Product ID:	NPC79810
*Common Name:**	ACRANQNXYMAQKJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ACRANQNXYMAQKJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H20Cl2O6/c1-9(2)5-6-11-13(25)7-14(26)12(8-24)15(11)19(27)16-20(28)17(22)10(3)18(23)21(16)29-4/h5,7-8,25-26,28H,6H2,1-4H3
SMILES:	CC(=CCc1c(cc(c(C=O)c1C(=O)c1c(c(c(C)c(c1OC)Cl)Cl)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10071878
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000120] Benzophenones

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO40998	Pestalotia sp. CNJ-328	Strain	Amphisphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11720529]
NPO40280	Pestalotiopsis neglecta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31829592]
NPO40280	Pestalotiopsis neglecta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32283019]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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
ED50	15
GI50	1
IC50	1
MIC	10

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1
Organism	20
Others	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT461	Cell Line	PANC-1	Homo sapiens	IC50	=	14000.0	nM	PMID[31829592]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	6000.0	nM	PMID[11720529]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.037	ug.mL-1	PMID[11720529]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	0.078	ug.mL-1	PMID[11720529]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.037	ug.mL-1	PMID[15844962]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	0.078	ug.mL-1	PMID[15844962]
NPT1209	Organism	Pseudomonas fluorescens	Pseudomonas fluorescens	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT610	Others	Molecular identity unknown		ED50	>	50.0	ug ml-1	PMID[23905700]
NPT21	Organism	Aspergillus niger	Aspergillus niger	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT826	Organism	Magnaporthe oryzae	Magnaporthe oryzae	ED50	=	28.6	ug ml-1	PMID[23905700]
NPT1276	Organism	Gibberella zeae	Gibberella zeae	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT1278	Organism	Fusarium culmorum	Fusarium culmorum	ED50	=	0.12	ug ml-1	PMID[23905700]
NPT610	Others	Molecular identity unknown		ED50	=	22.4	ug ml-1	PMID[23905700]
NPT610	Others	Molecular identity unknown		ED50	=	2.2	ug ml-1	PMID[23905700]
NPT827	Organism	Mycosphaerella graminicola	Mycosphaerella graminicola	ED50	=	26.7	ug ml-1	PMID[23905700]
NPT635	Organism	Botryotinia fuckeliana	Botryotinia fuckeliana	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT1494	Organism	Alternaria mali	Alternaria mali	ED50	=	22.4	ug ml-1	PMID[23905700]
NPT961	Organism	Pythium aphanidermatum	Pythium aphanidermatum	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT610	Others	Molecular identity unknown		ED50	=	33.9	ug ml-1	PMID[23905700]
NPT825	Organism	Phytophthora infestans	Phytophthora infestans	ED50	>	50.0	ug ml-1	PMID[23905700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	6.25	ug.mL-1	PMID[23905700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	3.1	ug.mL-1	PMID[23905700]
NPT2709	Organism	Bacillus subtilis subsp. subtilis str. 168	Bacillus subtilis subsp. subtilis str. 168	MIC	=	1.6	ug.mL-1	PMID[23905700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	16.0	ug.mL-1	PMID[23905700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	10.0	ug.mL-1	PMID[23905700]

☑ 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 NPC79810 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	477
0.1-0.2	2165
0.2-0.3	5865
0.3-0.4	13171
0.4-0.5	4737
0.5-0.6	6154
0.6-0.7	6852
0.7-0.8	3121
0.8-0.85	106
0.85-0.9	33
0.9-0.95	14
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID

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 NPC79810 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	427
0.1-0.2	1118
0.2-0.3	1980
0.3-0.4	2900
0.4-0.5	1701
0.5-0.6	739
0.6-0.7	248
0.7-0.8	37
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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