NPASS Compound

Structure

NPC484459 OpenBabel06302216212D 21 21 0 0 1 0 0 0 0 0999 V2000 1.3635 0.7288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3827 0.9239 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3827 1.9239 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 2.8478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7071 3.5549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6310 3.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6310 3.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5549 3.5549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2620 2.8478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6447 1.9239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6447 0.9239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2620 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5549 -0.7071 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6310 -1.0898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6310 -1.0898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7071 -0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1515 -1.5386 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 -4.1104 -1.5386 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0934 -0.5556 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3635 2.1190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 3 4 1 0 0 0 0 3 21 1 6 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 20 1 1 0 0 0 13 14 1 0 0 0 0 13 19 1 1 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	300.19
Volume:	315.414
LogP:	2.388
LogD:	1.718
LogS:	-2.242
# Rotatable Bonds:	0
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.669
Synthetic Accessibility Score:	3.91
Fsp3:	0.875
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.705
MDCK Permeability:	4.130930392420851e-05
Pgp-inhibitor:	0.969
Pgp-substrate:	0.665
Human Intestinal Absorption (HIA):	0.079
20% Bioavailability (F20%):	0.98
30% Bioavailability (F30%):	0.948

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.619
Plasma Protein Binding (PPB):	69.28569793701172%
Volume Distribution (VD):	0.875
Pgp-substrate:	25.281959533691406%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.452
CYP2C19-inhibitor:	0.043
CYP2C19-substrate:	0.085
CYP2C9-inhibitor:	0.047
CYP2C9-substrate:	0.899
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.09
CYP3A4-inhibitor:	0.085
CYP3A4-substrate:	0.082

ADMET: Excretion

Clearance (CL):	7.497
Half-life (T1/2):	0.922

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.138
Drug-inuced Liver Injury (DILI):	0.266
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.023
Maximum Recommended Daily Dose:	0.29
Skin Sensitization:	0.169
Carcinogencity:	0.075
Eye Corrosion:	0.015
Eye Irritation:	0.125
Respiratory Toxicity:	0.034

Download Data

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

Natural Product: NPC484459

Natural Product ID:	NPC484459
*Common Name:**	OXTXYWGSTRVDDS-MLCUHWOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OXTXYWGSTRVDDS-MLCUHWOYSA-N
Standard InCHI:	InChI=1S/C16H28O5/c1-12-13(17)8-6-4-2-3-5-7-9-14(18)15(19)10-11-16(20)21-12/h10-15,17-19H,2-9H2,1H3/b11-10+/t12-,13+,14+,15-/m1/s1
SMILES:	C[C@@H]1[C@H](CCCCCCCC[C@@H]([C@@H](/C=C/C(=O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	132967554
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues

*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
NPO40267	Penicillium clavigerum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28326781]
NPO41451	Penicillium fuscum + Penicillium camembertii/clavigerum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28326781]
NPO40270	Penicillium fuscum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28326781]
NPO40905	Penicillium camembertii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28326781]

☑ 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
IC50	1
MIC	6
Others	1

Activity Type	# Activity
Cell Line	1
Individual Protein	1
Organism	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT567	Individual Protein	Matrix metalloproteinase 3	Homo sapiens	IC50	=	150000.0	nM	PMID[28326781]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	GI	=	38.0	%	PMID[28326781]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	64000.0	nM	PMID[28326781]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	500000.0	nM	PMID[28326781]
NPT554	Organism	Candida glabrata	Candida glabrata	MIC	>	1000000.0	nM	PMID[28326781]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	1000000.0	nM	PMID[28326781]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	1000000.0	nM	PMID[28326781]
NPT1550	Organism	Bacillus anthracis	Bacillus anthracis	MIC	=	250000.0	nM	PMID[28326781]

☑ 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 NPC484459 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	177
0.1-0.2	1771
0.2-0.3	6634
0.3-0.4	17986
0.4-0.5	9736
0.5-0.6	4381
0.6-0.7	1502
0.7-0.8	440
0.8-0.85	39
0.85-0.9	26
0.9-0.95	4
0.95-1	1

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 NPC484459 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	145
0.1-0.2	2434
0.2-0.3	3822
0.3-0.4	2122
0.4-0.5	481
0.5-0.6	109
0.6-0.7	34
0.7-0.8	3
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