NPASS Compound

Structure

NPC486817 OpenBabel06302215572D 23 26 0 0 1 0 0 0 0 0999 V2000 -0.6323 -2.3997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3494 -3.0494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2705 -2.7532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4746 -1.8074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7576 -1.1578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8364 -1.4539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9676 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8505 -1.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8573 -2.4081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6890 -2.8806 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5140 -2.3965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5072 -1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6755 -0.9676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6755 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6755 0.9679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8250 1.4519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8184 2.4519 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4237 -2.9133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6963 -3.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3957 -1.5113 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9875 -3.4029 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 23 1 0 0 0 0 4 5 2 0 0 0 0 4 22 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 19 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 21 1 0 0 0 0 11 12 2 0 0 0 0 11 20 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 19 1 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 19 18 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	338.12
Volume:	349.03
LogP:	4.555
LogD:	2.795
LogS:	-3.087
# Rotatable Bonds:	3
TPSA:	90.9
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.626
Synthetic Accessibility Score:	2.679
Fsp3:	0.15
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:	-4.752
MDCK Permeability:	1.2738541045109741e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.428
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.891
30% Bioavailability (F30%):	0.708

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	97.41840362548828%
Volume Distribution (VD):	0.618
Pgp-substrate:	2.577284574508667%

ADMET: Metabolism

CYP1A2-inhibitor:	0.922
CYP1A2-substrate:	0.161
CYP2C19-inhibitor:	0.913
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.829
CYP2C9-substrate:	0.907
CYP2D6-inhibitor:	0.795
CYP2D6-substrate:	0.449
CYP3A4-inhibitor:	0.276
CYP3A4-substrate:	0.104

ADMET: Excretion

Clearance (CL):	7.019
Half-life (T1/2):	0.741

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.264
Drug-inuced Liver Injury (DILI):	0.492
AMES Toxicity:	0.058
Rat Oral Acute Toxicity:	0.377
Maximum Recommended Daily Dose:	0.05
Skin Sensitization:	0.929
Carcinogencity:	0.135
Eye Corrosion:	0.003
Eye Irritation:	0.844
Respiratory Toxicity:	0.093

Download Data

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

Natural Product: NPC486817

Natural Product ID:	NPC486817
*Common Name:**	NZKVZAOTASFTDL-POJUEXTFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NZKVZAOTASFTDL-POJUEXTFSA-N
Standard InCHI:	InChI=1S/C17H14O6/c18-11-2-1-7(3-12(11)19)16-9-5-14(21)13(20)4-8(9)10-6-15(22)23-17(10)16/h1-5,10,16-21H,6H2/t10-,16-,17-/m0/s1
SMILES:	c1cc(c(cc1[C@H]1c2cc(c(cc2[C@@H]2CC(=O)O[C@H]12)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000027] Indanes

*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
NPO29255	Salvia chinensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30370766]
NPO29255	Salvia chinensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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	3

Activity Type	# Activity
Cell Line	2
CELL-LINE	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6530	Cell Line	MOLM-13	Homo sapiens	IC50	=	2300.0	nM	PMID[30370766]
NPT1649	Cell Line	MV4-11	Homo sapiens	IC50	>	10000.0	nM	PMID[30370766]
NPT24396	CELL-LINE	MOLM-14	Homo sapiens	IC50	=	7100.0	nM	PMID[30370766]

☑ 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 NPC486817 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	303
0.1-0.2	1204
0.2-0.3	2666
0.3-0.4	6383
0.4-0.5	12714
0.5-0.6	6733
0.6-0.7	10792
0.7-0.8	1825
0.8-0.85	69
0.85-0.9	6
0.9-0.95	1
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 NPC486817 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	249
0.1-0.2	783
0.2-0.3	1522
0.3-0.4	2678
0.4-0.5	2224
0.5-0.6	1215
0.6-0.7	419
0.7-0.8	58
0.8-0.85	2
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