NPASS Compound

Structure

NPC182783 OpenBabel06302215072D 22 24 0 0 1 0 0 0 0 0999 V2000 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 1 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 1 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 -4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 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 -3.4641 2.0000 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 1.7321 -1.0000 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 22 1 6 0 0 0 4 5 1 0 0 0 0 4 21 1 1 0 0 0 5 6 1 0 0 0 0 5 18 1 1 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 10 11 1 0 0 0 0 10 20 1 6 0 0 0 11 12 1 0 0 0 0 11 19 1 6 0 0 0 12 13 1 6 0 0 0 12 16 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	322.09
Volume:	275.705
LogP:	-1.508
LogD:	-1.359
LogS:	-0.972
# Rotatable Bonds:	1
TPSA:	155.14
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.333
Synthetic Accessibility Score:	4.652
Fsp3:	0.917
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:	-6.492
MDCK Permeability:	0.00014468785957433283
Pgp-inhibitor:	0.001
Pgp-substrate:	0.983
Human Intestinal Absorption (HIA):	0.943
20% Bioavailability (F20%):	0.034
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.255
Plasma Protein Binding (PPB):	16.848234176635742%
Volume Distribution (VD):	0.36
Pgp-substrate:	75.67900848388672%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.05
CYP2C19-inhibitor:	0.037
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.108
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.232
Half-life (T1/2):	0.791

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.181
Drug-inuced Liver Injury (DILI):	0.953
AMES Toxicity:	0.139
Rat Oral Acute Toxicity:	0.188
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.393
Carcinogencity:	0.034
Eye Corrosion:	0.004
Eye Irritation:	0.107
Respiratory Toxicity:	0.224

Download Data

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

Natural Product: NPC182783

Natural Product ID:	NPC182783
*Common Name:**	GPNBVTXKEGZPLX-NFBQDZRMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GPNBVTXKEGZPLX-NFBQDZRMSA-N
Standard InCHI:	InChI=1S/C12H18O10/c1-2-3(13)4(14)8-11(19-2)21-9-6(16)5(15)7(10(17)18)20-12(9)22-8/h2-9,11-16H,1H3,(H,17,18)/t2-,3-,4+,5+,6-,7-,8+,9+,11+,12+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@@H]2[C@H](O1)O[C@@H]1[C@H]([C@H]([C@@H](C(=O)O)O[C@@H]1O2)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000215] Sugar acids and derivatives [CHEMONTID:0002094] Glucuronic acid derivatives

*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
NPO15057	Isodon gesneroides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO581	Conyza bonariensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21924	Althaea officinalis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11478	Aniba duckei	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21924	Althaea officinalis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11117	Xerula melanotricha	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12034	Dictamnus gymnostylis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO581	Conyza bonariensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28881	Virola sebifera	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16888	Sophora davidii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15057	Isodon gesneroides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11895	Nama johnstonii	Species	Namaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17117	Diaporthe amygdali	Species	Diaporthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7201	Rhodopila globiformis	Species	Acetobacteraceae	Bacteria	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC182783 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	970
0.1-0.2	6080
0.2-0.3	13588
0.3-0.4	12624
0.4-0.5	6527
0.5-0.6	2458
0.6-0.7	328
0.7-0.8	109
0.8-0.85	11
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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 NPC182783 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	998
0.1-0.2	4731
0.2-0.3	2264
0.3-0.4	733
0.4-0.5	256
0.5-0.6	115
0.6-0.7	35
0.7-0.8	12
0.8-0.85	5
0.85-0.9	0
0.9-0.95	1
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