NPASS Compound

Structure

NPC24161 OpenBabel06302215322D 28 30 0 0 1 0 0 0 0 0999 V2000 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 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 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 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 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 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 0.8660 -2.5000 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 1.7321 -1.0000 0.0000 C 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 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 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 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 -1.7321 2.0000 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 2.0000 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 3.4641 -3.0000 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 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 28 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 27 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 1 0 0 0 18 19 1 0 0 0 0 18 25 1 6 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 6 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.11
Volume:	372.168
LogP:	0.498
LogD:	0.229
LogS:	-2.052
# Rotatable Bonds:	5
TPSA:	156.91
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.369
Synthetic Accessibility Score:	3.628
Fsp3:	0.316
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:	-6.307
MDCK Permeability:	7.935708708828315e-06
Pgp-inhibitor:	0.021
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.472
20% Bioavailability (F20%):	0.049
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.14
Plasma Protein Binding (PPB):	93.19094848632812%
Volume Distribution (VD):	0.735
Pgp-substrate:	4.3175482749938965%

ADMET: Metabolism

CYP1A2-inhibitor:	0.244
CYP1A2-substrate:	0.039
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.249
CYP2D6-inhibitor:	0.259
CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.03
CYP3A4-substrate:	0.05

ADMET: Excretion

Clearance (CL):	7.373
Half-life (T1/2):	0.815

ADMET: Toxicity

hERG Blockers:	0.122
Human Hepatotoxicity (H-HT):	0.033
Drug-inuced Liver Injury (DILI):	0.956
AMES Toxicity:	0.759
Rat Oral Acute Toxicity:	0.044
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.572
Carcinogencity:	0.144
Eye Corrosion:	0.003
Eye Irritation:	0.567
Respiratory Toxicity:	0.03

Download Data

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

Natural Product: NPC24161

Natural Product ID:	NPC24161
*Common Name:**	CCXXIROIENJKKR-LQDZTQBFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CCXXIROIENJKKR-LQDZTQBFSA-N
Standard InCHI:	InChI=1S/C19H20O9/c20-8-13-16(24)17(25)18(26)19(28-13)27-12-7-10(21)6-11(22)14(12)15(23)9-4-2-1-3-5-9/h1-7,13,16-22,24-26H,8H2/t13-,16-,17+,18-,19-/m1/s1
SMILES:	c1ccc(cc1)C(=O)c1c(cc(cc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11003703
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic glycosides

*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
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0040-4039(00)90246-6]
NPO7811	Scleronephthya pallida	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075773]
NPO10376	Arcyria denudata	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16933891]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18464091]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18558747]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	stem bark	Pangradin village, Jasinga, West Java, Indonesia	2005-AUG	PMID[19839614]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20817450]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[24555285]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24717154]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	fruit hulls	Madras, Tamil Nadu, India	1993-MAR	PMID[9213587]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10849	Eucalyptus camaldulensis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10849	Eucalyptus camaldulensis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10391	Dolomiaea souliei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10391	Dolomiaea souliei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10221	Streptomyces alboniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10056	Nicotiana sylvestris	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7534	Leptogorgia sarmentosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24931	Myelochroa aurulenta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8560	Aplidium tabascum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10849	Eucalyptus camaldulensis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9741	Actinopyga agassizi	Species	Holothuriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8927	Poria selecta	Species	Coccinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3707	Chromatium okenii	Species	Chromatiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6249	Garcinia mangostana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27924	Serpocaulon triseriale	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7811	Scleronephthya pallida	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10391	Dolomiaea souliei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4064	Halimodendron halodendron	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10376	Arcyria denudata	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8354	Aster bellidiastrum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25216	Senecio vellereus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12600	Trametes cinnabarina	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3449	Lonicera hypoleuca	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9717	Wibelia divaricata	Species	Davalliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3806	Garcinia morella	Species	Clusiaceae	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

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 NPC24161 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	383
0.1-0.2	1590
0.2-0.3	3727
0.3-0.4	9071
0.4-0.5	9275
0.5-0.6	4164
0.6-0.7	5324
0.7-0.8	5497
0.8-0.85	2503
0.85-0.9	971
0.9-0.95	159
0.95-1	33

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 NPC24161 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	355
0.1-0.2	858
0.2-0.3	1732
0.3-0.4	2674
0.4-0.5	1916
0.5-0.6	1068
0.6-0.7	343
0.7-0.8	150
0.8-0.85	36
0.85-0.9	17
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