NPASS Compound

Structure

NPC52405 OpenBabel06302215182D 21 24 0 0 1 0 0 0 0 0999 V2000 -2.2299 -1.2234 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9333 -0.3106 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0205 -0.0140 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4564 -0.7905 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4564 -1.0871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3692 -0.7905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9333 -0.0140 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9333 0.9457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3692 1.7222 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4564 2.0188 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4586 1.8871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4564 1.7222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0205 0.9457 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9333 1.2423 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4975 0.4658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4572 0.4658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1696 2.6610 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8461 -0.3106 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9128 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3927 0.8312 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 15 1 0 0 0 0 3 4 1 0 0 0 0 3 13 1 0 0 0 0 4 5 1 6 0 0 0 4 21 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 19 1 0 0 0 0 7 8 1 0 0 0 0 7 18 1 1 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 10 17 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	294.11
Volume:	278.602
LogP:	1.202
LogD:	0.904
LogS:	-3.244
# Rotatable Bonds:	0
TPSA:	92.43
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.558
Synthetic Accessibility Score:	6.039
Fsp3:	0.667
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:	-5.451
MDCK Permeability:	3.258882134105079e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.038
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.322
Plasma Protein Binding (PPB):	56.71575927734375%
Volume Distribution (VD):	1.069
Pgp-substrate:	41.757347106933594%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.285
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.745
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.113
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.044
CYP3A4-substrate:	0.437

ADMET: Excretion

Clearance (CL):	11.698
Half-life (T1/2):	0.443

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.76
Drug-inuced Liver Injury (DILI):	0.663
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.833
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.291
Carcinogencity:	0.59
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.868

Download Data

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

Natural Product: NPC52405

Natural Product ID:	NPC52405
*Common Name:**	ITFJPAQQKHMDBK-QEPGURRYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ITFJPAQQKHMDBK-QEPGURRYSA-N
Standard InCHI:	InChI=1S/C15H18O6/c1-6-12-9-3-7(14(18)19-9)8(16)4-11-15(2,21-11)5-10(12)20-13(6)17/h3,6,8-12,16H,4-5H2,1-2H3/t6-,8-,9-,10+,11-,12+,15+/m1/s1
SMILES:	C[C@@H]1[C@H]2[C@H]3C=C([C@@H](C[C@@H]4[C@](C)(C[C@@H]2OC1=O)O4)O)C(=O)O3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101731027
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	barks	n.a.	n.a.	PMID[15620248]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19267453]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20430633]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20499851]
NPO23998	Auxarthron reticulatum	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24900275]
NPO6403	Phlegmariurus squarrosus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32941036]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24950	Eupatorium aschenbornianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23998	Auxarthron reticulatum	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1827	Morinda elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25341	Sanango racemosum	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24854	Beltrania rhombica	Species	Beltraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24950	Eupatorium aschenbornianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25602	Crotalaria barbata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25399	Patrinia intermedia	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25241	Cordyla africana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23866	Anisocycla cymosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25313	Satureja douglasii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24242	Haminoea cymbalum	Species	Haminoeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25683	Columba livia	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6403	Phlegmariurus squarrosus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25115	Psychotria calocarpa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24142	Cereus ocamponis	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24895	Parmelia springtonensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24662	Ulmus laevis	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23134	Artemisia kaschgarica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20331	Aerva tomentosa	Species	Amaranthaceae	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 NPC52405 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	227
0.1-0.2	1332
0.2-0.3	5211
0.3-0.4	9233
0.4-0.5	14795
0.5-0.6	6962
0.6-0.7	3704
0.7-0.8	1062
0.8-0.85	130
0.85-0.9	30
0.9-0.95	11
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 NPC52405 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	1973
0.2-0.3	3818
0.3-0.4	2105
0.4-0.5	673
0.5-0.6	288
0.6-0.7	73
0.7-0.8	11
0.8-0.85	1
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