NPASS Compound

Structure

NPC253769 OpenBabel06302215392D 22 24 0 0 1 0 0 0 0 0999 V2000 -1.6764 0.2399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7628 0.6466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7329 1.6462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5506 2.2218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2559 3.1773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2560 3.1923 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6514 3.6127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0672 2.2460 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0351 1.9944 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4418 1.0808 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4363 1.1854 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1054 0.4422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6442 2.1635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5578 2.5703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7782 2.6635 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9811 0.1933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5810 -0.6069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1879 -1.5264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1951 -1.6458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7878 -2.3265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1664 4.1883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 17 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 5 6 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 6 22 1 0 0 0 0 8 3 1 1 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 15 1 6 0 0 0 10 11 1 0 0 0 0 10 16 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 6 0 0 0 18 19 1 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:	306.15
Volume:	310.324
LogP:	1.547
LogD:	1.244
LogS:	-2.088
# Rotatable Bonds:	2
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.747
Synthetic Accessibility Score:	4.757
Fsp3:	0.647
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:	-4.751
MDCK Permeability:	4.419967808644287e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.013
Human Intestinal Absorption (HIA):	0.024
20% Bioavailability (F20%):	0.848
30% Bioavailability (F30%):	0.384

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.886
Plasma Protein Binding (PPB):	47.10028076171875%
Volume Distribution (VD):	1.022
Pgp-substrate:	55.54243469238281%

ADMET: Metabolism

CYP1A2-inhibitor:	0.177
CYP1A2-substrate:	0.083
CYP2C19-inhibitor:	0.034
CYP2C19-substrate:	0.565
CYP2C9-inhibitor:	0.017
CYP2C9-substrate:	0.041
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.051
CYP3A4-inhibitor:	0.666
CYP3A4-substrate:	0.44

ADMET: Excretion

Clearance (CL):	5.759
Half-life (T1/2):	0.734

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.831
Drug-inuced Liver Injury (DILI):	0.461
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.813
Maximum Recommended Daily Dose:	0.485
Skin Sensitization:	0.339
Carcinogencity:	0.332
Eye Corrosion:	0.064
Eye Irritation:	0.119
Respiratory Toxicity:	0.93

Download Data

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

Natural Product: NPC253769

Natural Product ID:	NPC253769
*Common Name:**	SYTRJRUSWMMZLV-KZVQMNAWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SYTRJRUSWMMZLV-KZVQMNAWSA-N
Standard InCHI:	InChI=1S/C17H22O5/c1-8-7-12(21-10(3)18)13-9(2)16(19)22-15(13)14-11(8)5-6-17(14,4)20/h5-6,9,12-15,20H,7H2,1-4H3/t9-,12-,13+,14-,15-,17+/m1/s1
SMILES:	CC1=C2C=C[C@@](C)([C@H]2[C@H]2[C@@H]([C@@H](C)C(=O)O2)[C@@H](C1)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
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
NPO22051	Litsea verticillata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762792]
NPO12907	Hypericum carinatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921431]
NPO6879	Laetia corymbulosa	Species	Salicaceae	Eukaryota	Bark	n.a.	n.a.	PMID[28290698]
NPO17203	Impatiens siculifer	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22051	Litsea verticillata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12656	Holarrhena febrifuga	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12656	Holarrhena febrifuga	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22051	Litsea verticillata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6879	Laetia corymbulosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17203	Impatiens siculifer	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22051	Litsea verticillata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17743	Solanum aculeatum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12907	Hypericum carinatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20253	Eucalyptus decorticans	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6879	Laetia corymbulosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28772	Polygonum mite	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20602	Trichomanes reniforme	Species	Hymenophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20180	Rabdosia loxothyrsa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12656	Holarrhena febrifuga	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19748	Aspergillus phoenicis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22051	Litsea verticillata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11665	Kloeckera brevis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10235	Castanopsis eyrei	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17203	Impatiens siculifer	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21477	Euryops rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13840	Streptomyces incarnatus	Species	Streptomycetaceae	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 NPC253769 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	191
0.1-0.2	985
0.2-0.3	4239
0.3-0.4	10580
0.4-0.5	14036
0.5-0.6	7971
0.6-0.7	3911
0.7-0.8	738
0.8-0.85	38
0.85-0.9	8
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 NPC253769 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	165
0.1-0.2	1481
0.2-0.3	3698
0.3-0.4	2527
0.4-0.5	803
0.5-0.6	398
0.6-0.7	53
0.7-0.8	25
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