NPASS Compound

Structure

NPC69543 OpenBabel06302215172D 27 31 0 0 1 0 0 0 0 0999 V2000 0.8660 -3.5000 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 -0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 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 -0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6238 -2.1249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2182 -2.3778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9409 -1.8771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8106 -2.3706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4483 1.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1554 2.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1213 2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3801 1.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6730 0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3788 1.1031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7371 2.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9600 2.6660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3747 -3.3655 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3082 -3.7238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2984 -2.8631 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2750 -2.6478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 3 1 1 0 0 0 4 13 1 0 0 0 0 4 5 1 0 0 0 0 4 8 1 0 0 0 0 5 6 1 6 0 0 0 5 14 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 26 1 0 0 0 0 10 11 1 0 0 0 0 10 24 1 0 0 0 0 11 12 2 0 0 0 0 13 11 1 6 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.14
Volume:	365.912
LogP:	2.464
LogD:	2.942
LogS:	-4.795
# Rotatable Bonds:	5
TPSA:	63.22
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.743
Synthetic Accessibility Score:	4.693
Fsp3:	0.476
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:	-4.827
MDCK Permeability:	1.872645952971652e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.061

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.135
Plasma Protein Binding (PPB):	87.26504516601562%
Volume Distribution (VD):	1.169
Pgp-substrate:	10.613306999206543%

ADMET: Metabolism

CYP1A2-inhibitor:	0.926
CYP1A2-substrate:	0.922
CYP2C19-inhibitor:	0.886
CYP2C19-substrate:	0.787
CYP2C9-inhibitor:	0.587
CYP2C9-substrate:	0.115
CYP2D6-inhibitor:	0.939
CYP2D6-substrate:	0.378
CYP3A4-inhibitor:	0.966
CYP3A4-substrate:	0.709

ADMET: Excretion

Clearance (CL):	12.768
Half-life (T1/2):	0.249

ADMET: Toxicity

hERG Blockers:	0.273
Human Hepatotoxicity (H-HT):	0.433
Drug-inuced Liver Injury (DILI):	0.349
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.068
Maximum Recommended Daily Dose:	0.792
Skin Sensitization:	0.214
Carcinogencity:	0.06
Eye Corrosion:	0.004
Eye Irritation:	0.069
Respiratory Toxicity:	0.907

Download Data

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

Natural Product: NPC69543

Natural Product ID:	NPC69543
*Common Name:**	CIYZXQSKZRSLTE-YMQVBBKESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CIYZXQSKZRSLTE-YMQVBBKESA-N
Standard InCHI:	InChI=1S/C21H22O6/c1-4-7-21-12-9-25-20(21)19(24-3)18(23-2)17(22)16(21)15(12)11-5-6-13-14(8-11)27-10-26-13/h4-6,8,12,15-16,20H,1,7,9-10H2,2-3H3/t12-,15-,16-,20+,21-/m1/s1
SMILES:	C=CC[C@@]12[C@@H]3CO[C@H]2C(=C(C(=O)[C@H]1[C@@H]3c1ccc2c(c1)OCO2)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000296] Benzodioxoles

*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
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	Stems	Tainan Hsien, Taiwan, Republic of China	2000-JAN	PMID[16038551]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	leaves	n.a.	n.a.	PMID[19938815]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	root	n.a.	PMID[23738470]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[23738470]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[25275213]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1187	Baccharis scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7346	Ligularia odontomanes	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1863	Alpinia pricei	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8078	Palaquium leiocarpum	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO474	Beilschmiedia kunstleri	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3390	Radermachia sinica	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20070.1	Crinum stuhlmannii subsp. delagoense	Subspecies	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11706	Gordonia terrae	Species	Gordoniaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12193	Metadina trichotoma	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15978	Nalanthamala diospyri	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12316	Pterospermum lanceolatum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11948	Ferulago sylvatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12080	Metrodorea flavida	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10161	Macaranga pleiostemona	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11817	Seiridium cardinale	Species	Sporocadaceae	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 NPC69543 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	421
0.1-0.2	1485
0.2-0.3	3167
0.3-0.4	7996
0.4-0.5	11263
0.5-0.6	5456
0.6-0.7	11401
0.7-0.8	1417
0.8-0.85	75
0.85-0.9	11
0.9-0.95	5
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 NPC69543 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	357
0.1-0.2	854
0.2-0.3	1787
0.3-0.4	2699
0.4-0.5	1984
0.5-0.6	1060
0.6-0.7	383
0.7-0.8	26
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