NPASS Compound

Structure

NPC195888 OpenBabel06302216032D 24 27 0 0 1 0 0 0 0 0999 V2000 -7.3250 2.2237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9182 1.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9237 1.2056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5170 0.2921 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3830 0.7921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2490 0.2921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2490 -0.7079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3830 -1.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3830 -2.2079 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5170 -0.7079 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9237 -1.6215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5659 -1.0169 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9781 -0.2079 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5659 0.6011 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2569 1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9781 -0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4781 -1.0739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 -1.0739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9781 -0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 1.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 0.9945 0.0000 C 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 2 2 0 0 0 0 2 3 1 0 0 0 0 4 3 1 6 0 0 0 4 14 1 0 0 0 0 4 5 1 0 0 0 0 4 10 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 16 1 1 0 0 0 14 15 1 6 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 24 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.13
Volume:	331.087
LogP:	3.328
LogD:	2.763
LogS:	-4.498
# Rotatable Bonds:	3
TPSA:	64.99
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.864
Synthetic Accessibility Score:	4.548
Fsp3:	0.421
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.629
MDCK Permeability:	3.3968019124586135e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.579
30% Bioavailability (F30%):	0.804

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.901
Plasma Protein Binding (PPB):	86.90619659423828%
Volume Distribution (VD):	1.123
Pgp-substrate:	10.07579517364502%

ADMET: Metabolism

CYP1A2-inhibitor:	0.907
CYP1A2-substrate:	0.822
CYP2C19-inhibitor:	0.546
CYP2C19-substrate:	0.785
CYP2C9-inhibitor:	0.105
CYP2C9-substrate:	0.05
CYP2D6-inhibitor:	0.847
CYP2D6-substrate:	0.342
CYP3A4-inhibitor:	0.946
CYP3A4-substrate:	0.725

ADMET: Excretion

Clearance (CL):	13.921
Half-life (T1/2):	0.3

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.234
Drug-inuced Liver Injury (DILI):	0.091
AMES Toxicity:	0.812
Rat Oral Acute Toxicity:	0.52
Maximum Recommended Daily Dose:	0.28
Skin Sensitization:	0.337
Carcinogencity:	0.95
Eye Corrosion:	0.004
Eye Irritation:	0.139
Respiratory Toxicity:	0.956

Download Data

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

Natural Product: NPC195888

Natural Product ID:	NPC195888
*Common Name:**	ZWZOJVXHAOTSDM-NVAWSTJUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZWZOJVXHAOTSDM-NVAWSTJUSA-N
Standard InCHI:	InChI=1S/C19H20O5/c1-3-8-18-9-4-5-16(20)19(18,21)24-17(12(18)2)13-6-7-14-15(10-13)23-11-22-14/h3-7,10,12,17,21H,1,8-9,11H2,2H3/t12-,17+,18+,19-/m1/s1
SMILES:	C=CC[C@]12CC=CC(=O)[C@@]2(O)O[C@@H]([C@H]1C)c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15126690
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
NPO21557	Woodsia manchuriensis	Species	Woodsiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10293	Diaporthe phaseolorum	Species	Diaporthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2243	Euphorbia splendens	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9616	Lunasia costulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8072	Rudbeckia speciosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9108	Leptotaenia multifida	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2649	Ocotea aciphylla	Species	Lauraceae	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 NPC195888 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	335
0.1-0.2	1286
0.2-0.3	2762
0.3-0.4	6360
0.4-0.5	11266
0.5-0.6	5933
0.6-0.7	9987
0.7-0.8	4576
0.8-0.85	161
0.85-0.9	23
0.9-0.95	7
0.95-1	1

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 NPC195888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	291
0.1-0.2	820
0.2-0.3	1662
0.3-0.4	2590
0.4-0.5	2076
0.5-0.6	1130
0.6-0.7	505
0.7-0.8	75
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