NPASS Compound

Structure

NPC95468 OpenBabel06302216152D 25 29 0 0 1 0 0 0 0 0999 V2000 -2.2945 2.0260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8177 1.2002 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3047 0.3566 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8177 -0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8436 -0.4870 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3566 0.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8436 1.2002 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8436 2.1743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.6613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8436 2.1743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6620 2.6469 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8436 1.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.7131 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 -0.0001 3.6064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8184 4.0790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2788 0.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7658 -0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7399 -0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2270 0.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7399 1.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7658 1.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3917 1.9241 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2816 1.5279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3288 1.3253 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 17 1 1 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 14 1 0 0 0 0 7 6 1 1 0 0 0 7 13 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 25 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	340.13
Volume:	339.826
LogP:	3.206
LogD:	2.82
LogS:	-4.966
# Rotatable Bonds:	2
TPSA:	53.99
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.827
Synthetic Accessibility Score:	5.483
Fsp3:	0.45
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:	-4.846
MDCK Permeability:	2.3071723262546584e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.989
30% Bioavailability (F30%):	0.585

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	99.12858581542969%
Volume Distribution (VD):	0.78
Pgp-substrate:	1.6884346008300781%

ADMET: Metabolism

CYP1A2-inhibitor:	0.869
CYP1A2-substrate:	0.565
CYP2C19-inhibitor:	0.969
CYP2C19-substrate:	0.834
CYP2C9-inhibitor:	0.928
CYP2C9-substrate:	0.637
CYP2D6-inhibitor:	0.97
CYP2D6-substrate:	0.369
CYP3A4-inhibitor:	0.972
CYP3A4-substrate:	0.716

ADMET: Excretion

Clearance (CL):	10.17
Half-life (T1/2):	0.291

ADMET: Toxicity

hERG Blockers:	0.12
Human Hepatotoxicity (H-HT):	0.879
Drug-inuced Liver Injury (DILI):	0.354
AMES Toxicity:	0.129
Rat Oral Acute Toxicity:	0.051
Maximum Recommended Daily Dose:	0.906
Skin Sensitization:	0.949
Carcinogencity:	0.831
Eye Corrosion:	0.029
Eye Irritation:	0.156
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC95468

Natural Product ID:	NPC95468
*Common Name:**	SXHVHWXETMBKPP-ZBQLUDKISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SXHVHWXETMBKPP-ZBQLUDKISA-N
Standard InCHI:	InChI=1S/C20H20O5/c1-11-14(12-3-4-16-17(5-12)24-10-23-16)6-13-8-20(11)9-18(22-2)15(21)7-19(20)25-13/h3-5,7,9,11,13-14H,6,8,10H2,1-2H3/t11-,13+,14+,20-/m0/s1
SMILES:	C[C@H]1[C@@H](C[C@@H]2C[C@@]31C=C(C(=O)C=C3O2)OC)c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101820916
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
NPO4682	Lindera aggregata	Species	Lauraceae	Eukaryota	n.a.	leaf	n.a.	PMID[17999353]
NPO4682	Lindera aggregata	Species	Lauraceae	Eukaryota	Roots; Tubers	n.a.	n.a.	PMID[19639966]
NPO9925	Rhododendron latoucheae	Species	Ericaceae	Eukaryota	Twigs; Leaves	n.a.	n.a.	PMID[30106288]
NPO9480	Huperzia miyoshiana	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9480	Huperzia miyoshiana	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4682	Lindera aggregata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4682	Lindera aggregata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9925	Rhododendron latoucheae	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19174	Anoplophora chinensis	Species	Cerambycidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9480	Huperzia miyoshiana	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1155	Forsythia japonica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4682	Lindera aggregata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6475	Gymnosporia trigyna	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7522	Streptomyces amakusaensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO313	Castilleja sulphurea	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9571	Pseudobrickellia brasiliensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9301	Dioscorea sativa	Species	Dioscoreaceae	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 NPC95468 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	431
0.1-0.2	1439
0.2-0.3	2902
0.3-0.4	7765
0.4-0.5	11494
0.5-0.6	6608
0.6-0.7	10361
0.7-0.8	1635
0.8-0.85	55
0.85-0.9	4
0.9-0.95	2
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 NPC95468 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	330
0.1-0.2	850
0.2-0.3	1481
0.3-0.4	2769
0.4-0.5	2108
0.5-0.6	1113
0.6-0.7	457
0.7-0.8	41
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