NPASS Compound

Structure

NPC4025 OpenBabel06302215552D 24 26 0 0 1 0 0 0 0 0999 V2000 2.6831 -4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0491 -0.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5491 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2872 1.1590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5962 2.1100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9563 0.4158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 17 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 8 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 16 17 1 6 0 0 0 16 20 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 1 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	336.19
Volume:	347.553
LogP:	3.144
LogD:	2.479
LogS:	-3.127
# Rotatable Bonds:	4
TPSA:	61.83
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.721
Synthetic Accessibility Score:	4.513
Fsp3:	0.789
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:	-4.639
MDCK Permeability:	7.731965888524428e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.963
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.498
Plasma Protein Binding (PPB):	71.88600158691406%
Volume Distribution (VD):	2.011
Pgp-substrate:	35.551387786865234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.179
CYP1A2-substrate:	0.066
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.587
CYP2C9-inhibitor:	0.111
CYP2C9-substrate:	0.041
CYP2D6-inhibitor:	0.395
CYP2D6-substrate:	0.126
CYP3A4-inhibitor:	0.513
CYP3A4-substrate:	0.397

ADMET: Excretion

Clearance (CL):	2.735
Half-life (T1/2):	0.237

ADMET: Toxicity

hERG Blockers:	0.141
Human Hepatotoxicity (H-HT):	0.859
Drug-inuced Liver Injury (DILI):	0.682
AMES Toxicity:	0.886
Rat Oral Acute Toxicity:	0.732
Maximum Recommended Daily Dose:	0.543
Skin Sensitization:	0.591
Carcinogencity:	0.972
Eye Corrosion:	0.914
Eye Irritation:	0.461
Respiratory Toxicity:	0.966

Download Data

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

Natural Product: NPC4025

Natural Product ID:	NPC4025
*Common Name:**	XOZIZCAYPORZCT-BCDMZGRMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XOZIZCAYPORZCT-BCDMZGRMSA-N
Standard InCHI:	InChI=1S/C19H28O5/c1-11(20)23-14-9-15-18(3,4)7-6-8-19(15,5)16-13(14)10-22-17(16)24-12(2)21/h10,14-17H,6-9H2,1-5H3/t14-,15+,16-,17+,19+/m1/s1
SMILES:	CC(=O)O[C@@H]1C[C@H]2C(C)(C)CCC[C@]2(C)[C@@H]2C1=CO[C@H]2OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14165763
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001634] Naphthofurans

*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
NPO18783	Garcinia fusca	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608849]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26394166]
NPO17862	Zanthoxylum planispinum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20535	Podocarpus spicatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12878	Cupressus sempervirens	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17862	Zanthoxylum planispinum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20535	Podocarpus spicatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20535	Podocarpus spicatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17862	Zanthoxylum planispinum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20535	Podocarpus spicatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18783	Garcinia fusca	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13734	Piper excelsum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17862	Zanthoxylum planispinum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21662	Geranium bellum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12878	Cupressus sempervirens	Species	Cupressaceae	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 NPC4025 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	214
0.1-0.2	1843
0.2-0.3	5944
0.3-0.4	15326
0.4-0.5	8806
0.5-0.6	7623
0.6-0.7	2674
0.7-0.8	256
0.8-0.85	7
0.85-0.9	4
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 NPC4025 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	181
0.1-0.2	2271
0.2-0.3	3968
0.3-0.4	1946
0.4-0.5	476
0.5-0.6	270
0.6-0.7	37
0.7-0.8	1
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