NPASS Compound

Structure

NPC56026 OpenBabel06302215392D 28 32 0 0 1 0 0 0 0 0999 V2000 -0.8839 -0.4582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8839 0.4948 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6681 0.9476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6683 1.8534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8837 2.3062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0995 1.8535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6846 2.3061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6847 3.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0995 3.6646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8840 3.2118 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8844 4.1173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0073 4.2752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4669 4.8106 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1578 5.6617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6682 3.6646 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9133 4.5792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4525 2.3062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0996 0.9478 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7710 1.3354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4087 0.6272 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3564 0.7268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8329 1.5521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7651 1.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8647 0.4062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9941 0.0186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9322 -0.1981 0.0000 O 0 0 0 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 -1.4164 -1.2753 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 18 1 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 17 1 0 0 0 0 5 10 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 18 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 6 0 0 0 10 15 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 18 27 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 1 0 0 0 20 26 1 0 0 0 0 21 25 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.15
Volume:	377.339
LogP:	2.091
LogD:	1.974
LogS:	-4.289
# Rotatable Bonds:	3
TPSA:	95.2
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.615
Synthetic Accessibility Score:	5.479
Fsp3:	0.619
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:	-5.242
MDCK Permeability:	5.095839878777042e-05
Pgp-inhibitor:	0.351
Pgp-substrate:	0.93
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.393

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.323
Plasma Protein Binding (PPB):	88.61585235595703%
Volume Distribution (VD):	2.604
Pgp-substrate:	10.717611312866211%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.773
CYP2C19-inhibitor:	0.493
CYP2C19-substrate:	0.827
CYP2C9-inhibitor:	0.826
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.201
CYP3A4-inhibitor:	0.747
CYP3A4-substrate:	0.568

ADMET: Excretion

Clearance (CL):	7.53
Half-life (T1/2):	0.24

ADMET: Toxicity

hERG Blockers:	0.067
Human Hepatotoxicity (H-HT):	0.688
Drug-inuced Liver Injury (DILI):	0.208
AMES Toxicity:	0.794
Rat Oral Acute Toxicity:	0.992
Maximum Recommended Daily Dose:	0.935
Skin Sensitization:	0.208
Carcinogencity:	0.921
Eye Corrosion:	0.003
Eye Irritation:	0.04
Respiratory Toxicity:	0.959

Download Data

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

Natural Product: NPC56026

Natural Product ID:	NPC56026
*Common Name:**	PRUZGIISEPDMEU-YDYULBBASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PRUZGIISEPDMEU-YDYULBBASA-N
Standard InCHI:	InChI=1S/C21H24O7/c1-11-8-14-16-13(4-3-6-20(16,17(22)25-2)18(23)27-14)21(11)9-15(28-19(21)24)12-5-7-26-10-12/h5,7,10-11,14-15,18,23H,3-4,6,8-9H2,1-2H3/t11-,14+,15+,18-,20+,21-/m1/s1
SMILES:	C[C@@H]1C[C@H]2C3=C(CCC[C@]3(C(=O)OC)[C@H](O)O2)[C@]21C[C@@H](c1ccoc1)OC2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000472] Hydroxy acids and derivatives [CHEMONTID:0001713] Beta hydroxy acids and derivatives

*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
NPO16699	Agave utahensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19645463]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11429	Matricaria parthenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13047	Epipolasis kushimotoensis	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14435	Mnium hornum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8606	Mallotus repandus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7720	Cyathocline purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12218	Pulicaria wightiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12393	Xanthoparmelia subincerta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16102	Senecio chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15984	Blainvillea rhomboidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13938	Plantago alpina	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11453	Centaurea cadmea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4754	Yucca flexilis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO642	Artemisia bigelovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15300	Bipolaris zeicola	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11633	Kelletia kelletii	Species	Buccinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16699	Agave utahensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16207	Acacia glaucescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	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 NPC56026 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	313
0.1-0.2	1261
0.2-0.3	3181
0.3-0.4	6833
0.4-0.5	11966
0.5-0.6	9705
0.6-0.7	8518
0.7-0.8	787
0.8-0.85	91
0.85-0.9	30
0.9-0.95	10
0.95-1	2

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 NPC56026 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	262
0.1-0.2	993
0.2-0.3	2296
0.3-0.4	2690
0.4-0.5	2009
0.5-0.6	708
0.6-0.7	185
0.7-0.8	7
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