NPASS Compound

Structure

NPC296556 OpenBabel06302215592D 30 32 0 0 1 0 0 0 0 0999 V2000 1.6796 4.8485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 3.8788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 3.3939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 1.9394 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1989 2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0387 1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0387 0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1989 0.4848 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1989 -0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0387 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0387 -1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1989 -2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 -1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 0.9697 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6796 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 -0.9697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8398 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8398 0.4848 0.0000 C 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 -0.0000 -0.9697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6796 1.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5193 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 1.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1989 3.3939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 3.3939 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 30 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 16 1 0 0 0 0 6 7 2 0 0 0 0 6 29 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 6 0 0 0 9 16 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 16 17 1 1 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 28 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 26 1 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	327.22
Volume:	361.498
LogP:	3.753
LogD:	3.452
LogS:	-4.855
# Rotatable Bonds:	2
TPSA:	60.16
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.613
Synthetic Accessibility Score:	4.456
Fsp3:	0.619
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.677
MDCK Permeability:	2.2929267288418487e-05
Pgp-inhibitor:	0.992
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.775
Plasma Protein Binding (PPB):	94.11585998535156%
Volume Distribution (VD):	1.64
Pgp-substrate:	6.394019603729248%

ADMET: Metabolism

CYP1A2-inhibitor:	0.649
CYP1A2-substrate:	0.642
CYP2C19-inhibitor:	0.562
CYP2C19-substrate:	0.742
CYP2C9-inhibitor:	0.484
CYP2C9-substrate:	0.074
CYP2D6-inhibitor:	0.876
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.852
CYP3A4-substrate:	0.255

ADMET: Excretion

Clearance (CL):	10.042
Half-life (T1/2):	0.178

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.668
Drug-inuced Liver Injury (DILI):	0.091
AMES Toxicity:	0.113
Rat Oral Acute Toxicity:	0.91
Maximum Recommended Daily Dose:	0.893
Skin Sensitization:	0.945
Carcinogencity:	0.833
Eye Corrosion:	0.015
Eye Irritation:	0.052
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC296556

Natural Product ID:	NPC296556
*Common Name:**	LYDZCXVWCFJAKQ-IMSXRSKXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LYDZCXVWCFJAKQ-IMSXRSKXSA-N
Standard InCHI:	InChI=1S/C26H30O4/c1-16(2)10-12-20-17(3)11-13-21(18-8-6-5-7-9-18)24(20)26(29)25-22(27)14-19(30-4)15-23(25)28/h5-11,14-15,20-21,24,27-28H,12-13H2,1-4H3/t20-,21+,24-/m0/s1
SMILES:	CC(=CC[C@H]1C(=CC[C@H](c2ccccc2)[C@H]1C(=O)c1c(cc(cc1O)OC)O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25023021
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	root	n.a.	PMID[10514313]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	roots	n.a.	n.a.	PMID[10514313]
NPO27986	Lonchocarpus chiricanus	Species	Fabaceae	Eukaryota	Root barks	n.a.	n.a.	PMID[11421729]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	roots	n.a.	n.a.	PMID[11575962]
NPO24946	Kaempferia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[15930750]
NPO27695	Centaurea sonchifolia	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[1624943]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	rhizomes	Pindaya Township, Shan State, Myanmar	2004-NOV	PMID[17896818]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27508308]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[28099006]
NPO19745	Esox lucius	Species	Esocidae	Eukaryota	n.a.	n.a.	n.a.	PMID[3349210]
NPO28159	Rubia akane	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8176404]
NPO19745	Esox lucius	Species	Esocidae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19745	Esox lucius	Species	Esocidae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO24946	Kaempferia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27397	Drymaria cordata	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24946	Kaempferia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23156	Maclura cochinchinensis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27882	Boswellia ovalifoliolata	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28159	Rubia akane	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27057	Matsucoccus josephi	Species	Margarodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25499	Campanula choziatowskyi	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4164	Salvia virgata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27145	Euphorbia hylonoma	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28044	Erythrina hypaphorus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28159	Rubia akane	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28289	Nepytia freemani	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16156	Mucuna holtonii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28385	Iris kashmiriana	Species	Tarachodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5970.1	Petunia axillaris subsp. parodii	Subspecies	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27916	Hardenbergia violacea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27455	Dysidea fragilis	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11849	Cynoglossum macrostylum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26476	Preussia terricola	Species	Sporormiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27234	Thalassiosira weissflogii	Species	Thalassiosiraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27986	Lonchocarpus chiricanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27506	Orgyia pseudotsugata	Species	Lymantriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27882	Boswellia ovalifoliolata	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26553	Lemonia spectabilis	Species	Lemoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28063	Beilschmiedia madang	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8738	Xylopia emarginata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27338	Senecio platyphylloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26321	Salvia patens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27613	Helleborus macranthus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27614	Salix rosmarinifolia	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28003	Astragalus circassicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27637	Heliotropium scabrum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27816	Pterocaulon serrulatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19383	Lactarius mitissimus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8961	Bethencourtia palmensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17337	Centaurea scoparia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28426	Etmopterus spinax	Species	Etmopteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26342	Dialium excelsum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27397	Drymaria cordata	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28313	Mentzelia decapetala	Species	Loasaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28412	Amorphophallus konjac	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16298	Quercus marilandica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27702	Matricaria sabulosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28206	Aniba santalodora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25835	Parmotrema nilgherrense	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9354	Lepechinia urbanii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28083	Salvia lavanduloides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19745	Esox lucius	Species	Esocidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27695	Centaurea sonchifolia	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23156	Maclura cochinchinensis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1184	Colchicum filifolium	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1373	Pulsatilla chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24946	Kaempferia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27642	Podocarpus dacrydioides	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2030	Mimosa pigra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27854	Sphaeria rousseliana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10367	Gaillardia coahuilensis	Species	Asteraceae	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 NPC296556 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	358
0.1-0.2	1496
0.2-0.3	3508
0.3-0.4	9017
0.4-0.5	9508
0.5-0.6	3500
0.6-0.7	5921
0.7-0.8	5885
0.8-0.85	2060
0.85-0.9	1078
0.9-0.95	350
0.95-1	16

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 NPC296556 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	325
0.1-0.2	940
0.2-0.3	1397
0.3-0.4	2509
0.4-0.5	2054
0.5-0.6	1240
0.6-0.7	486
0.7-0.8	142
0.8-0.85	42
0.85-0.9	10
0.9-0.95	5
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