NPASS Compound

Structure

NPC94581 OpenBabel06302215412D 29 32 0 0 1 0 0 0 0 0999 V2000 1.8632 0.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9972 -0.0747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9972 0.9253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5605 -0.9010 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2658 -1.8565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3349 -2.2219 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3349 -3.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5311 -3.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5311 -4.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3972 -5.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2632 -4.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2632 -3.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3972 -3.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3972 -2.2219 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2632 -1.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1292 -2.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9952 -1.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9952 -0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1292 -0.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2632 -0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1292 0.7781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2632 1.2781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8613 -0.2219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5311 -1.7219 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6802 -0.7331 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 -3.1292 -5.2219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3972 -6.2219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2632 -6.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 26 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 24 1 0 0 0 0 7 8 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 28 1 0 0 0 0 11 12 2 0 0 0 0 11 27 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 24 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 24 25 1 1 0 0 0 25 26 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	400.19
Volume:	409.061
LogP:	3.796
LogD:	3.376
LogS:	-4.395
# Rotatable Bonds:	3
TPSA:	77.38
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.816
Synthetic Accessibility Score:	3.785
Fsp3:	0.478
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.741
MDCK Permeability:	1.8794000425259583e-05
Pgp-inhibitor:	0.036
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.024
30% Bioavailability (F30%):	0.082

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.031
Plasma Protein Binding (PPB):	98.60710906982422%
Volume Distribution (VD):	0.724
Pgp-substrate:	1.7615275382995605%

ADMET: Metabolism

CYP1A2-inhibitor:	0.059
CYP1A2-substrate:	0.591
CYP2C19-inhibitor:	0.596
CYP2C19-substrate:	0.833
CYP2C9-inhibitor:	0.833
CYP2C9-substrate:	0.788
CYP2D6-inhibitor:	0.388
CYP2D6-substrate:	0.879
CYP3A4-inhibitor:	0.49
CYP3A4-substrate:	0.833

ADMET: Excretion

Clearance (CL):	11.456
Half-life (T1/2):	0.558

ADMET: Toxicity

hERG Blockers:	0.084
Human Hepatotoxicity (H-HT):	0.293
Drug-inuced Liver Injury (DILI):	0.937
AMES Toxicity:	0.055
Rat Oral Acute Toxicity:	0.156
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.234
Carcinogencity:	0.231
Eye Corrosion:	0.003
Eye Irritation:	0.224
Respiratory Toxicity:	0.657

Download Data

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

Natural Product: NPC94581

Natural Product ID:	NPC94581
*Common Name:**	SNCSNQKSYHFYSD-YHEJKZAPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SNCSNQKSYHFYSD-YHEJKZAPSA-N
Standard InCHI:	InChI=1S/C23H28O6/c1-23(2)28-11-15-7-14-9-21(27-4)19(25)10-16(14)22(17(15)12-29-23)13-5-6-18(24)20(8-13)26-3/h5-6,8-10,15,17,22,24-25H,7,11-12H2,1-4H3/t15-,17-,22-/m0/s1
SMILES:	CC1(C)OC[C@@H]2Cc3cc(c(cc3[C@H](c3ccc(c(c3)OC)O)[C@H]2CO1)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	91885030
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003425] Aryltetralin lignans

*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
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[11473432]
NPO25366	Sapium indicum	Species	Euphorbiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[12713411]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124776]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	bark	n.a.	n.a.	PMID[17907781]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18804027]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	bark	n.a.	n.a.	PMID[19646881]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20233596]
NPO25054	Phaleria macrocarpa	Species	Thymelaeaceae	Eukaryota	nut shell	n.a.	n.a.	PMID[23044367]
NPO25252	Nannocystis exedens	Species	Nannocystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24460410]
NPO25311	Guettarda platypoda	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2553871]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32058711]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8557595]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[8991951]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9644081]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24852	Helicia nilagirica	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22283	Alhagi maurorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15482	Vanderbylia fraxinea	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28460	Achyrocline tomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22152	Tecoma undulata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24566	Marasmiellus ramealis	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25389	Allium angulosum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25466	Lecanora sulphurella	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22283	Alhagi maurorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25492	Botryllus leachi	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23994	Ormosia macrophylla	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18706	Anemone thalictroides	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25054	Phaleria macrocarpa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23894	Pulicaria insignis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25311	Guettarda platypoda	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22618	Psolus eximius	Species	Psolidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14189	Osmundaria spiralis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24461	Clusia sandiensis	Species	Clusiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25366	Sapium indicum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24607	Goniothalamus dolichocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24852	Helicia nilagirica	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3721	Achyranthes obtusifolia	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24882	Erythrophleum chlorostachys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27390	Vernonia brevifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25252	Nannocystis exedens	Species	Nannocystaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO24802	Diploprion bifasciatum	Species	Serranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24730	Lactarius deliciosus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25277	Seiridium cupressi	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20264	Moonia heterophylla	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO25441	Desmodium pulchellu	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	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 NPC94581 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	380
0.1-0.2	1614
0.2-0.3	3904
0.3-0.4	11380
0.4-0.5	7447
0.5-0.6	5624
0.6-0.7	8819
0.7-0.8	3045
0.8-0.85	425
0.85-0.9	51
0.9-0.95	8
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 NPC94581 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	338
0.1-0.2	933
0.2-0.3	1648
0.3-0.4	2803
0.4-0.5	1718
0.5-0.6	978
0.6-0.7	638
0.7-0.8	88
0.8-0.85	6
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