NPASS Compound

Structure

NPC261416 OpenBabel06302215512D 38 42 0 0 1 0 0 0 0 0999 V2000 -1.7494 -2.3914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4401 -1.7007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -1.9535 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2294 -2.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 -0.9767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6130 0.4884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 2.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 3.9070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6130 3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6130 2.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4589 1.9535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 2.4419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 0.9767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -0.9767 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6918 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -0.4884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8459 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9535 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8459 -1.4651 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8459 -0.4884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6918 0.0000 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 1.6918 -1.9535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9302 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5110 -2.9219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 25 1 0 0 0 0 3 4 1 0 0 0 0 3 38 1 6 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 25 1 0 0 0 0 8 9 1 0 0 0 0 8 24 1 0 0 0 0 9 22 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 2 0 0 0 0 13 15 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 16 22 1 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 21 1 0 0 0 0 22 23 2 0 0 0 0 25 26 1 1 0 0 0 27 26 1 6 0 0 0 27 28 1 0 0 0 0 27 33 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 35 1 6 0 0 0 30 31 1 0 0 0 0 30 34 1 1 0 0 0 31 32 1 6 0 0 0 31 33 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	527.22
Volume:	519.079
LogP:	4.378
LogD:	1.72
LogS:	-3.061
# Rotatable Bonds:	4
TPSA:	163.31
# H-Bond Aceptor:	10
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.198
Synthetic Accessibility Score:	4.97
Fsp3:	0.429
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.947
MDCK Permeability:	5.994867478875676e-06
Pgp-inhibitor:	0.206
Pgp-substrate:	0.829
Human Intestinal Absorption (HIA):	0.9
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.092

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	97.02620697021484%
Volume Distribution (VD):	0.887
Pgp-substrate:	8.076367378234863%

ADMET: Metabolism

CYP1A2-inhibitor:	0.131
CYP1A2-substrate:	0.901
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.07
CYP2C9-inhibitor:	0.097
CYP2C9-substrate:	0.426
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.229
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.496

ADMET: Excretion

Clearance (CL):	6.639
Half-life (T1/2):	0.357

ADMET: Toxicity

hERG Blockers:	0.1
Human Hepatotoxicity (H-HT):	0.293
Drug-inuced Liver Injury (DILI):	0.96
AMES Toxicity:	0.79
Rat Oral Acute Toxicity:	0.16
Maximum Recommended Daily Dose:	0.851
Skin Sensitization:	0.941
Carcinogencity:	0.747
Eye Corrosion:	0.003
Eye Irritation:	0.177
Respiratory Toxicity:	0.689

Download Data

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

Natural Product: NPC261416

Natural Product ID:	NPC261416
*Common Name:**	HECQIFUUJRYFRO-SSEWAAHHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HECQIFUUJRYFRO-SSEWAAHHSA-N
Standard InCHI:	InChI=1S/C28H33NO9/c1-5-28(36)10-9-14-19(27(28)38-17-11-15(29(3)4)22(31)12(2)37-17)26(35)21-20(24(14)33)25(34)18-13(23(21)32)7-6-8-16(18)30/h6-8,12,15,17,22,27,30-31,33,35-36H,5,9-11H2,1-4H3/t12-,15-,17+,22-,27-,28-/m1/s1
SMILES:	CC[C@]1(CCc2c(c(c3c(c2O)C(=O)c2c(cccc2O)C3=O)O)[C@H]1O[C@H]1C[C@H]([C@@H]([C@@H](C)O1)O)N(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000022] Naphthacenes [CHEMONTID:0000155] Tetracenequinones

*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
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[1002/hlca.19760590517]
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[931752]
NPO25885	Drupella fragum	Species	Muricidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9722496]
NPO25782	Crotalaria trifoliastrum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9784166]
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26911	Mesua thwaitesii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25912	Leontice smirnowii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26911	Mesua thwaitesii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25912	Leontice smirnowii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26769	Montanoa tomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25782	Crotalaria trifoliastrum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25912	Leontice smirnowii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26713	Lasius umbratus	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26600	Glottiphyllum longum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26616	Piper novae-hollandiae	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28906	Cossus cossus	Species	Cossidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3732	Entoleuca mammata	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26891	Pinus nigra	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4085	Cephalaria lycica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26310	Panax ricinifolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25861	Helminthosporium catenarium	Species	Massarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26198	Halimeda scabra	Species	Halimedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27039	Poterium polygamum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26998	Goniotrichum elegans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO25885	Drupella fragum	Species	Muricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26911	Mesua thwaitesii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13835	Aristolochia serpentaria	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26796	Tropaeolum peregrinum	Species	Tropaeolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11483	Adenocarpus decorticans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19417	Cochliobolus pallescens	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26276	Haplopappus taeda	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26769	Montanoa tomentosa	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 NPC261416 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	280
0.1-0.2	1174
0.2-0.3	3129
0.3-0.4	8459
0.4-0.5	9927
0.5-0.6	7171
0.6-0.7	9424
0.7-0.8	2996
0.8-0.85	104
0.85-0.9	21
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 NPC261416 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	197
0.1-0.2	628
0.2-0.3	1337
0.3-0.4	2436
0.4-0.5	2540
0.5-0.6	1421
0.6-0.7	477
0.7-0.8	80
0.8-0.85	8
0.85-0.9	18
0.9-0.95	8
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