NPASS Compound

Structure

NPC219854 OpenBabel06302215392D 37 40 0 0 1 0 0 0 0 0999 V2000 6.0622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -6.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7942 -6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -6.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -5.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 3 2 1 1 0 0 0 3 4 1 0 0 0 0 3 13 1 0 0 0 0 4 5 1 0 0 0 0 4 15 1 6 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 13 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 6 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 17 37 1 6 0 0 0 18 19 1 0 0 0 0 18 36 1 1 0 0 0 19 20 1 0 0 0 0 19 24 1 6 0 0 0 20 21 1 1 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.3
Volume:	515.423
LogP:	5.655
LogD:	4.424
LogS:	-5.014
# Rotatable Bonds:	2
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.397
Synthetic Accessibility Score:	5.315
Fsp3:	0.733
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.86
MDCK Permeability:	3.0918821721570566e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.878
30% Bioavailability (F30%):	0.373

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	97.22852325439453%
Volume Distribution (VD):	2.409
Pgp-substrate:	3.084373712539673%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.263
CYP2C19-inhibitor:	0.709
CYP2C19-substrate:	0.863
CYP2C9-inhibitor:	0.77
CYP2C9-substrate:	0.645
CYP2D6-inhibitor:	0.702
CYP2D6-substrate:	0.091
CYP3A4-inhibitor:	0.92
CYP3A4-substrate:	0.774

ADMET: Excretion

Clearance (CL):	4.468
Half-life (T1/2):	0.228

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.805
Drug-inuced Liver Injury (DILI):	0.032
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.959
Skin Sensitization:	0.973
Carcinogencity:	0.121
Eye Corrosion:	0.049
Eye Irritation:	0.387
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC219854

Natural Product ID:	NPC219854
*Common Name:**	HDCDXJNXZKWABL-KHQKZOISSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HDCDXJNXZKWABL-KHQKZOISSA-N
Standard InCHI:	InChI=1S/C25H28O12/c1-2-15-23(34-12-16-22(31)33-10-9-25(15,16)32)37-24-20(30)19(29)21(17(11-26)35-24)36-18(28)8-5-13-3-6-14(27)7-4-13/h2-8,12,15,17,19-21,23-24,26-27,29-30,32H,1,9-11H2/b8-5+/t15-,17+,19+,20+,21+,23-,24-,25+/m0/s1
SMILES:	C=C[C@H]1[C@@H](OC=C2C(=O)OCC[C@@]12O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)OC(=O)/C=C/c1ccc(cc1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101394761
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0003002] Hydroxycinnamic acid esters [CHEMONTID:0000465] Coumaric acid esters

*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
NPO25228	Corollospora pulchella	Species	Halosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9666182]
NPO24661	Leontice leontopetalum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20828	Swertia leducii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20828	Swertia leducii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24468	Zanthoxylum macrophyllum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2825	Chiloscyphus pallescens	Species	Lophocoleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23292	Andrographis macrobotrys	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20828	Swertia leducii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24661	Leontice leontopetalum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21804	Dryopteris villarii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25228	Corollospora pulchella	Species	Halosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24875	Lithocarpus litseifolius	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25134	Cephalosporium chrysogenum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23166	Keteleeria evelyniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25070	Naranga aenescens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22424	Cetraria ornata	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13483	Silene praemixta	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19759	Begonia fagifolia	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22085	Cercospora traversiana	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11200.1	Paenibacillus larvae subsp. pulvifaciens	Subspecies	Paenibacillaceae	Bacteria	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 NPC219854 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	312
0.1-0.2	1175
0.2-0.3	2907
0.3-0.4	6799
0.4-0.5	10286
0.5-0.6	8130
0.6-0.7	10397
0.7-0.8	2447
0.8-0.85	174
0.85-0.9	56
0.9-0.95	13
0.95-1	1

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 NPC219854 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	261
0.1-0.2	733
0.2-0.3	1620
0.3-0.4	2910
0.4-0.5	2100
0.5-0.6	1163
0.6-0.7	335
0.7-0.8	27
0.8-0.85	1
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