NPASS Compound

Structure

NPC80616 OpenBabel06302215512D 22 24 0 0 0 0 0 0 0 0999 V2000 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 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 -0.8660 -0.5000 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 -1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 20 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 22 1 0 0 0 0 7 8 1 0 0 0 0 8 18 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 17 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 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	298.08
Volume:	299.778
LogP:	3.069
LogD:	1.929
LogS:	-3.501
# Rotatable Bonds:	2
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.385
Synthetic Accessibility Score:	2.932
Fsp3:	0.176
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:	-4.758
MDCK Permeability:	2.1961424863548018e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.372

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.02
Plasma Protein Binding (PPB):	98.06590270996094%
Volume Distribution (VD):	0.779
Pgp-substrate:	3.599581480026245%

ADMET: Metabolism

CYP1A2-inhibitor:	0.963
CYP1A2-substrate:	0.233
CYP2C19-inhibitor:	0.287
CYP2C19-substrate:	0.11
CYP2C9-inhibitor:	0.777
CYP2C9-substrate:	0.501
CYP2D6-inhibitor:	0.537
CYP2D6-substrate:	0.183
CYP3A4-inhibitor:	0.517
CYP3A4-substrate:	0.152

ADMET: Excretion

Clearance (CL):	4.816
Half-life (T1/2):	0.568

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.54
Drug-inuced Liver Injury (DILI):	0.96
AMES Toxicity:	0.938
Rat Oral Acute Toxicity:	0.624
Maximum Recommended Daily Dose:	0.438
Skin Sensitization:	0.257
Carcinogencity:	0.963
Eye Corrosion:	0.003
Eye Irritation:	0.056
Respiratory Toxicity:	0.884

Download Data

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

Natural Product: NPC80616

Natural Product ID:	NPC80616
*Common Name:**	VRARPPQMEQUQET-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VRARPPQMEQUQET-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C17H14O5/c1-2-22-8-12-13(18)7-11-14(17(12)21)16(20)10-6-4-3-5-9(10)15(11)19/h3-7,18,21H,2,8H2,1H3
SMILES:	CCOCc1c(cc2c(C(=O)c3ccccc3C2=O)c1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	28578
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO23980	Rhamnus nakaharai	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691213]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13324	Euphorbia ingens	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13324	Euphorbia ingens	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26368	Fomes tasmanicus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2868	Perna viridis	Species	Mytilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO861	Siphonaria funiculata	Species	Siphonariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13446	Stachys recta	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23980	Rhamnus nakaharai	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11734	Chara corallina	Species	Characeae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24656	Scabiosa olgae	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15917	Monilinia fructigena	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26859	Solanum curtipes	Species	Solanaceae	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 NPC80616 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	370
0.1-0.2	1572
0.2-0.3	3587
0.3-0.4	8938
0.4-0.5	9687
0.5-0.6	3830
0.6-0.7	6240
0.7-0.8	5652
0.8-0.85	2044
0.85-0.9	685
0.9-0.95	87
0.95-1	5

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 NPC80616 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	975
0.2-0.3	1444
0.3-0.4	2647
0.4-0.5	2015
0.5-0.6	1146
0.6-0.7	385
0.7-0.8	168
0.8-0.85	29
0.85-0.9	2
0.9-0.95	1
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