NPASS Compound

Structure

NPC64331 OpenBabel06302215182D 25 28 0 0 0 0 0 0 0 0999 V2000 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 O 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 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 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 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 -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 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 -1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7350 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 0.3090 0.0000 O 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 0.8660 0.5000 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 1.5000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 21 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 15 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 20 2 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 19 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 20 24 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	342.07
Volume:	326.098
LogP:	3.105
LogD:	2.81
LogS:	-5.77
# Rotatable Bonds:	3
TPSA:	80.29
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.722
Synthetic Accessibility Score:	2.392
Fsp3:	0.222
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.724
MDCK Permeability:	6.245847180252895e-05
Pgp-inhibitor:	0.987
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.138
Plasma Protein Binding (PPB):	90.46218872070312%
Volume Distribution (VD):	0.652
Pgp-substrate:	6.764712333679199%

ADMET: Metabolism

CYP1A2-inhibitor:	0.619
CYP1A2-substrate:	0.961
CYP2C19-inhibitor:	0.627
CYP2C19-substrate:	0.516
CYP2C9-inhibitor:	0.602
CYP2C9-substrate:	0.877
CYP2D6-inhibitor:	0.127
CYP2D6-substrate:	0.409
CYP3A4-inhibitor:	0.845
CYP3A4-substrate:	0.486

ADMET: Excretion

Clearance (CL):	10.022
Half-life (T1/2):	0.205

ADMET: Toxicity

hERG Blockers:	0.064
Human Hepatotoxicity (H-HT):	0.151
Drug-inuced Liver Injury (DILI):	0.672
AMES Toxicity:	0.644
Rat Oral Acute Toxicity:	0.084
Maximum Recommended Daily Dose:	0.544
Skin Sensitization:	0.036
Carcinogencity:	0.951
Eye Corrosion:	0.003
Eye Irritation:	0.165
Respiratory Toxicity:	0.325

Download Data

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

Natural Product: NPC64331

Natural Product ID:	NPC64331
*Common Name:**	DTRVNXUELKBJRX-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DTRVNXUELKBJRX-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H14O7/c1-21-13-6-10-14(18(23-3)17(13)22-2)16(20)9-5-12-11(24-7-25-12)4-8(9)15(10)19/h4-6H,7H2,1-3H3
SMILES:	COc1cc2c(C(=O)c3cc4c(cc3C2=O)OCO4)c(c1OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[12880307]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Stems	n.a.	n.a.	PMID[17663584]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[18186611]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Steamed Roots	n.a.	n.a.	PMID[26200131]
NPO7946	Navicula delognei	Species	Berkeleyaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6512534]
NPO22413	Dysosma aurantiocaulis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7946	Navicula delognei	Species	Berkeleyaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22208	Spiraea mongolica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22413	Dysosma aurantiocaulis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22208	Spiraea mongolica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22026	Sibthorpia africana	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22208	Spiraea mongolica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22413	Dysosma aurantiocaulis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23074	Achillea grandifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18381	Inula eupatorioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13152	Chalcas paniculata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO18134	Heliobacterium modesticaldum	Species	Heliobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO21288	Ficus rumphii	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3675	Actinobole uliginosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22726	Carthamus lanatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22783	Pteris arguta	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21763	Parmotrema subisidiosum	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22266	Fagus taurica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21892	Eisenibacter elegans	Species	Microscillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7946	Navicula delognei	Species	Berkeleyaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19243	Sarcophyton decaryi	Species	Orchidaceae	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 NPC64331 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	491
0.1-0.2	2030
0.2-0.3	4601
0.3-0.4	11030
0.4-0.5	6924
0.5-0.6	3788
0.6-0.7	5823
0.7-0.8	6966
0.8-0.85	926
0.85-0.9	113
0.9-0.95	5
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 NPC64331 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	424
0.1-0.2	1024
0.2-0.3	1880
0.3-0.4	2850
0.4-0.5	1671
0.5-0.6	859
0.6-0.7	289
0.7-0.8	143
0.8-0.85	9
0.85-0.9	1
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