NPASS Compound

Structure

NPC67790 OpenBabel06302216202D 26 31 0 0 1 0 0 0 0 0999 V2000 1.7895 -0.9589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6802 -1.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4658 -0.7768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3606 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4699 0.5838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6844 0.0089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8396 0.4927 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8396 1.4774 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8396 2.4624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0260 2.9550 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8656 2.4624 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.7104 2.9461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6781 2.8410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2531 3.6265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8603 4.5172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8925 4.6224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3176 3.8368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6935 5.5753 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5382 6.0591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1392 5.1711 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8656 1.4774 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8656 0.4927 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 4.2485 0.5901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9024 -0.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9495 0.0680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 26 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 24 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 23 1 0 0 0 0 8 9 1 1 0 0 0 8 21 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 21 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 20 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 1 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	354.11
Volume:	340.06
LogP:	3.644
LogD:	3.059
LogS:	-5.634
# Rotatable Bonds:	2
TPSA:	55.38
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.825
Synthetic Accessibility Score:	3.774
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.966
MDCK Permeability:	5.4007290600566193e-05
Pgp-inhibitor:	0.79
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.017

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.139
Plasma Protein Binding (PPB):	96.35446166992188%
Volume Distribution (VD):	1.005
Pgp-substrate:	2.2629778385162354%

ADMET: Metabolism

CYP1A2-inhibitor:	0.771
CYP1A2-substrate:	0.234
CYP2C19-inhibitor:	0.946
CYP2C19-substrate:	0.151
CYP2C9-inhibitor:	0.778
CYP2C9-substrate:	0.802
CYP2D6-inhibitor:	0.962
CYP2D6-substrate:	0.909
CYP3A4-inhibitor:	0.968
CYP3A4-substrate:	0.334

ADMET: Excretion

Clearance (CL):	19.003
Half-life (T1/2):	0.065

ADMET: Toxicity

hERG Blockers:	0.255
Human Hepatotoxicity (H-HT):	0.203
Drug-inuced Liver Injury (DILI):	0.857
AMES Toxicity:	0.823
Rat Oral Acute Toxicity:	0.095
Maximum Recommended Daily Dose:	0.489
Skin Sensitization:	0.682
Carcinogencity:	0.886
Eye Corrosion:	0.003
Eye Irritation:	0.477
Respiratory Toxicity:	0.743

Download Data

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

Natural Product: NPC67790

Natural Product ID:	NPC67790
*Common Name:**	PEYUIKBAABKQKQ-XIDAIZRNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PEYUIKBAABKQKQ-XIDAIZRNSA-N
Standard InCHI:	InChI=1S/C20H18O6/c1-3-15-17(25-9-23-15)5-11(1)19-13-7-22-20(14(13)8-21-19)12-2-4-16-18(6-12)26-10-24-16/h1-6,13-14,19-20H,7-10H2/t13-,14-,19-,20?/m1/s1
SMILES:	c1cc2c(cc1[C@@H]1[C@@H]3COC(c4ccc5c(c4)OCO5)[C@@H]3CO1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	233333
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid 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
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15388977]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	stem	n.a.	PMID[17202689]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[17625893]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[18293924]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	Stems; Barks	n.a.	n.a.	PMID[18303853]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[18303853]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20192247]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[20628994]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21319773]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	roots	n.a.	n.a.	PMID[22381047]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[22445674]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23623680]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[25735399]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28322565]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28968119]
NPO8500	Acanthopanax gracilistylus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32319765]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8500	Acanthopanax gracilistylus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12468	Asarum heterotropoides	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12468.2	Asarum heterotropoides f. schm. var. mandshuricum (maxim.) kitag.	Varieties	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8500	Acanthopanax gracilistylus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO753	Acanthopanax sessiliflorum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29078	Asiasarum sieboldii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4659	Asiasarum heterotropoides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12468	Asarum heterotropoides	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4659	Asiasarum heterotropoides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29078	Asiasarum sieboldii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO8500	Acanthopanax gracilistylus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12468	Asarum heterotropoides	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	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 NPC67790 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	515
0.1-0.2	1506
0.2-0.3	4213
0.3-0.4	11378
0.4-0.5	7597
0.5-0.6	8247
0.6-0.7	6937
0.7-0.8	1867
0.8-0.85	300
0.85-0.9	93
0.9-0.95	30
0.95-1	14

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 NPC67790 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	390
0.1-0.2	848
0.2-0.3	1852
0.3-0.4	2829
0.4-0.5	1742
0.5-0.6	1044
0.6-0.7	397
0.7-0.8	46
0.8-0.85	2
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