NPASS Compound

Structure

NPC35300 OpenBabel06302215272D 28 32 0 0 1 0 0 0 0 0999 V2000 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 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 0.8660 1.5000 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 0.8660 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 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 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 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 -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 6.1472 -1.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7350 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1472 -3.3090 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 -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 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 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 2 1 0 0 0 0 2 17 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 6 0 0 0 3 6 1 0 0 0 0 4 5 1 0 0 0 0 6 24 2 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 21 2 0 0 0 0 8 17 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 20 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	379.14
Volume:	380.142
LogP:	4.543
LogD:	3.392
LogS:	-6.574
# Rotatable Bonds:	3
TPSA:	60.39
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.748
Synthetic Accessibility Score:	3.192
Fsp3:	0.273
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:	-4.664
MDCK Permeability:	5.681745824404061e-05
Pgp-inhibitor:	0.794
Pgp-substrate:	0.974
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.731

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.405
Plasma Protein Binding (PPB):	95.12152862548828%
Volume Distribution (VD):	0.76
Pgp-substrate:	1.782217025756836%

ADMET: Metabolism

CYP1A2-inhibitor:	0.95
CYP1A2-substrate:	0.849
CYP2C19-inhibitor:	0.937
CYP2C19-substrate:	0.606
CYP2C9-inhibitor:	0.806
CYP2C9-substrate:	0.9
CYP2D6-inhibitor:	0.946
CYP2D6-substrate:	0.921
CYP3A4-inhibitor:	0.888
CYP3A4-substrate:	0.789

ADMET: Excretion

Clearance (CL):	11.275
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.102
Human Hepatotoxicity (H-HT):	0.089
Drug-inuced Liver Injury (DILI):	0.752
AMES Toxicity:	0.789
Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.955
Skin Sensitization:	0.704
Carcinogencity:	0.918
Eye Corrosion:	0.003
Eye Irritation:	0.046
Respiratory Toxicity:	0.882

Download Data

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

Natural Product: NPC35300

Natural Product ID:	NPC35300
*Common Name:**	GKBDCSXIKLSKMH-INIZCTEOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GKBDCSXIKLSKMH-INIZCTEOSA-N
Standard InCHI:	InChI=1S/C22H21NO5/c1-23-16(10-24)20-13(6-7-17(25-2)22(20)26-3)14-5-4-12-8-18-19(28-11-27-18)9-15(12)21(14)23/h4-9,16,24H,10-11H2,1-3H3/t16-/m0/s1
SMILES:	CN1[C@@H](CO)c2c(-c3ccc4cc5c(cc4c13)OCO5)ccc(c2OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002665] Benzophenanthridine alkaloids [CHEMONTID:0002667] Dihydrobenzophenanthridine alkaloids

*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
NPO26992	Sophora leachiana	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1016/0031-9422(90)85209-X]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	Caribbean	n.a.	PMID[10021943]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	Taiwan	n.a.	PMID[11277748]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921424]
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]
NPO26203	Dysidea villosa	Species	Dysideidae	Eukaryota	n.a.	Hainan, China	n.a.	PMID[19091557]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[23806071]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	China	n.a.	PMID[25115700]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26666037]
NPO25406	Celastrus monospermus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28006915]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798955]
NPO26992	Sophora leachiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25122	Conium maculatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24478	Morinda coreia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19672	Hosta sieboldiana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26992	Sophora leachiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25122	Conium maculatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19672	Hosta sieboldiana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13313	Talipariti tiliaceum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24478	Morinda coreia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19672	Hosta sieboldiana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25122	Conium maculatum	Species	Apiaceae	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]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25833	Asclepias subulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25358	Senecio gilliesi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25406	Celastrus monospermus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22264	Inula salsoloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26409	Plakortis simplex	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24918	Jacobaea cannabifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22890	Eutrochium purpureum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25259	Schrebera swietenoides	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25201	Aglaia pyramidata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26690	Lactarius subpiperatus	Species	Lactariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24478	Morinda coreia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26203	Dysidea villosa	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3963	Hortonia floribunda	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24547	Xanthoria parietina	Species	Teloschistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25802	Agave deserti	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26789	Tephrosia bidwilli	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25122	Conium maculatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1267	Acronychia laurifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13313	Talipariti tiliaceum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19672	Hosta sieboldiana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1818	Chelidonium japonicum	Species	Cerambycidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5491	Critonia daleoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9324	0techis scutatus	Species	Elapidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4574	Eriocephalus giessii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3005	Passiflora morifolia	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26160	Thielavia terricola	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25714	Solanum spirale	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26992	Sophora leachiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26849	Parmelia zollingeri	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28636	Vernonia lilacina	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 NPC35300 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	373
0.1-0.2	1887
0.2-0.3	8459
0.3-0.4	9170
0.4-0.5	7636
0.5-0.6	12020
0.6-0.7	2378
0.7-0.8	658
0.8-0.85	91
0.85-0.9	17
0.9-0.95	7
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 NPC35300 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	216
0.1-0.2	714
0.2-0.3	1013
0.3-0.4	1716
0.4-0.5	2727
0.5-0.6	2078
0.6-0.7	608
0.7-0.8	78
0.8-0.85	0
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