NPASS Compound

Structure

NPC260546 OpenBabel06302215182D 26 29 0 0 1 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4071 -2.0878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3581 -1.7788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5661 -0.8006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8229 -0.1315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0308 0.8467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9819 1.1557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7250 0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5171 -0.4916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5911 0.9865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3831 1.9647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3886 2.0692 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0981 -3.0388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7891 -2.0878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8380 -1.7788 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 2 1 0 0 0 0 2 3 1 0 0 0 0 3 25 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 24 2 0 0 0 0 7 8 2 0 0 0 0 8 22 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 6 0 0 0 9 20 1 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 14 1 0 0 0 0 14 19 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 17 1 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 21 22 1 0 0 0 0 22 23 2 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:	351.9
LogP:	3.441
LogD:	3.534
LogS:	-5.212
# Rotatable Bonds:	4
TPSA:	74.22
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.672
Synthetic Accessibility Score:	3.062
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.932
MDCK Permeability:	2.123168269463349e-05
Pgp-inhibitor:	0.912
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.028
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.067
Plasma Protein Binding (PPB):	99.53009796142578%
Volume Distribution (VD):	0.5
Pgp-substrate:	1.4936116933822632%

ADMET: Metabolism

CYP1A2-inhibitor:	0.98
CYP1A2-substrate:	0.421
CYP2C19-inhibitor:	0.978
CYP2C19-substrate:	0.103
CYP2C9-inhibitor:	0.905
CYP2C9-substrate:	0.717
CYP2D6-inhibitor:	0.98
CYP2D6-substrate:	0.751
CYP3A4-inhibitor:	0.951
CYP3A4-substrate:	0.353

ADMET: Excretion

Clearance (CL):	15.745
Half-life (T1/2):	0.369

ADMET: Toxicity

hERG Blockers:	0.109
Human Hepatotoxicity (H-HT):	0.226
Drug-inuced Liver Injury (DILI):	0.8
AMES Toxicity:	0.467
Rat Oral Acute Toxicity:	0.162
Maximum Recommended Daily Dose:	0.882
Skin Sensitization:	0.771
Carcinogencity:	0.85
Eye Corrosion:	0.003
Eye Irritation:	0.738
Respiratory Toxicity:	0.508

Download Data

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

Natural Product: NPC260546

Natural Product ID:	NPC260546
*Common Name:**	RDQYZETVAPDYFY-UUINEXAVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RDQYZETVAPDYFY-UUINEXAVSA-N
Standard InCHI:	InChI=1S/C20H18O6/c1-23-17-4-2-13(8-16(17)21)7-15-14(10-24-20(15)22)6-12-3-5-18-19(9-12)26-11-25-18/h2-5,7-9,14,21H,6,10-11H2,1H3/b15-7+/t14-/m0/s1
SMILES:	COc1ccc(/C=C/2[C@@H](Cc3ccc4c(c3)OCO4)COC2=O)cc1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001613] Dibenzylbutyrolactone 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
NPO12176	Streptomyces olivaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11376004]
NPO12176	Streptomyces olivaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1367428]
NPO2291	Saussurea pulchella	Species	Asteraceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[18314958]
NPO11237	Bupleurum salicifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24242108]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32100544]
NPO11237	Bupleurum salicifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7964800]
NPO12176	Streptomyces olivaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[Article]
NPO2291	Saussurea pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7991	Lactarius vellereus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4033	Corydalis gigantea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11400	Aster ptarmicoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4033	Corydalis gigantea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12874	Sedum cepaea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7991	Lactarius vellereus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6669	Dysosma delavayi	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2291	Saussurea pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2291	Saussurea pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4033	Corydalis gigantea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1164	Osteospermum hyoseroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11237	Bupleurum salicifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1460	Rubus phoenicolasius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11400	Aster ptarmicoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8414	Crella incrustans	Species	Crellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9018	Millettia rubiginosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9496	Gomphostemma crinitum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7653	Mosla japonica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12422	Pinus massoniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9648	Maharanga bicolor	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7327	Aeromonas hydrophila	Species	Aeromonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16792	0cardia pseudobrasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10354	Urbanodendron verrucosum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16343	Galium album	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12874	Sedum cepaea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4970	Torricellia tiliifolia	Species	Torricelliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12176	Streptomyces olivaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6235	Exobasidium vaccinii	Species	Exobasidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20210	Lophozia floerkei	Species	Scapaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17456	Echinochloa esculenta	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6669	Dysosma delavayi	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4033	Corydalis gigantea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2291	Saussurea pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3614	Echinopepon bigelovii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7991	Lactarius vellereus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12659	Hopea brevipetiolaris	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3017	Artemisia caucasica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2582	Plagiomnium undulatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10719	Centrosema haitense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10560	Adenia fruticosa	Species	Passifloraceae	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 NPC260546 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	294
0.1-0.2	1286
0.2-0.3	2919
0.3-0.4	7597
0.4-0.5	11417
0.5-0.6	4201
0.6-0.7	10262
0.7-0.8	4229
0.8-0.85	392
0.85-0.9	78
0.9-0.95	20
0.95-1	2

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 NPC260546 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	248
0.1-0.2	775
0.2-0.3	1518
0.3-0.4	2486
0.4-0.5	2216
0.5-0.6	1216
0.6-0.7	590
0.7-0.8	95
0.8-0.85	5
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