NPASS Compound

Structure

NPC64506 OpenBabel06302215172D 47 51 0 0 1 0 0 0 0 0999 V2000 -1.1964 -1.9344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4532 -1.2652 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4043 -0.9562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6122 0.0219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8690 0.6911 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0820 0.3821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2899 -0.5961 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2410 -0.9051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4489 -1.8833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7058 -2.5524 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2453 -2.2434 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9884 -2.9125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7805 -3.8906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1705 -4.1997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7805 -4.5087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5773 -5.1132 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5718 -5.0087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7797 -4.0305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9137 -3.5305 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3204 -2.6170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0773 -5.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9227 -5.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4227 -6.8453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9227 -7.7113 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4227 -8.5773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0773 -7.7113 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5773 -6.8453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9395 -2.6035 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -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 C 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 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 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 3.4641 -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 5.1962 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 N 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 O 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 7 1 0 0 0 0 2 11 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 6 1 0 0 0 0 5 29 1 6 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 19 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 28 1 1 0 0 0 13 14 1 0 0 0 0 14 19 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 21 1 6 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 27 2 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 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 3 0 0 0 34 47 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 36 44 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	658.36
Volume:	658.482
LogP:	-0.072
LogD:	0.502
LogS:	-2.298
# Rotatable Bonds:	13
TPSA:	227.77
# H-Bond Aceptor:	13
# H-Bond Donor:	8
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.087
Synthetic Accessibility Score:	5.304
Fsp3:	0.735
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.88
MDCK Permeability:	2.2294363589026034e-05
Pgp-inhibitor:	0.451
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.618
20% Bioavailability (F20%):	0.979
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.272
Plasma Protein Binding (PPB):	31.494482040405273%
Volume Distribution (VD):	0.587
Pgp-substrate:	57.87997817993164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.019
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.027
CYP2C9-substrate:	0.045
CYP2D6-inhibitor:	0.036
CYP2D6-substrate:	0.192
CYP3A4-inhibitor:	0.076
CYP3A4-substrate:	0.124

ADMET: Excretion

Clearance (CL):	1.649
Half-life (T1/2):	0.501

ADMET: Toxicity

hERG Blockers:	0.228
Human Hepatotoxicity (H-HT):	0.447
Drug-inuced Liver Injury (DILI):	0.036
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.247
Maximum Recommended Daily Dose:	0.955
Skin Sensitization:	0.905
Carcinogencity:	0.231
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.939

Download Data

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

Natural Product: NPC64506

Natural Product ID:	NPC64506
*Common Name:**	PEDUWTJUACTTDA-XDXHQNGOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PEDUWTJUACTTDA-XDXHQNGOSA-N
Standard InCHI:	InChI=1S/C34H50N4O9/c1-32-13-11-21(47-28(42)10-8-26(40)38-24(30(43)44)4-3-15-37-31(35)36)16-20(32)6-7-23-29(32)25(39)17-33(2)22(12-14-34(23,33)45)19-5-9-27(41)46-18-19/h5,9,18,20-25,29,39,45H,3-4,6-8,10-17H2,1-2H3,(H,38,40)(H,43,44)(H4,35,36,37)/t20-,21+,22-,23-,24+,25-,29-,32+,33-,34+/m1/s1
SMILES:	C[C@]12CC[C@@H](C[C@H]1CC[C@@H]1[C@@H]2[C@@H](C[C@]2(C)[C@H](CC[C@]12O)c1ccc(=O)oc1)O)OC(=O)CCC(=N[C@@H](CCCNC(=N)N)C(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001557] Bufanolides and derivatives

*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
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0040-4039(01)99818-1]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	roots	n.a.	n.a.	PMID[10346940]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11421725]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165135]
NPO3983	Piper futokadsura	Species	Piperaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[15635246]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15730237]
NPO664	Potentilla multifida	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17504571]
NPO9576	Bufo bufo	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21185919]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21954912]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	n.a.	twig	n.a.	PMID[21954912]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	twigs and leaves	Yunnan Province, China	2008-OCT	PMID[21954912]
NPO10672	Vitex megapotamica	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22708620]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26722868]
NPO18636	Cupressus macrocarpa	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223924]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18636	Cupressus macrocarpa	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10672	Vitex megapotamica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9576	Bufo bufo	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9576	Bufo bufo	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9398	Cortinarius rubellus	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2498	Kochia trichophylla	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12012	Saururus cernuus	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6011	Pleurotus citrinopileatus	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21463	Aruncus dioicus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11885	Dysoxylum lenticellatum	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18636	Cupressus macrocarpa	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7884	Centaurea amara	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO664	Potentilla multifida	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11515	Streptomyces plumbeus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2917	Artemisia oranensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26231	Vicia villosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12250	Strychnos fendleri	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7543	Haplopappus venetus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3983	Piper futokadsura	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4797	Gavia immer	Species	Gaviidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10672	Vitex megapotamica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12952	Cabucala madagascariensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10043	Phebalium ozothamnoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5177	Lecanora conizaeoides	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6887	Lytanthus salicinus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12735	Halimeda macroloba	Species	Halimedaceae	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 NPC64506 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	286
0.1-0.2	1259
0.2-0.3	3087
0.3-0.4	8933
0.4-0.5	13111
0.5-0.6	13691
0.6-0.7	2223
0.7-0.8	105
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
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 NPC64506 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	165
0.1-0.2	524
0.2-0.3	979
0.3-0.4	2317
0.4-0.5	3238
0.5-0.6	1681
0.6-0.7	242
0.7-0.8	4
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