NPASS Compound

Structure

NPC129159 OpenBabel06302215092D 53 59 0 0 1 0 0 0 0 0999 V2000 -0.1563 -1.1870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8516 -0.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7601 -0.8680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7032 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7032 0.9833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8516 1.4750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8516 2.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8516 2.4583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8516 4.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8516 1.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7032 0.9833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5548 1.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5548 2.4583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4064 2.9500 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4064 1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2580 2.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1095 2.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1095 3.9333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2580 4.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7496 5.2766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7663 5.2766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4064 3.9333 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5548 4.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7032 3.9333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7032 2.9500 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8516 3.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9611 4.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8127 3.9333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8127 2.9500 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.6643 2.4583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5159 2.9500 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.5159 3.9333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 9.3675 4.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2191 3.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6643 4.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3675 2.4583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6643 1.4750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9611 2.4583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9611 1.4750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1095 0.9833 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1095 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9611 -0.4917 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8127 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8127 0.9833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9611 -1.4750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2580 -0.4917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2580 1.4750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9833 0.0000 C 0 0 1 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 -1.7032 1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7032 2.9500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5548 1.4750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 50 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 49 1 0 0 0 0 6 7 1 0 0 0 0 6 51 1 6 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 6 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 11 49 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 6 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 6 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 29 28 1 1 0 0 0 29 30 1 0 0 0 0 29 36 1 0 0 0 0 30 31 1 0 0 0 0 30 39 1 6 0 0 0 31 32 1 0 0 0 0 31 38 1 1 0 0 0 32 33 1 0 0 0 0 32 37 1 6 0 0 0 33 34 1 1 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 40 39 1 1 0 0 0 40 41 1 0 0 0 0 40 45 1 0 0 0 0 41 42 1 0 0 0 0 41 48 1 6 0 0 0 42 43 1 0 0 0 0 42 47 1 1 0 0 0 43 44 1 0 0 0 0 43 46 1 6 0 0 0 44 45 1 0 0 0 0 49 50 1 1 0 0 0 51 52 2 0 0 0 0 51 53 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	562.28
Volume:	577.134
LogP:	2.665
LogD:	1.426
LogS:	-3.347
# Rotatable Bonds:	13
TPSA:	148.96
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.134
Synthetic Accessibility Score:	5.416
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.763
MDCK Permeability:	4.1560062527423725e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.108
Human Intestinal Absorption (HIA):	0.125
20% Bioavailability (F20%):	0.366
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.137
Plasma Protein Binding (PPB):	74.07173919677734%
Volume Distribution (VD):	2.187
Pgp-substrate:	12.243674278259277%

ADMET: Metabolism

CYP1A2-inhibitor:	0.03
CYP1A2-substrate:	0.245
CYP2C19-inhibitor:	0.682
CYP2C19-substrate:	0.713
CYP2C9-inhibitor:	0.892
CYP2C9-substrate:	0.025
CYP2D6-inhibitor:	0.073
CYP2D6-substrate:	0.022
CYP3A4-inhibitor:	0.928
CYP3A4-substrate:	0.539

ADMET: Excretion

Clearance (CL):	9.314
Half-life (T1/2):	0.519

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.956
Drug-inuced Liver Injury (DILI):	0.837
AMES Toxicity:	0.123
Rat Oral Acute Toxicity:	0.6
Maximum Recommended Daily Dose:	0.972
Skin Sensitization:	0.278
Carcinogencity:	0.226
Eye Corrosion:	0.067
Eye Irritation:	0.043
Respiratory Toxicity:	0.978

Download Data

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

Natural Product: NPC129159

Natural Product ID:	NPC129159
*Common Name:**	PDCALJUWWJEWKR-JOGRUJQXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PDCALJUWWJEWKR-JOGRUJQXSA-N
Standard InCHI:	InChI=1S/C41H66O12/c1-36(2)14-16-41(35(48)49)17-15-39(6)21(22(41)18-36)8-9-26-38(5)12-11-27(37(3,4)25(38)10-13-40(26,39)7)52-34-32(30(46)29(45)24(19-42)51-34)53-33-31(47)28(44)23(43)20-50-33/h8,22-34,42-47H,9-20H2,1-7H3,(H,48,49)/t22-,23+,24+,25-,26+,27-,28-,29+,30-,31+,32+,33-,34-,38-,39-,40-,41-/m1/s1
SMILES:	CC1(C)CC[C@]2(CC[C@]3(C)C(=CC[C@H]4[C@]5(C)CC[C@H](C(C)(C)[C@H]5CC[C@@]34C)O[C@@H]3[C@H]([C@@H]([C@H]([C@H](CO)O3)O)O)O[C@@H]3[C@H]([C@@H]([C@H](CO3)O)O)O)[C@H]2C1)C(=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:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO3245	Clavariopsis aquatica	Species		Eukaryota	n.a.	n.a.	n.a.	PMID[31244144]
NPO24689	Turraea nilotica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3245	Clavariopsis aquatica	Species		Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3100	Eupatorium villosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6820	Simsia foetida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2537	Ilex dumosa	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4548	Thermoplasma acidophilum	Species	Thermoplasmataceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO3945	Delphinium formosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5248	Eriocephalus pauperrimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2100	Rheum moorcroftianum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6650	Cereus blanckii	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5094	Dictyochaeta simplex	Species	Chaetosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24689	Turraea nilotica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2396	Daphnandra aromatica	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7741	Debregeasia orientalis	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15029	Liatris gracilis	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 NPC129159 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	257
0.1-0.2	1714
0.2-0.3	5022
0.3-0.4	11700
0.4-0.5	10437
0.5-0.6	6116
0.6-0.7	4148
0.7-0.8	1952
0.8-0.85	672
0.85-0.9	298
0.9-0.95	142
0.95-1	239

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 NPC129159 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	234
0.1-0.2	2008
0.2-0.3	3871
0.3-0.4	1977
0.4-0.5	605
0.5-0.6	273
0.6-0.7	147
0.7-0.8	20
0.8-0.85	11
0.85-0.9	4
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