NPASS Compound

Structure

NPC39082 OpenBabel06302215422D 37 40 0 0 1 0 0 0 0 0999 V2000 0.0015 -1.9566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8483 -1.4673 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6955 -1.9561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6957 -2.9341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5429 -3.4229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5431 -4.4009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6963 -4.8902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3903 -4.8897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3906 -5.8677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2371 -4.4004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -0.4893 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6946 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6943 0.9789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0003 0.9784 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8483 1.4677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8486 2.4467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6966 2.9360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5444 2.4462 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3918 2.9355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3921 3.9379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2599 3.4367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2390 2.4458 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2387 1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3913 0.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5441 1.4672 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5438 0.4648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6961 0.9779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6958 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8478 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1073 2.9466 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3860 1.6710 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5388 2.6374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4521 2.9883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7782 3.2529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 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 2 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 2 1 6 0 0 0 11 12 1 0 0 0 0 11 31 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 34 1 1 0 0 0 14 31 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 28 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 0 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 0 0 0 0 23 33 1 1 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 6 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	512.35
Volume:	558.571
LogP:	5.524
LogD:	4.277
LogS:	-4.706
# Rotatable Bonds:	7
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.305
Synthetic Accessibility Score:	5.321
Fsp3:	0.75
Lipinski Rule-of-5:	Rejected
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:	-5.101
MDCK Permeability:	1.9839038941427134e-05
Pgp-inhibitor:	0.871
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.923
30% Bioavailability (F30%):	0.725

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	96.33016967773438%
Volume Distribution (VD):	0.657
Pgp-substrate:	3.3790416717529297%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.099
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.86
CYP2C9-inhibitor:	0.078
CYP2C9-substrate:	0.838
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.159
CYP3A4-inhibitor:	0.292
CYP3A4-substrate:	0.483

ADMET: Excretion

Clearance (CL):	2.163
Half-life (T1/2):	0.351

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.769
Drug-inuced Liver Injury (DILI):	0.01
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.919
Skin Sensitization:	0.959
Carcinogencity:	0.068
Eye Corrosion:	0.045
Eye Irritation:	0.082
Respiratory Toxicity:	0.956

Download Data

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

Natural Product: NPC39082

Natural Product ID:	NPC39082
*Common Name:**	YCWGPALSXRBKTM-XGNRZNIMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YCWGPALSXRBKTM-XGNRZNIMSA-N
Standard InCHI:	InChI=1S/C32H48O5/c1-19(10-9-11-20(2)28(35)36)24-18-27(37-21(3)33)32(8)23-12-13-25-29(4,5)26(34)15-16-30(25,6)22(23)14-17-31(24,32)7/h11-12,14,19,24-27,34H,9-10,13,15-18H2,1-8H3,(H,35,36)/b20-11+/t19-,24-,25+,26-,27+,30-,31-,32-/m1/s1
SMILES:	C[C@H](CC/C=C(C)/C(=O)O)[C@H]1C[C@@H]([C@@]2(C)C3=CC[C@H]4C(C)(C)[C@@H](CC[C@]4(C)C3=CC[C@]12C)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101600075
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytochem.2005.10.025]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[11520245]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12045343]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14695801]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1791484]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	spore	n.a.	PMID[18827358]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	Nagano, Japan	2008-MAY	PMID[20039640]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20384295]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[20702092]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[21924611]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014750]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[22044278]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[22047696]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26222905]
NPO40519	Ganoderma orbiforme BCC 22325	Strain	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28504879]
NPO40520	Ganoderma sp. BCC 60695	Strain	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28504879]
NPO40518	Ganoderma australe BCC 22314	Strain	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28504879]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[9635497]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	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

Activity Type	# Activity
IC50	2
MIC	1

Activity Type	# Activity
Cell Line	1
Individual Protein	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	=	94000.0	nM	PMID[28504879]
NPT143	Individual Protein	DNA topoisomerase I	Homo sapiens	IC50	=	25000.0	nM	PMID[31035236]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	25.0	ug.mL-1	PMID[28504879]

☑ 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 NPC39082 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	170
0.1-0.2	1009
0.2-0.3	3985
0.3-0.4	10672
0.4-0.5	12015
0.5-0.6	7417
0.6-0.7	5510
0.7-0.8	1701
0.8-0.85	136
0.85-0.9	44
0.9-0.95	25
0.95-1	13

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 NPC39082 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	143
0.1-0.2	1183
0.2-0.3	3794
0.3-0.4	2737
0.4-0.5	793
0.5-0.6	189
0.6-0.7	211
0.7-0.8	100
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