NPASS Compound

Structure

NPC58085 OpenBabel06302216122D 38 41 0 0 1 0 0 0 0 0999 V2000 -3.5903 -1.4326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5903 -1.4326 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0903 -0.5665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5903 0.2995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0903 1.1655 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0957 1.2700 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1305 1.0086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5855 0.7422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3036 0.7960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8036 -0.0700 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7092 1.3909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4970 2.0790 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2060 2.7842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7538 2.7482 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8878 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0903 -2.2986 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0903 -2.2986 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5903 -3.1646 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4097 -3.1646 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9097 -2.2986 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4097 -1.4326 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9097 -0.5665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4097 0.2995 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9097 1.1655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4097 2.0315 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9097 1.1655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4097 0.2995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4097 0.2995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9097 1.1655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4097 2.0315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4097 2.0315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9097 2.8976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9097 1.1655 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9097 -0.5665 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5903 -1.4326 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9097 -2.2986 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9097 -4.0306 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0903 -4.0306 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 16 1 0 0 0 0 3 4 2 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 15 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 18 38 1 1 0 0 0 19 20 1 0 0 0 0 19 37 1 6 0 0 0 20 21 1 0 0 0 0 20 36 1 1 0 0 0 21 22 1 6 0 0 0 21 35 1 0 0 0 0 22 23 1 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 31 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 34 1 0 0 0 0 29 30 2 0 0 0 0 29 33 1 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	538.21
Volume:	513.69
LogP:	0.68
LogD:	0.043
LogS:	-2.651
# Rotatable Bonds:	8
TPSA:	192.44
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.16
Synthetic Accessibility Score:	5.812
Fsp3:	0.615
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.201
MDCK Permeability:	1.2601421076396946e-05
Pgp-inhibitor:	0.053
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.93
20% Bioavailability (F20%):	0.962
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	77.3521957397461%
Volume Distribution (VD):	0.428
Pgp-substrate:	8.45931625366211%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.659
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.073
CYP2C9-inhibitor:	0.037
CYP2C9-substrate:	0.115
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.125
CYP3A4-inhibitor:	0.157
CYP3A4-substrate:	0.104

ADMET: Excretion

Clearance (CL):	1.823
Half-life (T1/2):	0.919

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.114
Drug-inuced Liver Injury (DILI):	0.876
AMES Toxicity:	0.783
Rat Oral Acute Toxicity:	0.062
Maximum Recommended Daily Dose:	0.397
Skin Sensitization:	0.116
Carcinogencity:	0.056
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.038

Download Data

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

Natural Product: NPC58085

Natural Product ID:	NPC58085
*Common Name:**	LQVNYRWMNGPIEB-LJSMMZQXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LQVNYRWMNGPIEB-LJSMMZQXSA-N
Standard InCHI:	InChI=1S/C26H34O12/c1-12(4-5-18-25(2)8-14(27)9-26(18,3)36-11-25)37-24-22(33)21(32)20(31)17(38-24)10-35-23(34)13-6-15(28)19(30)16(29)7-13/h4-7,12,17-18,20-22,24,28-33H,8-11H2,1-3H3/b5-4+/t12-,17-,18-,20-,21+,22-,24-,25-,26-/m1/s1
SMILES:	C[C@H](/C=C/[C@@H]1[C@]2(C)CC(=O)C[C@@]1(C)OC2)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)c2cc(c(c(c2)O)O)O)O1)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:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11087590]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11421757]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11975480]
NPO10729	Lechevalieria aerocolonigenes	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15620255]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	leaves	Krachong waterfall area, Trang Province, Thailand	2001-APR	PMID[15974621]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15974621]
NPO3453	Elaeocarpus fuscoides	Species	Elaeocarpaceae	Eukaryota	leaves	n.a.	n.a.	PMID[17451272]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18844422]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[18844422]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	epidermis of the sclerotia	n.a.	n.a.	PMID[19746919]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27808511]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28972755]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8984162]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8543	Meconopsis horridula	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1209	Swartzia madagascariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6330	Croton caudatus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12330	Pseudophryne coriacea	Species	Myobatrachidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3280	Penicillium crustaceum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO477	Lepraria xanthina	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10729	Lechevalieria aerocolonigenes	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11884	Macaranga tanarius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7087	Oxera splendida	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO305	Vitex pinnata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8543	Meconopsis horridula	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3453	Elaeocarpus fuscoides	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23577	Wolfiporia cocos	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1209	Swartzia madagascariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5508	Stevia purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15164	Jacobaea adonidifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO896	Streptomyces kanamyceticus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5344	Calodendrum capense	Species	Rutaceae	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 NPC58085 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	369
0.1-0.2	1352
0.2-0.3	2702
0.3-0.4	5099
0.4-0.5	9428
0.5-0.6	8636
0.6-0.7	6412
0.7-0.8	7628
0.8-0.85	1007
0.85-0.9	57
0.9-0.95	7
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 NPC58085 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	316
0.1-0.2	816
0.2-0.3	1744
0.3-0.4	2653
0.4-0.5	2112
0.5-0.6	1056
0.6-0.7	319
0.7-0.8	125
0.8-0.85	9
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