NPASS Compound

Structure

NPC83818 OpenBabel06302215392D 32 35 0 0 1 0 0 0 0 0999 V2000 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 1 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 -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 -3.4641 -0.0000 0.0000 C 0 0 1 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 -3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7350 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8301 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8301 2.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.2321 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -4.8301 2.3660 0.0000 O 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 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 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 -2.0000 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 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 8 1 0 0 0 0 3 4 1 0 0 0 0 3 21 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 15 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 9 20 1 0 0 0 0 10 14 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 22 21 1 1 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 32 1 6 0 0 0 24 25 1 0 0 0 0 24 31 1 1 0 0 0 25 26 1 0 0 0 0 25 30 1 6 0 0 0 26 27 1 0 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 M CHG 1 19 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.18
Volume:	426.329
LogP:	-0.467
LogD:	-0.136
LogS:	-1.821
# Rotatable Bonds:	4
TPSA:	190.28
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.288
Synthetic Accessibility Score:	5.191
Fsp3:	0.762
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.36
MDCK Permeability:	9.337130177300423e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.76
Human Intestinal Absorption (HIA):	0.935
20% Bioavailability (F20%):	0.091
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.173
Plasma Protein Binding (PPB):	46.3568115234375%
Volume Distribution (VD):	0.391
Pgp-substrate:	31.680133819580078%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.072
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.078
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.046
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.089
CYP3A4-inhibitor:	0.018
CYP3A4-substrate:	0.038

ADMET: Excretion

Clearance (CL):	1.194
Half-life (T1/2):	0.677

ADMET: Toxicity

hERG Blockers:	0.072
Human Hepatotoxicity (H-HT):	0.274
Drug-inuced Liver Injury (DILI):	0.15
AMES Toxicity:	0.106
Rat Oral Acute Toxicity:	0.058
Maximum Recommended Daily Dose:	0.011
Skin Sensitization:	0.064
Carcinogencity:	0.082
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.945

Download Data

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

Natural Product: NPC83818

Natural Product ID:	NPC83818
*Common Name:**	MSKRHKRDZMIHDS-WHKIDCEGSA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MSKRHKRDZMIHDS-WHKIDCEGSA-M
Standard InCHI:	InChI=1S/C21H30O11/c1-8-10(31-18-14(25)13(24)12(23)11(7-22)32-18)3-5-20(2)15(8)21(29,19(27)28)17-9(16(20)26)4-6-30-17/h4,6,8,10-16,18,22-26,29H,3,5,7H2,1-2H3,(H,27,28)/p-1/t8-,10+,11+,12+,13-,14+,15-,16+,18+,20-,21+/m0/s1
SMILES:	C[C@H]1[C@@H](CC[C@@]2(C)[C@H]1[C@@](c1c(cco1)[C@H]2O)(C(=O)[O-])O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)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
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	Root barks	n.a.	n.a.	PMID[11473427]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	root bark	n.a.	n.a.	PMID[18198838]
NPO7171	Salvia polystachya	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29135252]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7171	Salvia polystachya	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10830	Dictamnus dasycarpus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3560	Trifolium montanum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5799	Streptomyces chryseus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO1329	Esenbeckia hartmanii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5451	Ageratina saltillensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11119	Salta triflora	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7171	Salvia polystachya	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7966	Grewia villosa	Species	Malvaceae	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 NPC83818 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	379
0.1-0.2	1388
0.2-0.3	2933
0.3-0.4	5493
0.4-0.5	9886
0.5-0.6	8295
0.6-0.7	6695
0.7-0.8	6912
0.8-0.85	574
0.85-0.9	127
0.9-0.95	15
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 NPC83818 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	325
0.1-0.2	870
0.2-0.3	1868
0.3-0.4	2593
0.4-0.5	2023
0.5-0.6	1031
0.6-0.7	307
0.7-0.8	126
0.8-0.85	6
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