NPASS Compound

Structure

NPC50855 OpenBabel06302215422D 23 24 0 0 1 0 0 0 0 0999 V2000 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 2 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 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 2 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 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 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 0 0 0 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 2 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 -0.8660 -0.5000 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 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 O 0 0 0 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 -4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 22 1 1 0 0 0 4 5 1 0 0 0 0 4 21 1 1 0 0 0 5 6 1 0 0 0 0 5 20 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 16 1 0 0 0 0 10 11 1 6 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 19 1 6 0 0 0 15 16 1 0 0 0 0 15 18 1 1 0 0 0 16 17 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	342.12
Volume:	295.688
LogP:	-2.629
LogD:	-2.723
LogS:	-0.197
# Rotatable Bonds:	4
TPSA:	189.53
# H-Bond Aceptor:	11
# H-Bond Donor:	8
# Rings:	2
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.243
Synthetic Accessibility Score:	4.282
Fsp3:	1.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.921
MDCK Permeability:	0.00018486716726329178
Pgp-inhibitor:	0.023
Pgp-substrate:	0.867
Human Intestinal Absorption (HIA):	0.937
20% Bioavailability (F20%):	0.13
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.256
Plasma Protein Binding (PPB):	15.07929801940918%
Volume Distribution (VD):	0.309
Pgp-substrate:	68.92107391357422%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.037
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.084
CYP3A4-inhibitor:	0.003
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	0.926
Half-life (T1/2):	0.876

ADMET: Toxicity

hERG Blockers:	0.233
Human Hepatotoxicity (H-HT):	0.11
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.106
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.0
Skin Sensitization:	0.806
Carcinogencity:	0.028
Eye Corrosion:	0.004
Eye Irritation:	0.286
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC50855

Natural Product ID:	NPC50855
*Common Name:**	GUBGYTABKSRVRQ-GFVAERMHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GUBGYTABKSRVRQ-GFVAERMHSA-N
Standard InCHI:	InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9+,10+,11-,12-/m0/s1
SMILES:	C([C@H]1[C@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H](CO)O[C@@H]([C@H]([C@@H]1O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO3762	Amentotaxus argotaenia	Species	Taxaceae	Eukaryota	Leaves; Twigs	n.a.	n.a.	PMID[32633512]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3102	Arachniodes exilis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9522	Pericopsis angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5205	Gymnoascus reesii	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9311	Parkia clappertoniana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2559	Mesua myrtifolia	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10588	Diploschistes violarius	Species	Graphidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9051	Delesseria sanguinea	Species	Delesseriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9522	Pericopsis angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10177	Eria linearifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11832	Pinus banksiana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3102	Arachniodes exilis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6194	Thalictrum pedunculatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO822	Cressa cretica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3762	Amentotaxus argotaenia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6796	Planchonella anteridifera	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6040	Svenzea zeai	Species	Dictyonellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1313	Aplophyllum bungei	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12895	Polypodiodes niponica	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO316	Fuligo aurea	Species	Physaraceae	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 NPC50855 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	1158
0.1-0.2	9214
0.2-0.3	17328
0.3-0.4	10075
0.4-0.5	3799
0.5-0.6	828
0.6-0.7	183
0.7-0.8	47
0.8-0.85	33
0.85-0.9	19
0.9-0.95	2
0.95-1	11

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 NPC50855 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1171
0.1-0.2	5393
0.2-0.3	1836
0.3-0.4	463
0.4-0.5	150
0.5-0.6	77
0.6-0.7	33
0.7-0.8	7
0.8-0.85	9
0.85-0.9	4
0.9-0.95	2
0.95-1	5

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