NPASS Compound

Structure

NPC25637 OpenBabel06302215552D 33 36 0 0 1 0 0 0 0 0999 V2000 -1.7321 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -5.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 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 -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 0 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 -0.8660 -0.5000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 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 0.0000 1.0000 0.0000 O 0 0 0 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 -1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -6.0000 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 7 1 0 0 0 0 3 4 1 0 0 0 0 3 33 1 6 0 0 0 4 5 1 0 0 0 0 4 32 1 1 0 0 0 5 6 1 0 0 0 0 5 31 1 6 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 30 1 0 0 0 0 12 27 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 26 2 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 26 27 1 0 0 0 0 26 29 1 0 0 0 0 27 28 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.12
Volume:	430.443
LogP:	2.142
LogD:	1.199
LogS:	-4.038
# Rotatable Bonds:	4
TPSA:	179.28
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.323
Synthetic Accessibility Score:	3.962
Fsp3:	0.318
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.224
MDCK Permeability:	1.1432350220275111e-05
Pgp-inhibitor:	0.198
Pgp-substrate:	0.973
Human Intestinal Absorption (HIA):	0.167
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013
Plasma Protein Binding (PPB):	90.33163452148438%
Volume Distribution (VD):	0.779
Pgp-substrate:	11.032784461975098%

ADMET: Metabolism

CYP1A2-inhibitor:	0.529
CYP1A2-substrate:	0.284
CYP2C19-inhibitor:	0.038
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.328
CYP2C9-substrate:	0.538
CYP2D6-inhibitor:	0.352
CYP2D6-substrate:	0.193
CYP3A4-inhibitor:	0.181
CYP3A4-substrate:	0.028

ADMET: Excretion

Clearance (CL):	4.452
Half-life (T1/2):	0.852

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.095
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.792
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.409
Carcinogencity:	0.296
Eye Corrosion:	0.003
Eye Irritation:	0.444
Respiratory Toxicity:	0.079

Download Data

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

Natural Product: NPC25637

Natural Product ID:	NPC25637
*Common Name:**	XLQFMBLUUSGXQY-NPQVZWJISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XLQFMBLUUSGXQY-NPQVZWJISA-N
Standard InCHI:	InChI=1S/C22H22O11/c1-8-16(25)18(27)20(29)22(31-8)32-10-6-12(24)15-14(7-10)33-21(19(28)17(15)26)9-3-4-11(23)13(5-9)30-2/h3-8,16,18,20,22-25,27-29H,1-2H3/t8-,16-,18+,20-,22+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)Oc1cc(c2c(c1)oc(c1ccc(c(c1)OC)O)c(c2=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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

*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
NPO28468	Aglaia duperreana	Species	Meliaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1021/np990242g]
NPO12203	Uvaria dulcis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27199	Croton macrostachys	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25238	Rheum coreanum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28284	Medicago arabica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27629	Rhododendron schlippenbachii	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27199	Croton macrostachys	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28536	Dictyostelium discoideum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12203	Uvaria dulcis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28468	Aglaia duperreana	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25238	Rheum coreanum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26376	Camptorrhiza strumosa	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25523	Ageratina ixiocladon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25985	Dryas octopetala	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29019	Aspergillus tamarii	Species	Aspergillaceae	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 NPC25637 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	433
0.1-0.2	1806
0.2-0.3	4144
0.3-0.4	9680
0.4-0.5	8342
0.5-0.6	4197
0.6-0.7	5140
0.7-0.8	5329
0.8-0.85	1725
0.85-0.9	1230
0.9-0.95	475
0.95-1	196

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 NPC25637 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	400
0.1-0.2	940
0.2-0.3	1926
0.3-0.4	2688
0.4-0.5	1801
0.5-0.6	920
0.6-0.7	300
0.7-0.8	133
0.8-0.85	15
0.85-0.9	13
0.9-0.95	13
0.95-1	1

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