NPASS Compound

Structure

NPC125733 OpenBabel06302215192D 23 25 0 0 1 0 0 0 0 0999 V2000 3.4641 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 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 -2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 2 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 -2.2321 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 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 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 23 1 0 0 0 0 5 15 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 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 1 0 0 0 13 14 1 0 0 0 0 13 17 1 0 0 0 0 13 21 1 1 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	320.09
Volume:	305.336
LogP:	1.903
LogD:	1.268
LogS:	-3.032
# Rotatable Bonds:	2
TPSA:	117.2
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.654
Synthetic Accessibility Score:	3.827
Fsp3:	0.375
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.846
MDCK Permeability:	1.2818260074709542e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.795
Human Intestinal Absorption (HIA):	0.036
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.177

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.443
Plasma Protein Binding (PPB):	83.64442443847656%
Volume Distribution (VD):	0.905
Pgp-substrate:	20.218952178955078%

ADMET: Metabolism

CYP1A2-inhibitor:	0.687
CYP1A2-substrate:	0.952
CYP2C19-inhibitor:	0.051
CYP2C19-substrate:	0.548
CYP2C9-inhibitor:	0.063
CYP2C9-substrate:	0.399
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.305
CYP3A4-inhibitor:	0.13
CYP3A4-substrate:	0.311

ADMET: Excretion

Clearance (CL):	3.153
Half-life (T1/2):	0.583

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.768
Drug-inuced Liver Injury (DILI):	0.893
AMES Toxicity:	0.65
Rat Oral Acute Toxicity:	0.638
Maximum Recommended Daily Dose:	0.876
Skin Sensitization:	0.489
Carcinogencity:	0.033
Eye Corrosion:	0.004
Eye Irritation:	0.027
Respiratory Toxicity:	0.09

Download Data

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

Natural Product: NPC125733

Natural Product ID:	NPC125733
*Common Name:**	YZMBEUQMDLBCDY-ZBEGNZNMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YZMBEUQMDLBCDY-ZBEGNZNMSA-N
Standard InCHI:	InChI=1S/C16H16O7/c1-7-5-8(17)12-10(6-7)23-9-3-4-11(18)16(21,15(20)22-2)13(9)14(12)19/h5-6,11,17-18,21H,3-4H2,1-2H3/t11-,16-/m0/s1
SMILES:	Cc1cc(c2c(c1)oc1CC[C@@H]([C@](c1c2=O)(C(=O)OC)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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
NPO12404	Trigonostemon chinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18611050]
NPO10023	Francoeuria undulata	Species	Asteraceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[28032767]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO12220	Hemerocallis thunbergii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12220	Hemerocallis thunbergii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8232	Sclerocarya caffra	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4866	Diospyros rotundifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11338	Muricella flexuosa	Species	Acanthogorgiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO678	Streptomyces spiroverticillatus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10023	Francoeuria undulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13202	Pseudodistoma kanoko	Species	Pseudodistomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6632	Lunaria biennis	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12220	Hemerocallis thunbergii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO897	Pinus gerardi	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10620	Monochoria elata	Species	Pontederiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12404	Trigonostemon chinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14605	Glochidion thomsonii	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8648	Gorgonia mariae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13302	Streptomyces nanchangensis	Species	Streptomycetaceae	Bacteria	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 NPC125733 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	374
0.1-0.2	1615
0.2-0.3	3786
0.3-0.4	8479
0.4-0.5	9933
0.5-0.6	4207
0.6-0.7	5653
0.7-0.8	5277
0.8-0.85	3022
0.85-0.9	337
0.9-0.95	12
0.95-1	2

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 NPC125733 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	352
0.1-0.2	925
0.2-0.3	1921
0.3-0.4	2577
0.4-0.5	1864
0.5-0.6	979
0.6-0.7	346
0.7-0.8	146
0.8-0.85	36
0.85-0.9	4
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