NPASS Compound

Structure

NPC123759 OpenBabel06302215422D 33 35 0 0 1 0 0 0 0 0999 V2000 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 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 0.8660 -1.5000 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 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 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 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -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 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 -0.8660 2.5000 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 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 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 O 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 -0.8660 -0.5000 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 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 33 1 0 0 0 0 3 4 1 0 0 0 0 3 32 1 6 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 29 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 18 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 2 0 0 0 0 20 31 1 0 0 0 0 21 22 1 0 0 0 0 21 29 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 29 30 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	452.11
Volume:	445.465
LogP:	1.779
LogD:	1.538
LogS:	-4.151
# Rotatable Bonds:	8
TPSA:	158.43
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.268
Synthetic Accessibility Score:	3.477
Fsp3:	0.167
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.009
MDCK Permeability:	8.909511961974204e-06
Pgp-inhibitor:	0.019
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.721
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	93.60863494873047%
Volume Distribution (VD):	0.232
Pgp-substrate:	0.6875825524330139%

ADMET: Metabolism

CYP1A2-inhibitor:	0.773
CYP1A2-substrate:	0.132
CYP2C19-inhibitor:	0.465
CYP2C19-substrate:	0.05
CYP2C9-inhibitor:	0.769
CYP2C9-substrate:	0.925
CYP2D6-inhibitor:	0.856
CYP2D6-substrate:	0.091
CYP3A4-inhibitor:	0.682
CYP3A4-substrate:	0.108

ADMET: Excretion

Clearance (CL):	1.793
Half-life (T1/2):	0.448

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.797
Drug-inuced Liver Injury (DILI):	0.99
AMES Toxicity:	0.322
Rat Oral Acute Toxicity:	0.237
Maximum Recommended Daily Dose:	0.713
Skin Sensitization:	0.389
Carcinogencity:	0.047
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.076

Download Data

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

Natural Product: NPC123759

Natural Product ID:	NPC123759
*Common Name:**	TXAZFHNEWZMHQF-QZXNXJAKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TXAZFHNEWZMHQF-QZXNXJAKSA-N
Standard InCHI:	InChI=1S/C24H20O9/c1-12(25)17(28)10-11-18(29)33-24-20(14-4-8-16(27)9-5-14)22(31)21(30)19(23(24)32)13-2-6-15(26)7-3-13/h2-12,17,25-28,30H,1H3/b11-10-/t12-,17+/m0/s1
SMILES:	C[C@@H]([C@@H](/C=CC(=O)OC1=C(c2ccc(cc2)O)C(=O)C(=C(c2ccc(cc2)O)C1=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:0001831] Carbonyl compounds [CHEMONTID:0000118] Ketones [CHEMONTID:0003487] Cyclic ketones [CHEMONTID:0002495] Quinones [CHEMONTID:0002384] Benzoquinones [CHEMONTID:0002494] P-benzoquinones

*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
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	Leaf Diffusate	n.a.	n.a.	Database[FooDB]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	Seeds	n.a.		Database[Phenol-Explorer]
NPO22014	Dysphania botrys	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28846	Doris nobilis	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18062	Tapinella atrotomentosa	Species	Tapinellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29532	Vigna angularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18494	Carassea connexa	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28886	Acacia latifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24755	Abies nordmanniana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28866	Haematomma ochrophaeum	Species	Haematommataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28900	Planobispora rosea	Species	Streptosporangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29128	Pimpinella heyneana	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29416	Rhodophyllus nidorosus	Species	Entolomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29173	Leucadendron adscendens	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28951	Manglietia phuthoensis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29489	Garcinia opaca	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28972	Comatula solaris	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22014	Dysphania botrys	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29451	Clostridium tertium	Species	Clostridiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29205	Vepris fitoravina	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29029	Ophistreptus levis	n.a.	n.a.	n.a.	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 NPC123759 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	254
0.1-0.2	1047
0.2-0.3	2967
0.3-0.4	7028
0.4-0.5	11360
0.5-0.6	5289
0.6-0.7	11272
0.7-0.8	3376
0.8-0.85	86
0.85-0.9	18
0.9-0.95	0
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 NPC123759 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	227
0.1-0.2	750
0.2-0.3	1398
0.3-0.4	2396
0.4-0.5	2283
0.5-0.6	1350
0.6-0.7	644
0.7-0.8	99
0.8-0.85	3
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