NPASS Compound

Structure

NPC121537 OpenBabel06302216212D 24 24 0 0 1 0 0 0 0 0999 V2000 -2.0000 2.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 1.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.1340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 S 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 -1.0000 -1.0000 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 1.5000 1.5981 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0000 2.4641 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0000 2.4641 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5000 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0000 0.7321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0000 0.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 -0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 -0.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 1.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 3.3301 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 3.3301 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.4641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 24 1 6 0 0 0 4 5 1 0 0 0 0 5 6 2 3 0 0 0 5 12 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 2 0 0 0 0 8 11 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 23 1 6 0 0 0 15 16 1 0 0 0 0 15 22 1 1 0 0 0 16 17 1 0 0 0 0 16 21 1 6 0 0 0 17 18 1 0 0 0 0 17 19 1 1 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	389.05
Volume:	320.9
LogP:	-1.38
LogD:	-1.557
LogS:	-0.06
# Rotatable Bonds:	8
TPSA:	186.34
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	1
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.089
Synthetic Accessibility Score:	4.817
Fsp3:	0.727
Lipinski Rule-of-5:	Rejected
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:	-6.122
MDCK Permeability:	5.358402995625511e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.042
Human Intestinal Absorption (HIA):	0.969
20% Bioavailability (F20%):	0.944
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.055
Plasma Protein Binding (PPB):	65.860595703125%
Volume Distribution (VD):	0.53
Pgp-substrate:	40.769840240478516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.033
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.05
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.486
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.102
CYP3A4-inhibitor:	0.006
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	0.931
Half-life (T1/2):	0.669

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.766
Drug-inuced Liver Injury (DILI):	0.531
AMES Toxicity:	0.038
Rat Oral Acute Toxicity:	0.118
Maximum Recommended Daily Dose:	0.215
Skin Sensitization:	0.152
Carcinogencity:	0.091
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.211

Download Data

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

Natural Product: NPC121537

Natural Product ID:	NPC121537
*Common Name:**	Progoitrin
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MYHSVHWQEVDFQT-ILPXZUKPSA-N
Standard InCHI:	InChI=1S/C11H19NO10S2/c1-2-5(14)3-7(12-22-24(18,19)20)23-11-10(17)9(16)8(15)6(4-13)21-11/h2,5-6,8-11,13-17H,1,3-4H2,(H,18,19,20)/t5-,6+,8+,9-,10+,11-/m0/s1
SMILES:	C=C[C@@H](CC(=NOS(=O)(=O)O)S[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5281139
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0001540] Monosaccharides [CHEMONTID:0001498] Hexoses [CHEMONTID:0000373] Glucosinolates [CHEMONTID:0003925] Alkylglucosinolates

*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
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	retail stores, supermarkets and market stalls in Forssa and in the Helsinki area	2003–2005	DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	1996-Sep	PMID[10352947]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15877880]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17011103]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	Northeastern Regional Plant Introduction Station at Geneva	1966, 1967, and 1968 crop seasons	PMID[18460139]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24014097]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24128451]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2831703]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	Roots	n.a.		Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7576.2	Brassica oleracea var. sabauda	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7576	Brassica oleracea	Species	Brassicaceae	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
NPO7576	NPC121537	Raw, Frozen	Leaf	3.337	2.909	3.765	umol/g of FW	PMID[FooDB]
NPO7576	NPC121537	Raw, Frozen	n.a.	51.79	49.064	54.516	umol/g of FW	PMID[FooDB]
NPO7576.1	NPC121537	n.a.	n.a.	0.45	n.a.	n.a.	µmol/100g of FW	PMID[17011103]
NPO7576.2	NPC121537	n.a.	n.a.	2.41	n.a.	n.a.	µmol/100g of FW	PMID[17011103]
NPO7576.2	NPC121537	n.a.	n.a.	3.33	n.a.	n.a.	µmol/100g of FW	PMID[17011103]
NPO7576.2	NPC121537	n.a.	n.a.	0.62	n.a.	n.a.	µmol/100g of FW	PMID[17011103]

☑ 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 NPC121537 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC121537 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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