NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	254.22
Volume:	297.6
LogP:	5.227
LogD:	3.16
LogS:	-3.367
# Rotatable Bonds:	13
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.356
Synthetic Accessibility Score:	2.052
Fsp3:	0.812
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.978
MDCK Permeability:	3.8469825085485354e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.026
20% Bioavailability (F20%):	0.987
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	98.34920501708984%
Volume Distribution (VD):	0.537
Pgp-substrate:	0.7379682660102844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.242
CYP1A2-substrate:	0.27
CYP2C19-inhibitor:	0.103
CYP2C19-substrate:	0.2
CYP2C9-inhibitor:	0.255
CYP2C9-substrate:	0.988
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.263
CYP3A4-inhibitor:	0.032
CYP3A4-substrate:	0.029

ADMET: Excretion

Clearance (CL):	2.613
Half-life (T1/2):	0.823

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.05
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.031
Skin Sensitization:	0.911
Carcinogencity:	0.137
Eye Corrosion:	0.947
Eye Irritation:	0.974
Respiratory Toxicity:	0.72

Download Data

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

Natural Product: NPC299545

Natural Product ID:	NPC299545
*Common Name:**	RVHDJZGRYYPEGM-FXKWVFHUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RVHDJZGRYYPEGM-FXKWVFHUSA-N
Standard InCHI:	InChI=1S/C5H9NO3S/c1-10(9)3-2-4(6)5(7)8/h2-4H,6H2,1H3,(H,7,8)/b3-2+/t4-,10+/m0/s1
SMILES:	C[S@@](=O)/C=C/[C@@H](C(=O)O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	56932118
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0002404] Alpha amino acids [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(01)00320-X]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11738417]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18071251]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	faeces	n.a.	PMID[18323202]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21462031]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31397570]
NPO16741.1	Codonopsis pilosula var. modesta	Varieties	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22659	Codonopsis subglobosa	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30421	Codonopsis tangshen	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14959.1	Codonopsis pilosula subsp. tangshen	Subspecies	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22659	Codonopsis subglobosa	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741.1	Codonopsis pilosula var. modesta	Varieties	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22659	Codonopsis subglobosa	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30421	Codonopsis tangshen	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14959.1	Codonopsis pilosula subsp. tangshen	Subspecies	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14959.1	Codonopsis pilosula subsp. tangshen	Subspecies	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22659	Codonopsis subglobosa	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22874	Bombyx mori	Species	Bombycidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16741.1	Codonopsis pilosula var. modesta	Varieties	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23429	Lycium barbarum	Species	Solanaceae	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 NPC299545 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	36
0.1-0.2	25223
0.2-0.3	15060
0.3-0.4	1998
0.4-0.5	265
0.5-0.6	79
0.6-0.7	26
0.7-0.8	7
0.8-0.85	3
0.85-0.9	0
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 NPC299545 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	35
0.1-0.2	4613
0.2-0.3	3742
0.3-0.4	607
0.4-0.5	100
0.5-0.6	37
0.6-0.7	13
0.7-0.8	3
0.8-0.85	0
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