NPASS Compound

Structure

CID161749 OpenBabel06191715532D 30 33 0 0 1 0 0 0 0 0999 V2000 6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 3.5000 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 4.3301 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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 4.5000 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 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 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 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 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 -0.0000 3.0000 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 1.7321 0.0000 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 3 1 0 0 0 0 1 10 2 0 0 0 0 2 4 2 0 0 0 0 2 10 1 0 0 0 0 3 11 2 0 0 0 0 4 11 1 0 0 0 0 5 6 2 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 7 12 2 0 0 0 0 7 15 1 0 0 0 0 8 22 1 0 0 0 0 9 14 2 0 0 0 0 9 28 1 0 0 0 0 10 14 1 0 0 0 0 11 23 1 0 0 0 0 12 29 1 0 0 0 0 13 15 2 0 0 0 0 13 17 1 0 0 0 0 14 17 1 0 0 0 0 15 28 1 0 0 0 0 16 8 1 6 0 0 0 16 18 1 0 0 0 0 16 30 1 0 0 0 0 17 24 2 0 0 0 0 18 19 1 0 0 0 0 18 25 1 1 0 0 0 19 20 1 0 0 0 0 19 26 1 6 0 0 0 20 21 1 0 0 0 0 20 27 1 1 0 0 0 21 29 1 6 0 0 0 21 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.11
Volume:	395.567
LogP:	0.829
LogD:	1.264
LogS:	-4.045
# Rotatable Bonds:	4
TPSA:	149.82
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.406
Synthetic Accessibility Score:	3.66
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.101
MDCK Permeability:	1.1897681361006107e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.14
Human Intestinal Absorption (HIA):	0.308
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.07
Plasma Protein Binding (PPB):	92.16301727294922%
Volume Distribution (VD):	0.995
Pgp-substrate:	5.06309700012207%

ADMET: Metabolism

CYP1A2-inhibitor:	0.299
CYP1A2-substrate:	0.046
CYP2C19-inhibitor:	0.091
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.027
CYP2C9-substrate:	0.477
CYP2D6-inhibitor:	0.719
CYP2D6-substrate:	0.601
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.057

ADMET: Excretion

Clearance (CL):	2.822
Half-life (T1/2):	0.633

ADMET: Toxicity

hERG Blockers:	0.191
Human Hepatotoxicity (H-HT):	0.061
Drug-inuced Liver Injury (DILI):	0.555
AMES Toxicity:	0.228
Rat Oral Acute Toxicity:	0.085
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.612
Carcinogencity:	0.665
Eye Corrosion:	0.003
Eye Irritation:	0.158
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC161749

Natural Product ID:	NPC161749
*Common Name:**	Daidzin
IUPAC Name:	3-(4-hydroxyphenyl)-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one
Synonyms:	Dadzin; Daidzin
Standard InCHIKey:	KYQZWONCHDNPDP-QNDFHXLGSA-N
Standard InCHI:	InChI=1S/C21H20O9/c22-8-16-18(25)19(26)20(27)21(30-16)29-12-5-6-13-15(7-12)28-9-14(17(13)24)10-1-3-11(23)4-2-10/h1-7,9,16,18-23,25-27H,8H2/t16-,18-,19+,20-,21-/m1/s1
SMILES:	c1cc(ccc1c1coc2cc(ccc2c1=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL486422
PubChem CID:	107971
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid 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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28809	Cullen corylifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9544566]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8882438]
NPO26158	Aspergillus carbonarius	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4837062]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[31861466]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[31159190]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30599958]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30583361]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	Guangzhou, China		PMID[30563201]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30236698]
NPO12182	Murraya exotica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29303577]

Showing 1 to 10 of 165 entries

Previous1 2 3 4 5…17Next

☑ 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

Show entries

Search:

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO13281	NPC161749	n.a.	Seeds	6.6	n.a.	n.a.	µg	PMID[31861466]
NPO13281	NPC161749	n.a.	Seeds	6.6	n.a.	n.a.	µg/g of Seed	PMID[24811150]
NPO7635	NPC161749	n.a.	Seeds	1.27	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO7635	NPC161749	n.a.	Seeds	3.785	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO7635	NPC161749	n.a.	Seeds	46.7	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]

Showing 1 to 5 of 14 entries

Previous1 2 3Next

☑ 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

Activity Type	# Activity
IC50	12
Kd	1
MIC	4
Others	33
Potency	13

Activity Type	# Activity
Cell Line	3
Individual Protein	22
NON-MOLECULAR	1
Organism	7
Others	18
Protein Family	4
SINGLE PROTEIN	4
Tissue	2
Uncleic Acid	2

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.09	%	PMID[448299]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-4.2	%	PMID[448298]
NPT2	Others	Unspecified		Inhibition	=	41.24	%	PMID[448297]
NPT2	Others	Unspecified		Inhibition	=	66.8	%	PMID[448297]
NPT2	Others	Unspecified		Inhibition	=	77.29	%	PMID[448297]
NPT2	Others	Unspecified		Inhibition	=	84.83	%	PMID[448297]
NPT2	Others	Unspecified		IC50	=	178300.0	nM	PMID[448297]
NPT2732	Individual Protein	Aldehyde dehydrogenase	Homo sapiens	IC50	=	3500.0	nM	PMID[448296]
NPT21253	SINGLE PROTEIN	Aldehyde dehydrogenase X	Homo sapiens	IC50	=	5100.0	nM	PMID[448296]
NPT21254	SINGLE PROTEIN	Retinal dehydrogenase 2	Homo sapiens	IC50	=	4500.0	nM	PMID[448296]

Showing 1 to 10 of 61 entries

Previous1 2 3 4 5 6 7Next

☑ 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 NPC161749 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	426
0.1-0.2	1734
0.2-0.3	3740
0.3-0.4	9326
0.4-0.5	9159
0.5-0.6	4352
0.6-0.7	5607
0.7-0.8	4991
0.8-0.85	2306
0.85-0.9	770
0.9-0.95	259
0.95-1	27

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC313163
1.0	High Similarity	NPC197896
1.0	High Similarity	NPC258035
1.0	High Similarity	NPC156457
0.9933	High Similarity	NPC73511

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC161749 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	393
0.1-0.2	909
0.2-0.3	1770
0.3-0.4	2704
0.4-0.5	1921
0.5-0.6	985
0.6-0.7	289
0.7-0.8	129
0.8-0.85	35
0.85-0.9	13
0.9-0.95	1
0.95-1	1

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4381	Clinical (unspecified phase)
0.9338	High Similarity	NPD4380	Phase 2
0.9308	High Similarity	NPD7804	Clinical (unspecified phase)
0.9245	High Similarity	NPD3818	Discontinued
0.9187	High Similarity	NPD7054	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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