NPASS Compound

Structure

CID26195 OpenBabel06191715352D 31 34 0 0 1 0 0 0 0 0999 V2000 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 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 1.5000 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 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 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 3.4641 0.0000 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 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 1 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 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 -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 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 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 -0.0000 1.0000 0.0000 C 0 0 2 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 6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 O 0 0 0 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 -2.5981 1.5000 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 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 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 9 2 0 0 0 0 2 4 2 0 0 0 0 2 9 1 0 0 0 0 3 11 2 0 0 0 0 4 11 1 0 0 0 0 5 10 2 0 0 0 0 5 12 1 0 0 0 0 6 10 1 0 0 0 0 6 15 2 0 0 0 0 7 13 1 0 0 0 0 7 14 1 0 0 0 0 8 22 1 0 0 0 0 10 23 1 0 0 0 0 11 29 1 0 0 0 0 12 17 2 0 0 0 0 12 24 1 0 0 0 0 13 17 1 0 0 0 0 13 25 2 0 0 0 0 14 9 1 6 0 0 0 14 30 1 0 0 0 0 15 17 1 0 0 0 0 15 30 1 0 0 0 0 16 8 1 6 0 0 0 16 18 1 0 0 0 0 16 31 1 0 0 0 0 18 19 1 0 0 0 0 18 26 1 1 0 0 0 19 20 1 0 0 0 0 19 27 1 6 0 0 0 20 21 1 0 0 0 0 20 28 1 1 0 0 0 21 29 1 6 0 0 0 21 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	434.12
Volume:	406.993
LogP:	0.797
LogD:	0.565
LogS:	-4.341
# Rotatable Bonds:	4
TPSA:	166.14
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.385
Synthetic Accessibility Score:	3.975
Fsp3:	0.381
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-6.444
MDCK Permeability:	1.4919351087883115e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.88
Human Intestinal Absorption (HIA):	0.143
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.095
Plasma Protein Binding (PPB):	82.93025970458984%
Volume Distribution (VD):	0.887
Pgp-substrate:	13.092449188232422%

ADMET: Metabolism

CYP1A2-inhibitor:	0.086
CYP1A2-substrate:	0.045
CYP2C19-inhibitor:	0.057
CYP2C19-substrate:	0.075
CYP2C9-inhibitor:	0.052
CYP2C9-substrate:	0.645
CYP2D6-inhibitor:	0.493
CYP2D6-substrate:	0.282
CYP3A4-inhibitor:	0.092
CYP3A4-substrate:	0.096

ADMET: Excretion

Clearance (CL):	6.645
Half-life (T1/2):	0.633

ADMET: Toxicity

hERG Blockers:	0.092
Human Hepatotoxicity (H-HT):	0.313
Drug-inuced Liver Injury (DILI):	0.953
AMES Toxicity:	0.608
Rat Oral Acute Toxicity:	0.282
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.758
Carcinogencity:	0.844
Eye Corrosion:	0.003
Eye Irritation:	0.174
Respiratory Toxicity:	0.25

Download Data

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

Natural Product: NPC26195

Natural Product ID:	NPC26195
*Common Name:**	Naringenin 4'-O-Beta-D-Glucopyranoside
IUPAC Name:	(2S)-5,7-dihydroxy-2-[4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]-2,3-dihydrochromen-4-one
Synonyms:
Standard InCHIKey:	KSDSYIXRWHRPMN-SFTVRKLSSA-N
Standard InCHI:	InChI=1S/C21H22O10/c22-8-16-18(26)19(27)20(28)21(31-16)29-11-3-1-9(2-4-11)14-7-13(25)17-12(24)5-10(23)6-15(17)30-14/h1-6,14,16,18-24,26-28H,7-8H2/t14-,16+,18+,19-,20+,21+/m0/s1
SMILES:	c1cc(ccc1[C@@H]1CC(=O)c2c(cc(cc2O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL453552
PubChem CID:	157745
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932124]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	stem	n.a.	PMID[12932124]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11087602]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
Others	1

Activity Type	# Activity
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	0.782	mM	PMID[551931]

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☑ 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 NPC26195 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	389
0.1-0.2	1539
0.2-0.3	3666
0.3-0.4	9116
0.4-0.5	9369
0.5-0.6	4192
0.6-0.7	5458
0.7-0.8	5872
0.8-0.85	1984
0.85-0.9	908
0.9-0.95	173
0.95-1	31

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC39351
1.0	High Similarity	NPC169248
1.0	High Similarity	NPC72649
1.0	High Similarity	NPC97052
0.9932	High Similarity	NPC206378

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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 NPC26195 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	844
0.2-0.3	1714
0.3-0.4	2694
0.4-0.5	1935
0.5-0.6	1084
0.6-0.7	350
0.7-0.8	140
0.8-0.85	28
0.85-0.9	13
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9733	High Similarity	NPD4381	Clinical (unspecified phase)
0.9304	High Similarity	NPD7804	Clinical (unspecified phase)
0.9245	High Similarity	NPD7074	Phase 3
0.9182	High Similarity	NPD7054	Approved
0.9125	High Similarity	NPD7472	Approved

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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