NPASS Compound

Structure

NPC106625 OpenBabel07101719512D 32 34 0 0 1 0 0 0 0 0999 V2000 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 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 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 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 -0.8660 -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 6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.0000 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 1.7321 4.0000 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 -0.8660 -0.5000 0.0000 C 0 0 2 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 -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 7.7942 4.5000 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 2.5981 4.5000 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 4.5000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 30 1 0 0 0 0 2 5 1 0 0 0 0 2 11 2 0 0 0 0 3 6 2 0 0 0 0 3 11 1 0 0 0 0 4 7 1 0 0 0 0 4 11 1 0 0 0 0 5 12 2 0 0 0 0 6 12 1 0 0 0 0 7 14 1 0 0 0 0 8 13 2 0 0 0 0 8 15 1 0 0 0 0 9 13 1 0 0 0 0 9 16 2 0 0 0 0 10 23 1 0 0 0 0 12 24 1 0 0 0 0 13 30 1 0 0 0 0 14 18 1 0 0 0 0 14 25 2 0 0 0 0 15 18 2 0 0 0 0 15 26 1 0 0 0 0 16 18 1 0 0 0 0 16 31 1 0 0 0 0 17 10 1 6 0 0 0 17 19 1 0 0 0 0 17 32 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 1 0 0 0 20 21 1 0 0 0 0 20 28 1 6 0 0 0 21 22 1 0 0 0 0 21 29 1 1 0 0 0 22 31 1 6 0 0 0 22 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.15
Volume:	432.846
LogP:	1.074
LogD:	1.175
LogS:	-3.541
# Rotatable Bonds:	8
TPSA:	166.14
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.304
Synthetic Accessibility Score:	3.726
Fsp3:	0.409
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:	-6.316
MDCK Permeability:	8.874130799085833e-06
Pgp-inhibitor:	0.012
Pgp-substrate:	0.087
Human Intestinal Absorption (HIA):	0.837
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.112
Plasma Protein Binding (PPB):	85.86642456054688%
Volume Distribution (VD):	0.741
Pgp-substrate:	4.678420543670654%

ADMET: Metabolism

CYP1A2-inhibitor:	0.339
CYP1A2-substrate:	0.076
CYP2C19-inhibitor:	0.068
CYP2C19-substrate:	0.106
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.789
CYP2D6-inhibitor:	0.646
CYP2D6-substrate:	0.578
CYP3A4-inhibitor:	0.062
CYP3A4-substrate:	0.076

ADMET: Excretion

Clearance (CL):	8.965
Half-life (T1/2):	0.785

ADMET: Toxicity

hERG Blockers:	0.211
Human Hepatotoxicity (H-HT):	0.06
Drug-inuced Liver Injury (DILI):	0.605
AMES Toxicity:	0.333
Rat Oral Acute Toxicity:	0.068
Maximum Recommended Daily Dose:	0.009
Skin Sensitization:	0.818
Carcinogencity:	0.19
Eye Corrosion:	0.003
Eye Irritation:	0.101
Respiratory Toxicity:	0.027

Download Data

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

Natural Product: NPC106625

Natural Product ID:	NPC106625
*Common Name:**	Asebotin
IUPAC Name:	1-[2-hydroxy-4-methoxy-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]-3-(4-hydroxyphenyl)propan-1-one
Synonyms:	Asebotin
Standard InCHIKey:	PQCIBORQLVRFMR-MIUGBVLSSA-N
Standard InCHI:	InChI=1S/C22H26O10/c1-30-13-8-15(26)18(14(25)7-4-11-2-5-12(24)6-3-11)16(9-13)31-22-21(29)20(28)19(27)17(10-23)32-22/h2-3,5-6,8-9,17,19-24,26-29H,4,7,10H2,1H3/t17-,19-,20+,21-,22-/m1/s1
SMILES:	OC[C@H]1O[C@@H](Oc2cc(OC)cc(c2C(=O)CCc2ccc(cc2)O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL490513
PubChem CID:	11190157
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
NPO19198	Kalmia latifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[521818]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31809052]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15787442]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	leaves	n.a.	n.a.	PMID[15787442]
NPO19198	Kalmia latifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19198	Kalmia latifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO19198	Kalmia latifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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	8

Activity Type	# Activity
NON-MOLECULAR	8

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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	=	35.16	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	40.73	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	47.42	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	79.57	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	87.19	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	89.78	10'-3cpm	PMID[539051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	100.0	%	PMID[539050]

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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 NPC106625 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	367
0.1-0.2	1426
0.2-0.3	3383
0.3-0.4	8347
0.4-0.5	10076
0.5-0.6	4262
0.6-0.7	5225
0.7-0.8	5749
0.8-0.85	2509
0.85-0.9	1126
0.9-0.95	191
0.95-1	36

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Similarity Score	Similarity Level	Natural Product ID
0.9932	High Similarity	NPC121001
0.9932	High Similarity	NPC259182
0.9932	High Similarity	NPC99233
0.9865	High Similarity	NPC127406
0.9865	High Similarity	NPC206378

Showing 1 to 5 of 200 entries

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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 NPC106625 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	313
0.1-0.2	841
0.2-0.3	1673
0.3-0.4	2637
0.4-0.5	1961
0.5-0.6	1125
0.6-0.7	391
0.7-0.8	161
0.8-0.85	29
0.85-0.9	17
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9667	High Similarity	NPD4381	Clinical (unspecified phase)
0.9241	High Similarity	NPD7804	Clinical (unspecified phase)
0.9182	High Similarity	NPD7074	Phase 3
0.9119	High Similarity	NPD7054	Approved
0.9062	High Similarity	NPD7472	Approved

Showing 1 to 5 of 200 entries

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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