NPASS Compound

Structure

NPC171651 OpenBabel07101718292D 30 32 0 0 1 0 0 0 0 0999 V2000 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 C 0 0 0 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 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 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 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 -1.7321 -1.0000 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 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 -6.0622 0.5000 0.0000 C 0 0 0 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 -3.4641 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 -1.7321 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 -1.0000 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 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 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 1 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 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 4 15 1 0 0 0 0 5 7 1 0 0 0 0 5 14 2 0 0 0 0 6 8 1 0 0 0 0 6 15 2 0 0 0 0 7 16 1 0 0 0 0 8 17 1 0 0 0 0 9 10 1 0 0 0 0 9 18 2 0 0 0 0 10 20 2 0 0 0 0 11 16 2 0 0 0 0 11 18 1 0 0 0 0 12 17 2 0 0 0 0 12 19 1 0 0 0 0 13 21 2 0 0 0 0 13 22 1 0 0 0 0 16 20 1 0 0 0 0 17 21 1 0 0 0 0 19 22 2 0 0 0 0 19 23 1 0 0 0 0 20 26 1 0 0 0 0 21 27 1 0 0 0 0 22 30 1 0 0 0 0 23 24 1 0 0 0 0 23 28 2 0 0 0 0 24 25 1 0 0 0 0 24 29 1 1 0 0 0 25 18 1 6 0 0 0 25 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	408.19
Volume:	435.51
LogP:	5.551
LogD:	3.887
LogS:	-3.057
# Rotatable Bonds:	5
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.619
Synthetic Accessibility Score:	3.765
Fsp3:	0.32
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:	-4.827
MDCK Permeability:	1.5340438039856963e-05
Pgp-inhibitor:	0.904
Pgp-substrate:	0.071
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.946
30% Bioavailability (F30%):	0.506

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	94.20446014404297%
Volume Distribution (VD):	0.813
Pgp-substrate:	5.504602909088135%

ADMET: Metabolism

CYP1A2-inhibitor:	0.186
CYP1A2-substrate:	0.165
CYP2C19-inhibitor:	0.778
CYP2C19-substrate:	0.076
CYP2C9-inhibitor:	0.87
CYP2C9-substrate:	0.918
CYP2D6-inhibitor:	0.909
CYP2D6-substrate:	0.563
CYP3A4-inhibitor:	0.504
CYP3A4-substrate:	0.185

ADMET: Excretion

Clearance (CL):	11.258
Half-life (T1/2):	0.176

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.705
Drug-inuced Liver Injury (DILI):	0.645
AMES Toxicity:	0.124
Rat Oral Acute Toxicity:	0.285
Maximum Recommended Daily Dose:	0.165
Skin Sensitization:	0.25
Carcinogencity:	0.088
Eye Corrosion:	0.003
Eye Irritation:	0.256
Respiratory Toxicity:	0.07

Download Data

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

Natural Product: NPC171651

Natural Product ID:	NPC171651
*Common Name:**	Lespeflorin B1
IUPAC Name:	(2R,3R)-3,7-dihydroxy-2-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]-6-(3-methylbut-2-enyl)-2,3-dihydrochromen-4-one
Synonyms:	Lespeflorin B1
Standard InCHIKey:	YELBDRXMPXVGQT-LOSJGSFVSA-N
Standard InCHI:	InChI=1S/C25H28O5/c1-14(2)5-7-16-11-18(9-10-20(16)26)25-24(29)23(28)19-12-17(8-6-15(3)4)21(27)13-22(19)30-25/h5-6,9-13,24-27,29H,7-8H2,1-4H3/t24-,25+/m0/s1
SMILES:	CC(=CCc1cc(ccc1O)[C@@H]1[C@H](C(=O)c2cc(CC=C(C)C)c(cc2O1)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL561905
PubChem CID:	25243246
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003646] 6-prenylated flavans [CHEMONTID:0003507] 6-prenylated flavanones

*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
NPO13293	Lespedeza floribunda	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[19132934]
NPO13293	Lespedeza floribunda	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[19132934]
NPO13293	Lespedeza floribunda	Species	Fabaceae	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
IC50	1

Activity Type	# Activity
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	2870.0	nM	PMID[566531]

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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 NPC171651 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	385
0.1-0.2	1424
0.2-0.3	3612
0.3-0.4	8597
0.4-0.5	9763
0.5-0.6	3661
0.6-0.7	5114
0.7-0.8	5159
0.8-0.85	2749
0.85-0.9	1575
0.9-0.95	573
0.95-1	85

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC35567
1.0	High Similarity	NPC243171
0.9932	High Similarity	NPC293286
0.9931	High Similarity	NPC278476
0.9931	High Similarity	NPC262038

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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 NPC171651 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	334
0.1-0.2	866
0.2-0.3	1666
0.3-0.4	2560
0.4-0.5	1891
0.5-0.6	1124
0.6-0.7	480
0.7-0.8	168
0.8-0.85	35
0.85-0.9	17
0.9-0.95	9
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.947	High Similarity	NPD7075	Discontinued
0.9459	High Similarity	NPD4380	Phase 2
0.94	High Similarity	NPD7096	Clinical (unspecified phase)
0.9384	High Similarity	NPD4378	Clinical (unspecified phase)
0.9272	High Similarity	NPD2393	Clinical (unspecified phase)

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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