NPASS Compound

Structure

CID293286 OpenBabel06191716102D 35 37 0 0 1 0 0 0 0 0999 V2000 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 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 -1.7321 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 3.4641 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 -2.5981 1.5000 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 -3.4641 -2.0000 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 -1.7321 1.0000 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 1.7321 1.0000 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 3.4641 4.0000 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 -2.5981 2.5000 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 -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 -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 -0.0000 -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 -0.8660 -0.5000 0.0000 C 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 -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 17 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 4 18 1 0 0 0 0 5 19 1 0 0 0 0 6 19 1 0 0 0 0 7 10 1 0 0 0 0 7 17 2 0 0 0 0 8 11 1 0 0 0 0 8 18 2 0 0 0 0 9 13 1 0 0 0 0 9 19 2 0 0 0 0 10 20 1 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 22 2 0 0 0 0 13 23 1 0 0 0 0 14 25 2 0 0 0 0 15 20 2 0 0 0 0 15 22 1 0 0 0 0 16 21 2 0 0 0 0 16 24 1 0 0 0 0 20 25 1 0 0 0 0 21 26 1 0 0 0 0 23 26 2 0 0 0 0 23 30 1 0 0 0 0 24 27 1 0 0 0 0 24 30 2 0 0 0 0 25 31 1 0 0 0 0 26 32 1 0 0 0 0 27 28 1 0 0 0 0 27 33 2 0 0 0 0 28 29 1 0 0 0 0 28 34 1 1 0 0 0 29 22 1 6 0 0 0 29 35 1 0 0 0 0 30 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	476.26
Volume:	519.353
LogP:	7.424
LogD:	4.441
LogS:	-2.768
# Rotatable Bonds:	7
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.408
Synthetic Accessibility Score:	4.033
Fsp3:	0.367
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:	-4.867
MDCK Permeability:	1.6034351574489847e-05
Pgp-inhibitor:	0.972
Pgp-substrate:	0.227
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.97
30% Bioavailability (F30%):	0.336

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016
Plasma Protein Binding (PPB):	86.08329772949219%
Volume Distribution (VD):	1.687
Pgp-substrate:	13.926011085510254%

ADMET: Metabolism

CYP1A2-inhibitor:	0.079
CYP1A2-substrate:	0.144
CYP2C19-inhibitor:	0.79
CYP2C19-substrate:	0.098
CYP2C9-inhibitor:	0.886
CYP2C9-substrate:	0.934
CYP2D6-inhibitor:	0.585
CYP2D6-substrate:	0.273
CYP3A4-inhibitor:	0.308
CYP3A4-substrate:	0.173

ADMET: Excretion

Clearance (CL):	11.75
Half-life (T1/2):	0.057

ADMET: Toxicity

hERG Blockers:	0.067
Human Hepatotoxicity (H-HT):	0.861
Drug-inuced Liver Injury (DILI):	0.163
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.359
Maximum Recommended Daily Dose:	0.166
Skin Sensitization:	0.701
Carcinogencity:	0.045
Eye Corrosion:	0.003
Eye Irritation:	0.057
Respiratory Toxicity:	0.146

Download Data

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

Natural Product: NPC293286

Natural Product ID:	NPC293286
*Common Name:**	Lespeflorin B3
IUPAC Name:	(2R,3R)-3,7-dihydroxy-2-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]-6,8-bis(3-methylbut-2-enyl)-2,3-dihydrochromen-4-one
Synonyms:	Lespeflorin B3
Standard InCHIKey:	IKKCPYPLJMVWMP-URLMMPGGSA-N
Standard InCHI:	InChI=1S/C30H36O5/c1-17(2)7-10-20-15-22(12-14-25(20)31)29-28(34)27(33)24-16-21(11-8-18(3)4)26(32)23(30(24)35-29)13-9-19(5)6/h7-9,12,14-16,28-29,31-32,34H,10-11,13H2,1-6H3/t28-,29+/m0/s1
SMILES:	CC(=CCc1c2O[C@H](c3ccc(c(c3)CC=C(C)C)O)[C@H](C(=O)c2cc(c1O)CC=C(C)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL549408
PubChem CID:	25243247
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans [CHEMONTID:0003508] 8-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	=	680.0	nM	PMID[555588]

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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 NPC293286 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	387
0.1-0.2	1396
0.2-0.3	3394
0.3-0.4	8342
0.4-0.5	10138
0.5-0.6	3771
0.6-0.7	5179
0.7-0.8	5285
0.8-0.85	2804
0.85-0.9	1441
0.9-0.95	498
0.95-1	62

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Similarity Score	Similarity Level	Natural Product ID
0.9932	High Similarity	NPC138288
0.9932	High Similarity	NPC171651
0.9932	High Similarity	NPC35567
0.9932	High Similarity	NPC243171
0.9863	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 NPC293286 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	868
0.2-0.3	1667
0.3-0.4	2558
0.4-0.5	1926
0.5-0.6	1100
0.6-0.7	469
0.7-0.8	168
0.8-0.85	37
0.85-0.9	18
0.9-0.95	4
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9536	High Similarity	NPD7075	Discontinued
0.9467	High Similarity	NPD7096	Clinical (unspecified phase)
0.9396	High Similarity	NPD4380	Phase 2
0.932	High Similarity	NPD4378	Clinical (unspecified phase)
0.9211	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