NPASS Compound

Structure

CID55615 OpenBabel06191715392D 31 33 0 0 1 0 0 0 0 0999 V2000 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 6.0000 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8660 0.5000 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 3.4641 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 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 5.0000 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 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 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 0.8660 1.5000 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 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 1 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 2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 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 13 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 4 14 1 0 0 0 0 5 24 1 0 0 0 0 6 24 1 0 0 0 0 7 9 2 0 0 0 0 7 15 1 0 0 0 0 8 10 2 0 0 0 0 8 15 1 0 0 0 0 9 16 1 0 0 0 0 10 17 1 0 0 0 0 11 13 1 0 0 0 0 11 18 1 0 0 0 0 12 14 1 0 0 0 0 12 19 1 0 0 0 0 15 21 2 0 0 0 0 16 20 2 0 0 0 0 16 31 1 0 0 0 0 17 25 2 0 0 0 0 17 28 1 0 0 0 0 18 26 2 0 0 0 0 18 29 1 0 0 0 0 19 27 2 0 0 0 0 19 30 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 21 28 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 1 0 0 0 24 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	430.2
Volume:	441.067
LogP:	5.178
LogD:	4.267
LogS:	-4.433
# Rotatable Bonds:	8
TPSA:	92.04
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.49
Synthetic Accessibility Score:	3.672
Fsp3:	0.542
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:	-4.683
MDCK Permeability:	3.98982701881323e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.059
Plasma Protein Binding (PPB):	89.4212875366211%
Volume Distribution (VD):	0.42
Pgp-substrate:	7.034782886505127%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.097
CYP2C19-inhibitor:	0.714
CYP2C19-substrate:	0.281
CYP2C9-inhibitor:	0.769
CYP2C9-substrate:	0.501
CYP2D6-inhibitor:	0.122
CYP2D6-substrate:	0.072
CYP3A4-inhibitor:	0.644
CYP3A4-substrate:	0.304

ADMET: Excretion

Clearance (CL):	11.612
Half-life (T1/2):	0.372

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.972
Drug-inuced Liver Injury (DILI):	0.962
AMES Toxicity:	0.102
Rat Oral Acute Toxicity:	0.432
Maximum Recommended Daily Dose:	0.025
Skin Sensitization:	0.193
Carcinogencity:	0.71
Eye Corrosion:	0.004
Eye Irritation:	0.026
Respiratory Toxicity:	0.186

Download Data

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

Natural Product: NPC55615

Natural Product ID:	NPC55615
*Common Name:**	3',4'-Diisovalerylkhellactone
IUPAC Name:	[(9S,10S)-8,8-dimethyl-9-(3-methylbutanoyloxy)-2-oxo-9,10-dihydropyrano[2,3-f]chromen-10-yl] 3-methylbutanoate
Synonyms:	Cis-3',4'-Diisovalerylkhellactone
Standard InCHIKey:	LJYPJWICCCIAKW-GOTSBHOMSA-N
Standard InCHI:	InChI=1S/C24H30O7/c1-13(2)11-18(26)29-22-20-16(9-7-15-8-10-17(25)28-21(15)20)31-24(5,6)23(22)30-19(27)12-14(3)4/h7-10,13-14,22-23H,11-12H2,1-6H3/t22-,23-/m0/s1
SMILES:	CC(C)CC(=O)O[C@H]1c2c(ccc3ccc(=O)oc23)OC(C)(C)[C@H]1OC(=O)CC(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL477694
PubChem CID:	44584701
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0003484] Pyranocoumarins [CHEMONTID:0003485] Angular pyranocoumarins

*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
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[25068578]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24813739]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[22784551]
NPO16675	Peucedanum japonicum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1453177]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16675	Peucedanum japonicum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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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
Others	5

Activity Type	# Activity
Cell Line	2
NON-MOLECULAR	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	7400.0	nM	PMID[561966]
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	>	90.0	%	PMID[561966]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	8.8	%	PMID[561965]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	49.8	%	PMID[561965]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	39.3	%	PMID[561965]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	0.0	%	PMID[561965]

Showing 1 to 6 of 6 entries

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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 NPC55615 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	416
0.1-0.2	1646
0.2-0.3	4074
0.3-0.4	9180
0.4-0.5	9424
0.5-0.6	4062
0.6-0.7	5920
0.7-0.8	5532
0.8-0.85	1848
0.85-0.9	392
0.9-0.95	154
0.95-1	49

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC149320
1.0	High Similarity	NPC160727
1.0	High Similarity	NPC476455
1.0	High Similarity	NPC128529
1.0	High Similarity	NPC177281

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 NPC55615 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	360
0.1-0.2	951
0.2-0.3	1755
0.3-0.4	2640
0.4-0.5	1889
0.5-0.6	1034
0.6-0.7	361
0.7-0.8	116
0.8-0.85	34
0.85-0.9	8
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.875	High Similarity	NPD5123	Clinical (unspecified phase)
0.875	High Similarity	NPD5124	Phase 1
0.8322	Intermediate Similarity	NPD1652	Phase 2
0.8212	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.8134	Intermediate Similarity	NPD422	Phase 1

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