NPASS Compound

Structure

CID80781 OpenBabel06191715422D 31 33 0 0 1 0 0 0 0 0999 V2000 -3.4641 3.0000 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 1.7321 3.0000 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 2.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 0.8660 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 0.8660 -1.5000 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 -0.0000 -1.0000 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 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 -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 -0.8660 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 -2.5981 0.5000 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 -0.0000 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 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 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 0.0000 -0.0000 0.0000 C 0 0 1 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 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 -3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 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 1 11 1 0 0 0 0 2 11 1 0 0 0 0 3 12 1 0 0 0 0 4 13 1 0 0 0 0 5 23 1 0 0 0 0 6 23 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 9 23 1 0 0 0 0 10 24 1 0 0 0 0 11 14 1 0 0 0 0 12 25 2 0 0 0 0 12 30 1 0 0 0 0 13 26 2 0 0 0 0 13 31 1 0 0 0 0 14 17 1 0 0 0 0 14 18 2 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 15 20 1 0 0 0 0 16 19 1 0 0 0 0 16 24 1 0 0 0 0 17 27 2 0 0 0 0 18 19 1 0 0 0 0 18 28 1 0 0 0 0 19 29 2 0 0 0 0 20 21 1 0 0 0 0 20 30 1 6 0 0 0 21 22 1 0 0 0 0 21 31 1 1 0 0 0 22 23 1 0 0 0 0 22 24 1 1 0 0 0 24 7 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.21
Volume:	443.704
LogP:	4.512
LogD:	2.814
LogS:	-4.109
# Rotatable Bonds:	5
TPSA:	113.29
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.356
Synthetic Accessibility Score:	4.279
Fsp3:	0.583
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.96
MDCK Permeability:	2.6169542252318934e-05
Pgp-inhibitor:	0.775
Pgp-substrate:	0.133
Human Intestinal Absorption (HIA):	0.932
20% Bioavailability (F20%):	0.935
30% Bioavailability (F30%):	0.88

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.421
Plasma Protein Binding (PPB):	95.34908294677734%
Volume Distribution (VD):	1.151
Pgp-substrate:	15.274761199951172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.293
CYP1A2-substrate:	0.094
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.118
CYP2C9-inhibitor:	0.46
CYP2C9-substrate:	0.661
CYP2D6-inhibitor:	0.032
CYP2D6-substrate:	0.136
CYP3A4-inhibitor:	0.137
CYP3A4-substrate:	0.221

ADMET: Excretion

Clearance (CL):	0.975
Half-life (T1/2):	0.32

ADMET: Toxicity

hERG Blockers:	0.0
Human Hepatotoxicity (H-HT):	0.016
Drug-inuced Liver Injury (DILI):	0.204
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.098
Maximum Recommended Daily Dose:	0.078
Skin Sensitization:	0.516
Carcinogencity:	0.046
Eye Corrosion:	0.016
Eye Irritation:	0.872
Respiratory Toxicity:	0.762

Download Data

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

Natural Product: NPC80781

Natural Product ID:	NPC80781
*Common Name:**	IJUVPYONTOHMDC-HYVLGVRCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IJUVPYONTOHMDC-HYVLGVRCSA-N
Standard InCHI:	InChI=1S/C24H32O7/c1-11(2)14-17(27)15-16(19(29)18(14)28)24(7)10-8-9-23(5,6)22(24)21(31-13(4)26)20(15)30-12(3)25/h11,20-22,28H,8-10H2,1-7H3/t20-,21+,22-,24+/m0/s1
SMILES:	CC(=O)O[C@H]1C2=C(C(=O)C(=C(C2=O)C(C)C)O)[C@@]2([C@@H]([C@@H]1OC(=O)C)C(C)(C)CCC2)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2425666
PubChem CID:	NA
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014350]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31347365]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	twig	n.a.	PMID[22474975]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 7 of 7 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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	5

Activity Type	# Activity
Cell Line	5

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	23300.0	nM	PMID[557096]
NPT926	Cell Line	SK-MEL-1	Homo sapiens	IC50	=	16200.0	nM	PMID[557096]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	15900.0	nM	PMID[557096]
NPT466	Cell Line	U-937	Homo sapiens	IC50	=	12100.0	nM	PMID[557096]
NPT793	Cell Line	MOLT-3	Homo sapiens	IC50	=	5400.0	nM	PMID[557096]

Showing 1 to 5 of 5 entries

Previous1Next

☑ 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 NPC80781 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	226
0.1-0.2	1400
0.2-0.3	4492
0.3-0.4	8547
0.4-0.5	13787
0.5-0.6	7705
0.6-0.7	5368
0.7-0.8	1140
0.8-0.85	27
0.85-0.9	2
0.9-0.95	2
0.95-1	1

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9149	High Similarity	NPC271652
0.8936	High Similarity	NPC113393
0.8723	High Similarity	NPC307298
0.8416	Intermediate Similarity	NPC198880
0.8367	Intermediate Similarity	NPC477436

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC80781 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	217
0.1-0.2	1770
0.2-0.3	3623
0.3-0.4	2225
0.4-0.5	863
0.5-0.6	255
0.6-0.7	187
0.7-0.8	10
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7788	Intermediate Similarity	NPD7115	Discovery
0.7619	Intermediate Similarity	NPD4225	Approved
0.7573	Intermediate Similarity	NPD7748	Approved
0.7545	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.7524	Intermediate Similarity	NPD7902	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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