NPASS Compound

Structure

CID100454 OpenBabel06191715442D 44 46 0 0 1 0 0 0 0 0999 V2000 18.6461 5.0969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 -1.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.8371 5.6847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.9235 5.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.8190 4.2834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.9054 3.8767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.8009 2.8821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2814 3.1973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3860 4.1919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3679 2.7906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.8874 2.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2995 4.5986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2634 1.7961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7828 1.4809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4040 5.5931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3498 1.3893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8693 1.0741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3176 5.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2453 0.3948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.7648 0.0796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1266 5.4121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0912 -0.0483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.7821 4.1388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5034 0.7607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3699 3.3298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5227 0.5759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3317 -0.0119 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 12.8512 -0.3271 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 9.0221 4.4175 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.0422 0.2607 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 9.8311 3.8298 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.0912 1.5697 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 10.7821 2.5207 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2272 -1.0064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.7467 -1.3216 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1085 4.0108 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6386 1.6637 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 12.0422 1.2607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.8311 2.8298 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 28 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 11 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 9 12 1 0 0 0 0 10 13 1 0 0 0 0 11 14 1 0 0 0 0 12 15 1 0 0 0 0 13 16 1 0 0 0 0 14 17 1 0 0 0 0 15 18 1 0 0 0 0 16 19 1 0 0 0 0 17 20 1 0 0 0 0 18 21 1 0 0 0 0 19 30 1 0 0 0 0 20 31 1 0 0 0 0 21 32 1 0 0 0 0 22 24 1 0 0 0 0 22 33 1 0 0 0 0 23 25 1 0 0 0 0 23 34 1 0 0 0 0 24 35 1 0 0 0 0 25 36 1 0 0 0 0 26 28 1 0 0 0 0 26 29 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 28 42 1 0 0 0 0 29 37 1 0 0 0 0 30 38 1 0 0 0 0 31 39 1 0 0 0 0 32 40 1 6 0 0 0 33 31 1 1 0 0 0 33 43 1 0 0 0 0 34 32 1 1 0 0 0 34 44 1 0 0 0 0 35 36 1 0 0 0 0 35 43 1 0 0 0 0 36 44 1 0 0 0 0 37 41 2 0 0 0 0 37 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.48
Volume:	679.097
LogP:	8.798
LogD:	5.012
LogS:	-5.41
# Rotatable Bonds:	25
TPSA:	112.52
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.081
Synthetic Accessibility Score:	4.662
Fsp3:	0.892
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.259
MDCK Permeability:	1.3828807823301759e-05
Pgp-inhibitor:	0.015
Pgp-substrate:	0.284
Human Intestinal Absorption (HIA):	0.028
20% Bioavailability (F20%):	0.994
30% Bioavailability (F30%):	0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	97.60294342041016%
Volume Distribution (VD):	1.147
Pgp-substrate:	2.4406354427337646%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.372
CYP2C19-inhibitor:	0.061
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.047
CYP2C9-substrate:	0.963
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.141
CYP3A4-inhibitor:	0.119
CYP3A4-substrate:	0.021

ADMET: Excretion

Clearance (CL):	5.965
Half-life (T1/2):	0.067

ADMET: Toxicity

hERG Blockers:	0.096
Human Hepatotoxicity (H-HT):	0.148
Drug-inuced Liver Injury (DILI):	0.062
AMES Toxicity:	0.044
Rat Oral Acute Toxicity:	0.218
Maximum Recommended Daily Dose:	0.506
Skin Sensitization:	0.965
Carcinogencity:	0.025
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.335

Download Data

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

Natural Product: NPC100454

Natural Product ID:	NPC100454
*Common Name:**	4-[(13R)-2,13-Dihydroxy-13-[(2R)-5-[(5R)-5-(1-Hydroxyundecyl)Oxolan-2-Yl]Oxolan-2-Yl]Tridecyl]-2-Methyl-2H-Furan-5-One
IUPAC Name:	4-[(13R)-2,13-dihydroxy-13-[(2R)-5-[(5R)-5-(1-hydroxyundecyl)oxolan-2-yl]oxolan-2-yl]tridecyl]-2-methyl-2H-furan-5-one
Synonyms:
Standard InCHIKey:	MBABCNBNDNGODA-XRLPKKPGSA-N
Standard InCHI:	InChI=1S/C37H66O7/c1-3-4-5-6-7-11-14-17-20-31(39)33-22-24-35(43-33)36-25-23-34(44-36)32(40)21-18-15-12-9-8-10-13-16-19-30(38)27-29-26-28(2)42-37(29)41/h26,28,30-36,38-40H,3-25,27H2,1-2H3/t28?,30?,31?,32-,33-,34-,35?,36?/m1/s1
SMILES:	CCCCCCCCCCC([C@H]1CCC(C2CC[C@H]([C@@H](CCCCCCCCCCC(CC3=CC(C)OC3=O)O)O)O2)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1996175
PubChem CID:	6711271
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002518] Annonaceous acetogenins

*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
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6387056]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 10 of 14 entries

Previous1 2Next

☑ 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
GI50	67

Activity Type	# Activity
Cell Line	67

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT367	Cell Line	MDA-N	Homo sapiens	GI50	n.a.	1496.24	nM	PMID[522288]
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	2254.24	nM	PMID[522288]
NPT369	Cell Line	ACHN	Homo sapiens	GI50	n.a.	1238.8	nM	PMID[522288]
NPT370	Cell Line	NCI-H23	Homo sapiens	GI50	n.a.	49.32	nM	PMID[522288]
NPT371	Cell Line	UO-31	Homo sapiens	GI50	n.a.	1148.15	nM	PMID[522288]
NPT372	Cell Line	HOP-92	Homo sapiens	GI50	n.a.	2443.43	nM	PMID[522288]
NPT116	Cell Line	HL-60	Homo sapiens	GI50	n.a.	1766.04	nM	PMID[522288]
NPT374	Cell Line	SF-539	Homo sapiens	GI50	n.a.	1563.15	nM	PMID[522288]
NPT90	Cell Line	DU-145	Homo sapiens	GI50	n.a.	4570.88	nM	PMID[522288]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI50	n.a.	564.94	nM	PMID[522288]

Showing 1 to 10 of 67 entries

Previous1 2 3 4 5 6 7Next

☑ 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 NPC100454 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	202
0.1-0.2	1446
0.2-0.3	5840
0.3-0.4	14569
0.4-0.5	10950
0.5-0.6	6593
0.6-0.7	2464
0.7-0.8	441
0.8-0.85	19
0.85-0.9	33
0.9-0.95	72
0.95-1	68

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC133730
1.0	High Similarity	NPC274446
1.0	High Similarity	NPC151403
1.0	High Similarity	NPC191929
1.0	High Similarity	NPC287164

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 NPC100454 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	182
0.1-0.2	2220
0.2-0.3	3919
0.3-0.4	2007
0.4-0.5	586
0.5-0.6	194
0.6-0.7	40
0.7-0.8	2
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
0.7849	Intermediate Similarity	NPD46	Approved
0.7849	Intermediate Similarity	NPD6698	Approved
0.7647	Intermediate Similarity	NPD7899	Clinical (unspecified phase)
0.7474	Intermediate Similarity	NPD7838	Discovery
0.7216	Intermediate Similarity	NPD7983	Approved

Showing 1 to 5 of 142 entries

Previous1 2 3 4 5…29Next

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