NPASS Compound

Structure

CID137345 OpenBabel06191715492D 38 40 0 0 1 0 0 0 0 0999 V2000 -3.7253 -4.2876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8608 -5.8505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9103 -3.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1671 -2.4612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3118 -1.4476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3359 -0.8124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5037 -1.4696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7446 0.8637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5924 -3.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6720 -2.2804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5037 0.5277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5378 0.7865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9576 -0.5968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 -1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4360 -4.5585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9811 -3.2315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5260 -3.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6939 -2.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0240 -0.2385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2024 -1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9053 -1.5955 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5561 -0.4710 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9932 -0.0522 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.5024 -4.9169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9592 -3.4394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6824 -2.2248 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3849 -1.1215 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3947 -1.0156 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8731 -5.6940 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6701 -2.3812 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5928 -0.1433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2464 -4.5984 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6225 -0.8293 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9394 -1.8543 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 4.2682 -4.3905 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 9 15 2 0 0 0 0 9 17 1 0 0 0 0 10 16 2 0 0 0 0 10 18 1 0 0 0 0 11 12 1 0 0 0 0 13 19 1 0 0 0 0 13 21 1 0 0 0 0 14 20 1 0 0 0 0 14 22 1 0 0 0 0 15 25 1 0 0 0 0 16 26 1 0 0 0 0 17 27 1 0 0 0 0 18 28 1 0 0 0 0 19 29 1 0 0 0 0 20 30 1 0 0 0 0 21 27 1 1 0 0 0 21 36 1 0 0 0 0 22 28 1 1 0 0 0 22 37 1 0 0 0 0 23 11 1 1 0 0 0 23 29 1 0 0 0 0 23 35 1 0 0 0 0 24 12 1 6 0 0 0 24 30 1 0 0 0 0 24 35 1 0 0 0 0 25 31 1 0 0 0 0 26 38 1 0 0 0 0 27 5 1 1 0 0 0 27 32 1 0 0 0 0 28 6 1 6 0 0 0 28 33 1 0 0 0 0 29 7 1 6 0 0 0 29 36 1 0 0 0 0 30 8 1 6 0 0 0 30 37 1 0 0 0 0 34 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	540.37
Volume:	566.816
LogP:	3.622
LogD:	2.692
LogS:	-3.652
# Rotatable Bonds:	11
TPSA:	117.84
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.167
Synthetic Accessibility Score:	5.566
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
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:	-4.857
MDCK Permeability:	1.56624610099243e-05
Pgp-inhibitor:	0.986
Pgp-substrate:	0.041
Human Intestinal Absorption (HIA):	0.036
20% Bioavailability (F20%):	0.841
30% Bioavailability (F30%):	0.769

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.065
Plasma Protein Binding (PPB):	87.92644500732422%
Volume Distribution (VD):	0.568
Pgp-substrate:	8.146940231323242%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.141
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.771
CYP2C9-inhibitor:	0.031
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.104
CYP3A4-inhibitor:	0.451
CYP3A4-substrate:	0.34

ADMET: Excretion

Clearance (CL):	3.027
Half-life (T1/2):	0.512

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.622
Drug-inuced Liver Injury (DILI):	0.048
AMES Toxicity:	0.031
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.472
Carcinogencity:	0.78
Eye Corrosion:	0.009
Eye Irritation:	0.13
Respiratory Toxicity:	0.047

Download Data

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

Natural Product: NPC137345

Natural Product ID:	NPC137345
*Common Name:**	(E,6S)-6-[(2R,5S)-5-[(2R,5R)-5-[(2S,5R)-5-[(E,2S)-6-Hydroperoxy-2-Hydroxy-6-Methylhept-4-En-2-Yl]-2-Methyloxolan-2-Yl]Oxolan-2-Yl]-5-Methyloxolan-2-Yl]-2-Methylhept-3-Ene-2,6-Diol
IUPAC Name:	(E,6S)-6-[(2R,5S)-5-[(2R,5R)-5-[(2S,5R)-5-[(E,2S)-6-hydroperoxy-2-hydroxy-6-methylhept-4-en-2-yl]-2-methyloxolan-2-yl]oxolan-2-yl]-5-methyloxolan-2-yl]-2-methylhept-3-ene-2,6-diol
Synonyms:
Standard InCHIKey:	QLFRXAKUUDRERJ-BOWISWASSA-N
Standard InCHI:	InChI=1S/C30H52O8/c1-25(2,31)15-9-17-27(5,32)21-13-19-29(7,36-21)23-11-12-24(35-23)30(8)20-14-22(37-30)28(6,33)18-10-16-26(3,4)38-34/h9-10,15-16,21-24,31-34H,11-14,17-20H2,1-8H3/b15-9+,16-10+/t21-,22-,23-,24-,27+,28+,29+,30+/m1/s1
SMILES:	CC(C)(/C=C/C[C@@](C)([C@H]1CC[C@@](C)([C@H]2CC[C@H]([C@]3(C)CC[C@H]([C@](C)(C/C=C/C(C)(C)OO)O)O3)O2)O1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL64580
PubChem CID:	10896840
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO9644	Euphorbia resinifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29667820]
NPO5401	Monanchora unguiculata	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28368118]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25905468]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[25066952]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24467387]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23403897]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[19931461]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919052]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[19715321]
NPO11530	Heterosigma akashiwo	Species	Chattonellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19659728]

Showing 1 to 10 of 59 entries

Previous1 2 3 4 5 6Next

☑ 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	1

Activity Type	# Activity
Others	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT27	Others	Unspecified		IC50	=	5.3	ug.mL-1	PMID[555737]

Showing 1 to 1 of 1 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 NPC137345 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	190
0.1-0.2	1632
0.2-0.3	6730
0.3-0.4	18052
0.4-0.5	10434
0.5-0.6	5032
0.6-0.7	603
0.7-0.8	20
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC181838
0.8904	High Similarity	NPC306085
0.8378	Intermediate Similarity	NPC16964
0.8125	Intermediate Similarity	NPC476701
0.7895	Intermediate Similarity	NPC472947

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 NPC137345 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	167
0.1-0.2	2291
0.2-0.3	4208
0.3-0.4	1929
0.4-0.5	442
0.5-0.6	97
0.6-0.7	16
0.7-0.8	0
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
0.6813	Remote Similarity	NPD7524	Approved
0.6774	Remote Similarity	NPD7838	Discovery
0.6702	Remote Similarity	NPD7983	Approved
0.663	Remote Similarity	NPD4250	Approved
0.663	Remote Similarity	NPD4251	Approved

Showing 1 to 5 of 83 entries

Previous1 2 3 4 5…17Next

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