NPASS Compound

Structure

NPC206394 OpenBabel06302215362D 40 46 0 0 1 0 0 0 0 0999 V2000 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 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 -0.0000 0.0000 C 0 0 0 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 -1.5000 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 N 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 -1.4210 -0.7254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0191 -0.7584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5954 -0.5954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0877 -0.2541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4424 0.2285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6592 0.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9475 0.1047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6212 0.8002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6047 1.3990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5862 1.5907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8330 1.1178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0469 1.5336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0139 2.4223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3947 1.9599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5036 2.7360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9191 2.8670 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3238 2.8011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7821 2.5454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3527 2.1278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1568 2.6158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4161 3.0732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9355 3.1557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1582 3.5539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6083 3.6281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9470 3.3223 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8410 2.6826 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3978 1.8520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0823 1.5933 0.0000 O 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 0.8660 1.5000 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 39 1 0 0 0 0 3 4 2 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 40 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 40 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 25 24 1 1 0 0 0 25 26 1 0 0 0 0 25 34 1 0 0 0 0 26 31 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 37 1 0 0 0 0 29 30 2 0 0 0 0 29 35 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 40 38 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	534.25
Volume:	562.242
LogP:	6.265
LogD:	3.805
LogS:	-6.268
# Rotatable Bonds:	2
TPSA:	61.31
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	8
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.407
Synthetic Accessibility Score:	6.187
Fsp3:	0.324
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.667
MDCK Permeability:	1.3087280422041658e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.81
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.988
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.411
Plasma Protein Binding (PPB):	96.0207748413086%
Volume Distribution (VD):	0.628
Pgp-substrate:	2.9543445110321045%

ADMET: Metabolism

CYP1A2-inhibitor:	0.152
CYP1A2-substrate:	0.615
CYP2C19-inhibitor:	0.678
CYP2C19-substrate:	0.852
CYP2C9-inhibitor:	0.131
CYP2C9-substrate:	0.373
CYP2D6-inhibitor:	0.902
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.243
CYP3A4-substrate:	0.93

ADMET: Excretion

Clearance (CL):	4.063
Half-life (T1/2):	0.103

ADMET: Toxicity

hERG Blockers:	0.924
Human Hepatotoxicity (H-HT):	0.506
Drug-inuced Liver Injury (DILI):	0.558
AMES Toxicity:	0.375
Rat Oral Acute Toxicity:	0.463
Maximum Recommended Daily Dose:	0.995
Skin Sensitization:	0.957
Carcinogencity:	0.054
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.682

Download Data

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

Natural Product: NPC206394

Natural Product ID:	NPC206394
*Common Name:**	VQSMHQHVINQAFK-SRYFTIFFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VQSMHQHVINQAFK-SRYFTIFFSA-N
Standard InCHI:	InChI=1S/C34H34N2O4/c1-37-27-17-24-11-13-36-30-15-21-6-8-25(9-7-21)39-26-5-3-4-22(14-26)16-29-28-20-32(40-33(19-27)34(24)30)31(38-2)18-23(28)10-12-35-29/h3-9,14,17-20,24,29,34-35H,10-13,15-16H2,1-2H3/t24-,29+,34-/m0/s1
SMILES:	COC1=C[C@@H]2CCN=C3Cc4ccc(cc4)Oc4cccc(c4)C[C@@H]4c5cc(c(cc5CCN4)OC)OC(=C1)[C@@H]23
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds

*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
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[4421158]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30169038]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26231157]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23944995]
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	Twigs	Yangming mountain, Taiwan	2008-APR	PMID[20873721]
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	n.a.	twig	n.a.	DOI[10.1021/np1003593]
NPO16279	Croptilon divaricatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5150	Mephitis mephitis	Species	Mephitidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3436	Taraxacum linearisquameum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6090	Caulerpa prolifera	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 17 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

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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 NPC206394 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	358
0.1-0.2	1709
0.2-0.3	10127
0.3-0.4	7496
0.4-0.5	10103
0.5-0.6	10537
0.6-0.7	1698
0.7-0.8	614
0.8-0.85	47
0.85-0.9	7
0.9-0.95	1
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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 NPC206394 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	199
0.1-0.2	641
0.2-0.3	1094
0.3-0.4	1554
0.4-0.5	2949
0.5-0.6	1877
0.6-0.7	688
0.7-0.8	140
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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