NPASS Compound

Structure

NPC198179 OpenBabel06302215222D 29 30 0 0 1 0 0 0 0 0999 V2000 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 2 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 -3.4641 0.0000 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 -2.5981 -1.5000 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 -4.3301 -1.5000 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 -5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 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 1.5000 0.0000 C 0 0 2 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 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 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 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 O 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 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 13 1 0 0 0 0 3 4 1 0 0 0 0 4 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 12 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 1 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	402.2
Volume:	423.537
LogP:	3.872
LogD:	3.706
LogS:	-4.676
# Rotatable Bonds:	10
TPSA:	74.22
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.621
Synthetic Accessibility Score:	3.273
Fsp3:	0.435
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.751
MDCK Permeability:	3.096849104622379e-05
Pgp-inhibitor:	0.991
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.021
30% Bioavailability (F30%):	0.736

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.083
Plasma Protein Binding (PPB):	96.26951599121094%
Volume Distribution (VD):	0.99
Pgp-substrate:	4.225377082824707%

ADMET: Metabolism

CYP1A2-inhibitor:	0.176
CYP1A2-substrate:	0.898
CYP2C19-inhibitor:	0.862
CYP2C19-substrate:	0.864
CYP2C9-inhibitor:	0.918
CYP2C9-substrate:	0.874
CYP2D6-inhibitor:	0.539
CYP2D6-substrate:	0.899
CYP3A4-inhibitor:	0.926
CYP3A4-substrate:	0.845

ADMET: Excretion

Clearance (CL):	7.719
Half-life (T1/2):	0.761

ADMET: Toxicity

hERG Blockers:	0.119
Human Hepatotoxicity (H-HT):	0.141
Drug-inuced Liver Injury (DILI):	0.912
AMES Toxicity:	0.157
Rat Oral Acute Toxicity:	0.032
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.207
Carcinogencity:	0.098
Eye Corrosion:	0.004
Eye Irritation:	0.108
Respiratory Toxicity:	0.062

Download Data

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

Natural Product: NPC198179

Natural Product ID:	NPC198179
*Common Name:**	VUUHIXIUHGVFKO-HUYGQZFBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VUUHIXIUHGVFKO-HUYGQZFBSA-N
Standard InCHI:	InChI=1S/C23H30O6/c1-14(11-17-7-9-19(25)21(12-17)27-5)15(2)23(29-16(3)24)18-8-10-20(26-4)22(13-18)28-6/h7-10,12-15,23,25H,11H2,1-6H3/t14-,15+,23-/m1/s1
SMILES:	C[C@H](Cc1ccc(c(c1)OC)O)[C@H](C)[C@H](c1ccc(c(c1)OC)OC)OC(=O)C
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 [CHEMONTID:0001969] Dibenzylbutane lignans

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27465	Sinularia erecta	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27142697]
NPO27520	Casuarina equisetifolia	Species	Casuarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27742	Mollugo pentaphylla	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27520	Casuarina equisetifolia	Species	Casuarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27742	Mollugo pentaphylla	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27520	Casuarina equisetifolia	Species	Casuarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27635	Laurencia dendroidea	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27339	Lactarius blennius	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16221	Dolichos kilimandscharicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27130	Tsuga sieboldii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27520	Casuarina equisetifolia	Species	Casuarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27777	Artemisia phaeolepis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5146	Tuta absoluta	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26934	Naucleopsis mello-barretoi	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27465	Sinularia erecta	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27593	Silene dioica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27742	Mollugo pentaphylla	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27570	Paederia foetida	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC198179 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	290
0.1-0.2	1245
0.2-0.3	3270
0.3-0.4	8422
0.4-0.5	10445
0.5-0.6	3819
0.6-0.7	8861
0.7-0.8	4779
0.8-0.85	1044
0.85-0.9	426
0.9-0.95	94
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID

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 NPC198179 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	245
0.1-0.2	813
0.2-0.3	1651
0.3-0.4	2577
0.4-0.5	1850
0.5-0.6	1056
0.6-0.7	749
0.7-0.8	200
0.8-0.85	8
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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