NPASS Compound

Structure

CID209298 OpenBabel06191716002D 31 34 0 0 1 0 0 0 0 0999 V2000 2.1183 -0.5724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1279 2.6550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0233 3.5446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9079 2.1131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7840 2.1131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5639 -0.8761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1279 -0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3459 -0.4515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 -1.8059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7820 -0.4515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2335 -0.5725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8866 2.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0233 2.6685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7820 -1.3545 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7819 -1.3545 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1279 0.9029 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7820 1.3544 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7820 -0.4515 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5639 0.9029 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9030 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9029 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3459 1.3544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5639 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6453 2.6550 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7354 2.2305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5481 -1.7968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3453 0.7663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7587 1.3410 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8866 1.3409 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7820 2.2305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 11 2 0 0 0 0 2 12 1 0 0 0 0 3 13 1 0 0 0 0 4 22 1 0 0 0 0 5 22 1 0 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 23 1 0 0 0 0 9 15 1 0 0 0 0 10 14 1 0 0 0 0 11 14 1 0 0 0 0 11 20 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 9 1 6 0 0 0 15 18 1 0 0 0 0 15 27 1 6 0 0 0 16 22 1 0 0 0 0 16 30 1 6 0 0 0 17 19 1 0 0 0 0 17 21 1 0 0 0 0 17 31 1 1 0 0 0 18 23 1 1 0 0 0 18 24 1 0 0 0 0 19 22 1 0 0 0 0 19 23 1 1 0 0 0 20 24 1 0 0 0 0 20 28 2 0 0 0 0 21 24 1 6 0 0 0 21 29 1 0 0 0 0 23 6 1 1 0 0 0 24 10 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	250.16
Volume:	263.425
LogP:	2.153
LogD:	2.511
LogS:	-2.359
# Rotatable Bonds:	0
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.53
Synthetic Accessibility Score:	4.41
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.673
MDCK Permeability:	3.233676034142263e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.204
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.05

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.785
Plasma Protein Binding (PPB):	48.532257080078125%
Volume Distribution (VD):	0.889
Pgp-substrate:	64.6376953125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.181
CYP1A2-substrate:	0.373
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.754
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.086
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.309
CYP3A4-inhibitor:	0.27
CYP3A4-substrate:	0.249

ADMET: Excretion

Clearance (CL):	14.118
Half-life (T1/2):	0.329

ADMET: Toxicity

hERG Blockers:	0.057
Human Hepatotoxicity (H-HT):	0.692
Drug-inuced Liver Injury (DILI):	0.225
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.907
Maximum Recommended Daily Dose:	0.208
Skin Sensitization:	0.137
Carcinogencity:	0.154
Eye Corrosion:	0.021
Eye Irritation:	0.027
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC209298

Natural Product ID:	NPC209298
*Common Name:**	Melissoidesin G
IUPAC Name:	n.a.
Synonyms:	Melissoidesin G
Standard InCHIKey:	JSXKRCUMUDUIGE-HZWKRDQHSA-N
Standard InCHI:	InChI=1S/C24H34O7/c1-11-14-9-15(27)18-23(6)8-7-16(30-12(2)25)22(4,5)19(23)17(31-13(3)26)21(29)24(18,10-14)20(11)28/h14-19,21,27,29H,1,7-10H2,2-6H3/t14-,15+,16+,17-,18+,19-,21+,23+,24+/m1/s1
SMILES:	C=C1[C@@H]2C[C@@H]([C@H]3[C@]4(C)CC[C@@H](C(C)(C)[C@H]4[C@H]([C@@H]([C@]3(C2)C1=O)O)OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL514251
PubChem CID:	10342874
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003782] Kaurane 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25590529]
NPO12522	Isodon melissoides	Species	Lamiaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[15387638]
NPO13092	Reticulidia fungia	Species	Phyllidiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10514331]
NPO12522	Isodon melissoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13092	Reticulidia fungia	Species	Phyllidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12757	Caragana alaica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12522	Isodon melissoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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☑ 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

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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

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☑ 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
Cell Line	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT547	Cell Line	BGC-823	Homo sapiens	IC50	=	6.62	ug.mL-1	PMID[533597]

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☑ 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 NPC209298 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	236
0.1-0.2	1649
0.2-0.3	5386
0.3-0.4	9223
0.4-0.5	11376
0.5-0.6	5942
0.6-0.7	5346
0.7-0.8	2999
0.8-0.85	338
0.85-0.9	127
0.9-0.95	64
0.95-1	11

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC277074
0.9792	High Similarity	NPC122811
0.9694	High Similarity	NPC166993
0.9684	High Similarity	NPC470388
0.9596	High Similarity	NPC273155

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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 NPC209298 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	224
0.1-0.2	2088
0.2-0.3	3956
0.3-0.4	1837
0.4-0.5	560
0.5-0.6	228
0.6-0.7	160
0.7-0.8	96
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8131	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD8034	Phase 2
0.8	Intermediate Similarity	NPD8035	Phase 2
0.7982	Intermediate Similarity	NPD6319	Approved
0.7928	Intermediate Similarity	NPD4632	Approved

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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