NPASS Compound

Structure

NPC147561 OpenBabel07101718192D 29 32 0 0 1 0 0 0 0 0999 V2000 -2.4616 0.0129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0039 -2.2708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4135 0.4593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 1.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 0.7775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6350 -1.0987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7690 -1.5987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6350 -0.0987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9030 -1.0987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7690 0.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3458 -0.9839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6577 -1.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3587 1.1194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0827 1.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5060 -0.2819 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0483 -1.9761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9030 -0.0987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1691 1.6092 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1298 -0.7064 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3049 0.4013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0370 0.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2900 -0.0043 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9781 0.2079 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3152 -2.6562 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0370 1.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8258 -1.0011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1709 -0.0987 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 1 15 1 0 0 0 0 2 16 1 0 0 0 0 3 22 1 0 0 0 0 4 22 1 0 0 0 0 5 23 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 8 10 2 0 0 0 0 9 17 2 0 0 0 0 10 17 1 0 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 19 1 0 0 0 0 13 20 1 0 0 0 0 14 18 1 0 0 0 0 15 24 1 1 0 0 0 16 25 2 0 0 0 0 16 27 1 0 0 0 0 17 21 1 0 0 0 0 18 13 1 1 0 0 0 18 22 1 0 0 0 0 19 23 1 1 0 0 0 19 27 1 0 0 0 0 20 23 1 6 0 0 0 20 28 1 0 0 0 0 21 26 2 0 0 0 0 21 28 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 6 0 0 0 24 14 1 1 0 0 0 24 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	400.22
Volume:	420.203
LogP:	4.781
LogD:	3.796
LogS:	-4.816
# Rotatable Bonds:	5
TPSA:	61.83
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.697
Synthetic Accessibility Score:	5.326
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.814
MDCK Permeability:	2.2399819499696605e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.915
30% Bioavailability (F30%):	0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.092
Plasma Protein Binding (PPB):	94.69339752197266%
Volume Distribution (VD):	2.018
Pgp-substrate:	8.394794464111328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.118
CYP1A2-substrate:	0.084
CYP2C19-inhibitor:	0.111
CYP2C19-substrate:	0.538
CYP2C9-inhibitor:	0.417
CYP2C9-substrate:	0.125
CYP2D6-inhibitor:	0.037
CYP2D6-substrate:	0.169
CYP3A4-inhibitor:	0.632
CYP3A4-substrate:	0.394

ADMET: Excretion

Clearance (CL):	7.313
Half-life (T1/2):	0.23

ADMET: Toxicity

hERG Blockers:	0.577
Human Hepatotoxicity (H-HT):	0.567
Drug-inuced Liver Injury (DILI):	0.867
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.144
Maximum Recommended Daily Dose:	0.875
Skin Sensitization:	0.859
Carcinogencity:	0.427
Eye Corrosion:	0.027
Eye Irritation:	0.626
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC147561

Natural Product ID:	NPC147561
*Common Name:**	MDUQZKJGFROTKT-JSJPKNAYSA-N
IUPAC Name:	n.a.
Synonyms:	Triptogelin G-2
Standard InCHIKey:	MDUQZKJGFROTKT-JSJPKNAYSA-N
Standard InCHI:	InChI=1S/C24H32O5/c1-15-11-12-19(27-16(2)25)23(5)20(28-21(26)17-9-7-6-8-10-17)13-18-14-24(15,23)29-22(18,3)4/h6-10,15,18-20H,11-14H2,1-5H3/t15-,18-,19+,20+,23+,24+/m1/s1
SMILES:	C[C@@H]1CC[C@@H]([C@@]2(C)[C@H](C[C@@H]3C[C@]12OC3(C)C)OC(=O)c1ccccc1)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL374470
PubChem CID:	44419629
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

*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
NPO11250	Celastrus flagellaris	Species	Celastraceae	Eukaryota	seeds	Jilin, China	n.a.	PMID[26295746]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18590313]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	root	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	roots	n.a.	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	leaves	n.a.	n.a.	PMID[17125218]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	stem	n.a.	n.a.	PMID[16643054]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11250	Celastrus flagellaris	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11250	Celastrus flagellaris	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11250	Celastrus flagellaris	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 10 of 10 entries

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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
MIC	1
Others	6

Activity Type	# Activity
Cell Line	2
Organism	1
Others	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	60.0	%	PMID[568953]
NPT2	Others	Unspecified	""	Activity	=	4.6	%	PMID[568953]
NPT2	Others	Unspecified	""	Activity	=	36.6	%	PMID[568953]
NPT2	Others	Unspecified	""	Activity	=	76.8	%	PMID[568953]
NPT2	Others	Unspecified	""	Activity	=	100.0	%	PMID[568953]
NPT519	Cell Line	SH-SY5Y	Homo sapiens	Activity	=	74.4	%	PMID[568952]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	26000.0	nM	PMID[568951]

Showing 1 to 7 of 7 entries

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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 NPC147561 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	293
0.1-0.2	1194
0.2-0.3	2082
0.3-0.4	4445
0.4-0.5	9118
0.5-0.6	13313
0.6-0.7	10355
0.7-0.8	1501
0.8-0.85	189
0.85-0.9	108
0.9-0.95	85
0.95-1	14

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Search:

Similarity Score	Similarity Level	Natural Product ID
0.9683	High Similarity	NPC474608
0.9606	High Similarity	NPC66761
0.9606	High Similarity	NPC17877
0.9606	High Similarity	NPC472577
0.9606	High Similarity	NPC291638

Showing 1 to 5 of 200 entries

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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 NPC147561 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	251
0.1-0.2	768
0.2-0.3	1241
0.3-0.4	2722
0.4-0.5	2370
0.5-0.6	1336
0.6-0.7	427
0.7-0.8	33
0.8-0.85	2
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
0.8298	Intermediate Similarity	NPD7236	Approved
0.8074	Intermediate Similarity	NPD5952	Clinical (unspecified phase)
0.8065	Intermediate Similarity	NPD2181	Clinical (unspecified phase)
0.8014	Intermediate Similarity	NPD7239	Suspended
0.776	Intermediate Similarity	NPD2182	Approved

Showing 1 to 5 of 200 entries

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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