NPASS Compound

Structure

CID217201 OpenBabel06191716012D 34 37 0 0 1 0 0 0 0 0999 V2000 -4.7388 -0.7474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2780 0.0954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5325 -0.5228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0014 -2.9223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2785 -1.5911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3048 -1.5914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6872 -0.9741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6871 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3761 1.9494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8442 1.4621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3760 -0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8441 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7651 -0.7477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5325 1.4620 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8442 0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6884 1.9494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2196 1.4620 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2196 0.4873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6883 -0.9741 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8442 -1.4615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8182 -2.4349 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6883 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5325 0.4873 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.9741 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8445 -2.4352 0.0000 C 0 0 1 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 1.6884 2.9595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0945 1.9669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0945 -0.0177 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5631 -1.4791 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3053 -3.2780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8448 -3.4089 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 14 1 0 0 0 0 4 25 1 0 0 0 0 6 7 1 0 0 0 0 6 14 1 0 0 0 0 7 22 1 0 0 0 0 8 9 1 0 0 0 0 8 21 1 0 0 0 0 9 27 1 0 0 0 0 10 15 1 0 0 0 0 10 18 1 0 0 0 0 11 16 2 0 0 0 0 11 17 1 0 0 0 0 12 19 1 0 0 0 0 12 24 1 0 0 0 0 13 20 1 0 0 0 0 13 25 1 0 0 0 0 15 17 1 0 0 0 0 15 24 1 6 0 0 0 16 23 1 0 0 0 0 16 27 1 0 0 0 0 17 28 2 0 0 0 0 18 19 1 0 0 0 0 18 29 1 1 0 0 0 19 30 1 1 0 0 0 20 23 1 0 0 0 0 20 31 1 6 0 0 0 21 25 1 1 0 0 0 21 26 1 0 0 0 0 22 26 1 0 0 0 0 22 32 1 6 0 0 0 23 24 1 1 0 0 0 24 3 1 1 0 0 0 25 27 1 1 0 0 0 26 5 1 6 0 0 0 26 33 1 0 0 0 0 27 34 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	480.31
Volume:	497.581
LogP:	1.865
LogD:	0.601
LogS:	-3.327
# Rotatable Bonds:	5
TPSA:	138.45
# H-Bond Aceptor:	7
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.33
Synthetic Accessibility Score:	5.411
Fsp3:	0.889
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.167
MDCK Permeability:	5.459634394355817e-06
Pgp-inhibitor:	0.011
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.084
20% Bioavailability (F20%):	0.38
30% Bioavailability (F30%):	0.14

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	49.94859313964844%
Volume Distribution (VD):	1.378
Pgp-substrate:	30.29755973815918%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.171
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.746
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.151
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.027
CYP3A4-inhibitor:	0.167
CYP3A4-substrate:	0.295

ADMET: Excretion

Clearance (CL):	2.644
Half-life (T1/2):	0.241

ADMET: Toxicity

hERG Blockers:	0.103
Human Hepatotoxicity (H-HT):	0.343
Drug-inuced Liver Injury (DILI):	0.129
AMES Toxicity:	0.247
Rat Oral Acute Toxicity:	0.868
Maximum Recommended Daily Dose:	0.988
Skin Sensitization:	0.512
Carcinogencity:	0.188
Eye Corrosion:	0.01
Eye Irritation:	0.089
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC217201

Natural Product ID:	NPC217201
*Common Name:**	Ajugasterone C
IUPAC Name:	(2S,3R,5R,9R,10R,11R,13R,14S,17S)-17-[(2R,3R)-2,3-dihydroxy-6-methylheptan-2-yl]-2,3,11,14-tetrahydroxy-10,13-dimethyl-2,3,4,5,9,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-6-one
Synonyms:
Standard InCHIKey:	LQGNCUXDDPRDJH-UKTRSHMFSA-N
Standard InCHI:	InChI=1S/C27H44O7/c1-14(2)6-7-22(32)26(5,33)21-8-9-27(34)16-11-17(28)15-10-18(29)19(30)12-24(15,3)23(16)20(31)13-25(21,27)4/h11,14-15,18-23,29-34H,6-10,12-13H2,1-5H3/t15-,18+,19-,20+,21-,22+,23+,24-,25+,26+,27+/m0/s1
SMILES:	CC(CC[C@H]([C@@]([C@H]1CC[C@@]2([C@]1(C)C[C@@H](O)[C@H]1C2=CC(=O)[C@H]2[C@]1(C)C[C@H](O)[C@@H](C2)O)O)(O)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3793486
PubChem CID:	441826
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives

*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
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[9397205]
NPO362	Gentiana crassicaulis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33052051]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[22233034]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[16335823]
NPO20352	Gentiana straminea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO362	Gentiana crassicaulis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO362	Gentiana crassicaulis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

Showing 1 to 10 of 23 entries

Previous1 2 3Next

☑ 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
EC50	4
Others	2

Activity Type	# Activity
Organism	4
Others	2

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		Ratio CC50/EC50	>	69.7	n.a.	PMID[542046]
NPT27	Others	Unspecified		CC50	>	700000.0	nM	PMID[542046]
NPT4328	Organism	Dengue virus type 4	Dengue virus 4	EC50	=	12150.0	nM	PMID[542046]
NPT5238	Organism	Dengue virus 3	Dengue virus 3	EC50	=	9480.0	nM	PMID[542046]
NPT5239	Organism	Dengue virus 1	Dengue virus 1	EC50	=	15700.0	nM	PMID[542046]
NPT194	Organism	Dengue virus 2	Dengue virus 2	EC50	=	10050.0	nM	PMID[542046]

Showing 1 to 6 of 6 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 NPC217201 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	208
0.1-0.2	1333
0.2-0.3	4263
0.3-0.4	8363
0.4-0.5	12861
0.5-0.6	6746
0.6-0.7	6022
0.7-0.8	2580
0.8-0.85	244
0.85-0.9	36
0.9-0.95	11
0.95-1	30

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.99	High Similarity	NPC11710
0.9899	High Similarity	NPC475060
0.9899	High Similarity	NPC220229
0.9798	High Similarity	NPC149047
0.9798	High Similarity	NPC202167

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 NPC217201 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	176
0.1-0.2	1591
0.2-0.3	3905
0.3-0.4	2310
0.4-0.5	675
0.5-0.6	175
0.6-0.7	154
0.7-0.8	125
0.8-0.85	36
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8558	High Similarity	NPD5211	Phase 2
0.8529	High Similarity	NPD4755	Approved
0.8396	Intermediate Similarity	NPD5141	Approved
0.8384	Intermediate Similarity	NPD5328	Approved
0.8365	Intermediate Similarity	NPD4696	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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