NPASS Compound

Structure

CID165873 OpenBabel06191715532D 38 41 0 0 1 0 0 0 0 0999 V2000 -4.6298 -1.4266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8061 -1.9025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2983 2.8913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1527 2.3981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5040 -0.4934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8253 -3.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6494 1.9045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8247 1.4284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2035 -3.2021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1548 -3.2018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2982 -0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8247 -1.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4741 1.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4741 0.4761 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1224 0.4760 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8247 0.4761 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7276 -2.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6494 -0.9517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6483 -0.9516 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8247 -1.4278 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.1224 1.4283 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6482 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6301 -2.3778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2983 1.9044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9517 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6494 -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 1 0 0 0 0 0 0 0 0 0 -0.8250 -2.3790 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9770 -0.0173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2029 -1.5545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5041 -1.4450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5030 -1.4448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9684 1.9166 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3389 0.6907 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5814 -2.3775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0014 -2.8549 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 5 27 1 0 0 0 0 9 10 1 0 0 0 0 9 15 2 0 0 0 0 10 18 1 0 0 0 0 11 12 1 0 0 0 0 11 19 1 0 0 0 0 12 25 1 0 0 0 0 13 16 1 0 0 0 0 13 17 1 0 0 0 0 14 20 1 0 0 0 0 14 27 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 28 1 1 0 0 0 17 23 1 0 0 0 0 17 31 1 1 0 0 0 18 28 1 6 0 0 0 18 29 1 0 0 0 0 19 30 1 0 0 0 0 19 32 2 0 0 0 0 20 28 1 0 0 0 0 20 33 2 0 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 21 34 1 6 0 0 0 22 27 1 0 0 0 0 22 30 1 0 0 0 0 23 26 1 0 0 0 0 23 35 1 6 0 0 0 24 29 1 0 0 0 0 24 36 2 0 0 0 0 25 37 1 0 0 0 0 27 29 1 1 0 0 0 28 6 1 1 0 0 0 29 7 1 6 0 0 0 30 8 1 6 0 0 0 30 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	534.32
Volume:	552.986
LogP:	2.111
LogD:	1.057
LogS:	-3.236
# Rotatable Bonds:	5
TPSA:	152.36
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.336
Synthetic Accessibility Score:	5.63
Fsp3:	0.833
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.012
MDCK Permeability:	1.1324150364089292e-05
Pgp-inhibitor:	0.895
Pgp-substrate:	0.731
Human Intestinal Absorption (HIA):	0.056
20% Bioavailability (F20%):	0.841
30% Bioavailability (F30%):	0.045

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.771
Plasma Protein Binding (PPB):	65.20571899414062%
Volume Distribution (VD):	0.469
Pgp-substrate:	22.718481063842773%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.131
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.592
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.162
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.213
CYP3A4-substrate:	0.228

ADMET: Excretion

Clearance (CL):	4.625
Half-life (T1/2):	0.621

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.168
Drug-inuced Liver Injury (DILI):	0.047
AMES Toxicity:	0.042
Rat Oral Acute Toxicity:	0.515
Maximum Recommended Daily Dose:	0.245
Skin Sensitization:	0.062
Carcinogencity:	0.3
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC165873

Natural Product ID:	NPC165873
*Common Name:**	(2S,3S,8R,9S,10R,13R,14S,16S)-17-[(2R)-2,6-Dihydroxy-6-Methyl-3-Oxoheptan-2-Yl]-2,3,16-Trihydroxy-4,4,9,13,14-Pentamethyl-2,3,7,8,10,12,16,17-Octahydro-1H-Cyclopenta[A]Phenanthrene-11,15-Dione
IUPAC Name:	(2S,3S,8R,9S,10R,13R,14S,16S)-17-[(2R)-2,6-dihydroxy-6-methyl-3-oxoheptan-2-yl]-2,3,16-trihydroxy-4,4,9,13,14-pentamethyl-2,3,7,8,10,12,16,17-octahydro-1H-cyclopenta[a]phenanthrene-11,15-dione
Synonyms:
Standard InCHIKey:	JXOVARVKBWXWKT-OVYJLHBXSA-N
Standard InCHI:	InChI=1S/C30H46O8/c1-25(2,37)12-11-19(32)30(8,38)22-21(34)24(36)29(7)18-10-9-15-16(13-17(31)23(35)26(15,3)4)28(18,6)20(33)14-27(22,29)5/h9,16-18,21-23,31,34-35,37-38H,10-14H2,1-8H3/t16-,17+,18-,21+,22?,23-,27-,28+,29-,30+/m1/s1
SMILES:	CC(C)(CCC(=O)[C@@](C)(C1[C@@H](C(=O)[C@@]2(C)[C@@H]3CC=C4[C@@H](C[C@@H]([C@H](C4(C)C)O)O)[C@]3(C)C(=O)C[C@]12C)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL27456
PubChem CID:	455562
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001686] Cucurbitacins

*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
NPO7131	Cowania mexicana	Species	Tachinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7131	Cowania mexicana	Species	Tachinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 2 of 2 entries

Previous1Next

☑ 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	1
IC50	1
Others	1

Activity Type	# Activity
Cell Line	2
Others	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT759	Cell Line	H9	Homo sapiens	IC50	=	38.0	ug.mL-1	PMID[456332]
NPT759	Cell Line	H9	Homo sapiens	EC50	=	2.5	ug.mL-1	PMID[456332]
NPT2	Others	Unspecified	""	Therapeutic index	=	15.2	n.a.	PMID[456332]

Showing 1 to 3 of 3 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 NPC165873 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	212
0.1-0.2	1447
0.2-0.3	5028
0.3-0.4	10734
0.4-0.5	11109
0.5-0.6	6225
0.6-0.7	5781
0.7-0.8	1965
0.8-0.85	134
0.85-0.9	53
0.9-0.95	7
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9694	High Similarity	NPC191892
0.9143	High Similarity	NPC280782
0.9109	High Similarity	NPC117185
0.9082	High Similarity	NPC49371
0.9057	High Similarity	NPC108721

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 NPC165873 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	1746
0.2-0.3	4161
0.3-0.4	2028
0.4-0.5	557
0.5-0.6	173
0.6-0.7	149
0.7-0.8	103
0.8-0.85	45
0.85-0.9	5
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8614	High Similarity	NPD4755	Approved
0.8447	Intermediate Similarity	NPD4700	Approved
0.8447	Intermediate Similarity	NPD4696	Approved
0.8447	Intermediate Similarity	NPD5285	Approved
0.8447	Intermediate Similarity	NPD5286	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