NPASS Compound

Structure

NPC232925 OpenBabel07101718272D 33 36 0 0 1 0 0 0 0 0999 V2000 -1.5180 4.8564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1653 4.3212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5909 2.0032 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 0.4067 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2382 1.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5472 2.4190 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9000 2.9543 0.0000 C 0 0 0 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 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2308 3.6974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1871 4.1132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 1.2601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8781 3.1622 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 1 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 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 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 -0.5398 4.6485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 -2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 17 1 0 0 0 0 6 7 1 0 0 0 0 6 18 1 0 0 0 0 8 11 1 0 0 0 0 8 20 1 0 0 0 0 9 12 1 0 0 0 0 9 22 1 0 0 0 0 10 13 1 0 0 0 0 10 19 1 0 0 0 0 11 28 1 0 0 0 0 12 29 1 0 0 0 0 13 30 1 0 0 0 0 14 20 1 0 0 0 0 14 24 1 0 0 0 0 15 25 1 0 0 0 0 16 23 1 0 0 0 0 16 26 1 0 0 0 0 17 19 1 0 0 0 0 18 3 1 1 0 0 0 18 23 1 0 0 0 0 19 7 1 1 0 0 0 20 31 1 6 0 0 0 21 15 1 1 0 0 0 21 22 1 0 0 0 0 21 27 1 0 0 0 0 22 28 1 6 0 0 0 23 29 1 6 0 0 0 24 25 1 0 0 0 0 24 28 1 6 0 0 0 25 32 1 6 0 0 0 26 27 1 0 0 0 0 26 33 1 1 0 0 0 27 29 1 6 0 0 0 28 4 1 6 0 0 0 29 5 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.39
Volume:	511.075
LogP:	5.233
LogD:	4.995
LogS:	-4.435
# Rotatable Bonds:	7
TPSA:	80.92
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.426
Synthetic Accessibility Score:	4.923
Fsp3:	1.0
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:	-4.808
MDCK Permeability:	5.003347905585542e-05
Pgp-inhibitor:	0.953
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.821
30% Bioavailability (F30%):	0.287

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.067
Plasma Protein Binding (PPB):	96.11628723144531%
Volume Distribution (VD):	1.056
Pgp-substrate:	1.3955398797988892%

ADMET: Metabolism

CYP1A2-inhibitor:	0.044
CYP1A2-substrate:	0.294
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.777
CYP2C9-inhibitor:	0.121
CYP2C9-substrate:	0.115
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.054
CYP3A4-inhibitor:	0.313
CYP3A4-substrate:	0.344

ADMET: Excretion

Clearance (CL):	8.205
Half-life (T1/2):	0.452

ADMET: Toxicity

hERG Blockers:	0.659
Human Hepatotoxicity (H-HT):	0.182
Drug-inuced Liver Injury (DILI):	0.056
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.097
Skin Sensitization:	0.959
Carcinogencity:	0.035
Eye Corrosion:	0.992
Eye Irritation:	0.915
Respiratory Toxicity:	0.579

Download Data

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

Natural Product: NPC232925

Natural Product ID:	NPC232925
*Common Name:**	Certonardosterol E2
IUPAC Name:	(3S,5S,6R,8R,9S,10R,13R,14S,15S,17R)-17-[(2R,5R)-5-(2-hydroxyethyl)-6-methylheptan-2-yl]-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,6,15-triol
Synonyms:	Certonardosterol E2
Standard InCHIKey:	BKDLTBPGTMXGMR-JRLYYEQVSA-N
Standard InCHI:	InChI=1S/C29H52O4/c1-17(2)19(10-13-30)7-6-18(3)23-16-26(33)27-21-15-25(32)24-14-20(31)8-11-28(24,4)22(21)9-12-29(23,27)5/h17-27,30-33H,6-16H2,1-5H3/t18-,19-,20+,21-,22+,23-,24-,25-,26+,27-,28-,29-/m1/s1
SMILES:	OCC[C@H](C(C)C)CC[C@H]([C@H]1C[C@@H]([C@@H]2[C@]1(C)CC[C@H]1[C@H]2C[C@H]([C@@H]2[C@]1(C)CC[C@@H](C2)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464938
PubChem CID:	21577265
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes 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
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497935]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104487]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662097]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444692]

Showing 1 to 4 of 4 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
ED50	5

Activity Type	# Activity
Cell Line	5

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	0.48	ug ml-1	PMID[475941]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	0.83	ug ml-1	PMID[475941]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	0.28	ug ml-1	PMID[475941]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	0.4	ug ml-1	PMID[475941]
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	1.26	ug ml-1	PMID[475941]

Showing 1 to 5 of 5 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 NPC232925 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	373
0.1-0.2	4397
0.2-0.3	16019
0.3-0.4	9562
0.4-0.5	4702
0.5-0.6	4374
0.6-0.7	2410
0.7-0.8	644
0.8-0.85	124
0.85-0.9	48
0.9-0.95	32
0.95-1	12

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC251201
1.0	High Similarity	NPC63588
0.9846	High Similarity	NPC477820
0.9701	High Similarity	NPC470610
0.9559	High Similarity	NPC304499

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 NPC232925 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	389
0.1-0.2	4348
0.2-0.3	3143
0.3-0.4	717
0.4-0.5	223
0.5-0.6	196
0.6-0.7	101
0.7-0.8	22
0.8-0.85	9
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8696	High Similarity	NPD4267	Clinical (unspecified phase)
0.8571	High Similarity	NPD4787	Phase 1
0.8289	Intermediate Similarity	NPD6928	Phase 2
0.8267	Intermediate Similarity	NPD6118	Approved
0.8267	Intermediate Similarity	NPD6697	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