NPASS Compound

Structure

CID202688 OpenBabel06191715592D 35 38 0 0 1 0 0 0 0 0999 V2000 -2.5433 4.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0824 6.8403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9287 7.3286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4164 4.5282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4394 4.5285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5421 3.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 1.9916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2356 4.3979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2359 5.3749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2347 2.4433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2345 1.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6926 0.9785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8477 2.4443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6949 2.9331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 1.4673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6941 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8466 -0.4888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3893 3.9096 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0821 5.8632 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.7747 6.8398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6929 0.0005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6944 0.9776 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3890 2.9326 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5416 1.4663 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8475 1.4668 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8469 -0.4893 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9282 5.3745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5418 2.4438 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0003 0.9780 0.0000 C 0 0 1 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 -7.6210 7.3281 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5591 -0.4991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 -1.4893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7744 5.8627 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3 20 1 0 0 0 0 4 27 1 0 0 0 0 5 27 1 0 0 0 0 7 29 1 0 0 0 0 8 9 1 0 0 0 0 8 18 1 0 0 0 0 9 19 1 0 0 0 0 10 11 1 0 0 0 0 10 23 1 0 0 0 0 11 24 1 0 0 0 0 12 15 1 0 0 0 0 12 21 1 0 0 0 0 13 14 1 0 0 0 0 13 25 1 0 0 0 0 14 28 1 0 0 0 0 15 29 1 0 0 0 0 16 26 1 0 0 0 0 17 21 1 0 0 0 0 17 30 1 0 0 0 0 18 1 1 1 0 0 0 18 23 1 0 0 0 0 19 2 1 1 0 0 0 19 27 1 0 0 0 0 20 31 2 0 0 0 0 20 35 1 0 0 0 0 21 32 1 6 0 0 0 22 16 1 1 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 23 28 1 6 0 0 0 24 28 1 6 0 0 0 25 29 1 6 0 0 0 26 30 1 6 0 0 0 26 33 1 0 0 0 0 27 35 1 0 0 0 0 28 6 1 6 0 0 0 29 30 1 6 0 0 0 30 34 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	492.38
Volume:	534.525
LogP:	5.915
LogD:	4.988
LogS:	-4.661
# Rotatable Bonds:	7
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.427
Synthetic Accessibility Score:	4.927
Fsp3:	0.967
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:	-4.724
MDCK Permeability:	3.2470779842697084e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.858
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.848
30% Bioavailability (F30%):	0.862

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.089
Plasma Protein Binding (PPB):	96.97632598876953%
Volume Distribution (VD):	0.96
Pgp-substrate:	1.5593165159225464%

ADMET: Metabolism

CYP1A2-inhibitor:	0.039
CYP1A2-substrate:	0.142
CYP2C19-inhibitor:	0.06
CYP2C19-substrate:	0.811
CYP2C9-inhibitor:	0.227
CYP2C9-substrate:	0.159
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.096
CYP3A4-inhibitor:	0.557
CYP3A4-substrate:	0.362

ADMET: Excretion

Clearance (CL):	5.769
Half-life (T1/2):	0.171

ADMET: Toxicity

hERG Blockers:	0.346
Human Hepatotoxicity (H-HT):	0.582
Drug-inuced Liver Injury (DILI):	0.588
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.023
Maximum Recommended Daily Dose:	0.217
Skin Sensitization:	0.968
Carcinogencity:	0.1
Eye Corrosion:	0.964
Eye Irritation:	0.633
Respiratory Toxicity:	0.927

Download Data

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

Natural Product: NPC202688

Natural Product ID:	NPC202688
*Common Name:**	(24S)-Ergostane-3Beta,5Alpha,6Beta,25-Tetraol 25-Monoacetate
IUPAC Name:	[(3S,6R)-2,3-dimethyl-6-[(3S,5R,6R,8S,9S,10R,13R,14S,17R)-3,5,6-trihydroxy-10,13-dimethyl-1,2,3,4,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]heptan-2-yl] acetate
Synonyms:
Standard InCHIKey:	NTYRSMDNACWFJE-GCYJJEFRSA-N
Standard InCHI:	InChI=1S/C30H52O5/c1-18(8-9-19(2)27(4,5)35-20(3)31)23-10-11-24-22-16-26(33)30(34)17-21(32)12-15-29(30,7)25(22)13-14-28(23,24)6/h18-19,21-26,32-34H,8-17H2,1-7H3/t18-,19+,21+,22+,23-,24+,25+,26-,28-,29-,30+/m1/s1
SMILES:	O[C@H]1CC[C@]2([C@@](C1)(O)[C@H](O)C[C@@H]1[C@@H]2CC[C@]2([C@H]1CC[C@@H]2[C@@H](CC[C@@H](C(OC(=O)C)(C)C)C)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1762128
PubChem CID:	14034721
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids [CHEMONTID:0001403] Ergosterols 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	Antarctic	n.a.	PMID[8882433]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32603106]
NPO16560	Palhinhaea cernua	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31994397]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25960261]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25043228]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23513740]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	Stems	n.a.	n.a.	PMID[23078294]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[22014827]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20932054]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19917748]

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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	2

Activity Type	# Activity
Cell Line	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	36450.0	nM	PMID[461001]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	42760.0	nM	PMID[461001]

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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 NPC202688 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	389
0.1-0.2	3286
0.2-0.3	9998
0.3-0.4	13423
0.4-0.5	5712
0.5-0.6	4515
0.6-0.7	4091
0.7-0.8	1069
0.8-0.85	146
0.85-0.9	53
0.9-0.95	10
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC60018
1.0	High Similarity	NPC154043
0.962	High Similarity	NPC266651
0.9259	High Similarity	NPC215968
0.9259	High Similarity	NPC155531

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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 NPC202688 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	390
0.1-0.2	3620
0.2-0.3	3448
0.3-0.4	1006
0.4-0.5	333
0.5-0.6	213
0.6-0.7	116
0.7-0.8	17
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8421	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.8272	Intermediate Similarity	NPD6115	Approved
0.8272	Intermediate Similarity	NPD6114	Approved
0.8272	Intermediate Similarity	NPD6118	Approved
0.8272	Intermediate Similarity	NPD6697	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