NPASS Compound

Structure

NPC469943 OpenBabel07101718192D 43 47 0 0 1 0 0 0 0 0999 V2000 0.4385 6.4018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 5.2428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4459 4.1723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6036 1.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4896 3.7565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7986 4.7076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1587 3.0134 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 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 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 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1295 5.4507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1369 3.2213 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8060 2.4781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 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 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 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 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 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 20 1 0 0 0 0 2 20 1 0 0 0 0 4 22 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 7 20 1 0 0 0 0 8 21 1 0 0 0 0 9 10 1 0 0 0 0 9 23 1 0 0 0 0 11 12 1 0 0 0 0 11 26 1 0 0 0 0 12 27 1 0 0 0 0 13 16 1 0 0 0 0 13 24 1 0 0 0 0 14 15 1 0 0 0 0 14 28 1 0 0 0 0 15 34 1 0 0 0 0 16 35 1 0 0 0 0 17 23 2 0 0 0 0 17 24 1 0 0 0 0 18 37 1 0 0 0 0 19 42 1 0 0 0 0 21 3 1 1 0 0 0 21 26 1 0 0 0 0 22 36 2 3 0 0 0 22 38 1 0 0 0 0 23 35 1 0 0 0 0 24 39 1 1 0 0 0 25 10 1 6 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 26 34 1 1 0 0 0 27 34 1 1 0 0 0 28 35 1 1 0 0 0 29 18 1 1 0 0 0 29 31 1 0 0 0 0 29 43 1 0 0 0 0 30 32 1 0 0 0 0 30 33 1 0 0 0 0 30 36 1 6 0 0 0 31 32 1 0 0 0 0 31 40 1 6 0 0 0 32 41 1 1 0 0 0 33 42 1 1 0 0 0 33 43 1 0 0 0 0 34 5 1 1 0 0 0 35 19 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	605.43
Volume:	638.389
LogP:	4.761
LogD:	4.632
LogS:	-3.813
# Rotatable Bonds:	11
TPSA:	128.48
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.235
Synthetic Accessibility Score:	5.147
Fsp3:	0.914
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:	-5.126
MDCK Permeability:	9.97357437881874e-06
Pgp-inhibitor:	0.806
Pgp-substrate:	0.757
Human Intestinal Absorption (HIA):	0.025
20% Bioavailability (F20%):	0.961
30% Bioavailability (F30%):	0.877

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.029
Plasma Protein Binding (PPB):	94.1019058227539%
Volume Distribution (VD):	0.92
Pgp-substrate:	2.2616899013519287%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.231
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.707
CYP2C9-inhibitor:	0.176
CYP2C9-substrate:	0.027
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.067
CYP3A4-inhibitor:	0.804
CYP3A4-substrate:	0.237

ADMET: Excretion

Clearance (CL):	2.317
Half-life (T1/2):	0.292

ADMET: Toxicity

hERG Blockers:	0.139
Human Hepatotoxicity (H-HT):	0.283
Drug-inuced Liver Injury (DILI):	0.237
AMES Toxicity:	0.223
Rat Oral Acute Toxicity:	0.414
Maximum Recommended Daily Dose:	0.296
Skin Sensitization:	0.301
Carcinogencity:	0.116
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC469943

Natural Product ID:	NPC469943
*Common Name:**	19-O-Beta-D-N-Acetyl-2-Aminoglucopyranosyl-Cholest-4-En-3B,19-Diol
IUPAC Name:	N-[(2R,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[[(3S,8S,9S,10S,13R,14S,17R)-3-hydroxy-13-methyl-17-[(2R)-6-methylheptan-2-yl]-2,3,6,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-10-yl]methoxy]oxan-3-yl]acetamide
Synonyms:
Standard InCHIKey:	NLQPIKCKRZEVKY-PEPCZXFMSA-N
Standard InCHI:	InChI=1S/C35H59NO7/c1-20(2)7-6-8-21(3)26-11-12-27-25-10-9-23-17-24(39)13-16-35(23,28(25)14-15-34(26,27)5)19-42-33-30(36-22(4)38)32(41)31(40)29(18-37)43-33/h17,20-21,24-33,37,39-41H,6-16,18-19H2,1-5H3,(H,36,38)/t21-,24+,25+,26-,27+,28+,29-,30-,31-,32-,33-,34-,35-/m1/s1
SMILES:	CC(C)CCCC(C)C1CCC2C1(CCC3C2CCC4=CC(CCC34COC5C(C(C(C(O5)CO)O)O)NC(=O)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1288407
PubChem CID:	52947463
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003566] Cholestane steroids [CHEMONTID:0001469] Cholesterols 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
NPO33255	peyssonnelia sp.	Species	Peyssonneliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21036050]

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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	11

Activity Type	# Activity
Cell Line	9
NON-MOLECULAR	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1900	Cell Line	DU-4475	Homo sapiens	IC50	=	6120.0	nM	PMID[474080]
NPT784	Cell Line	MDA-MB-468	Homo sapiens	IC50	=	7130.0	nM	PMID[474080]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	9610.0	nM	PMID[474080]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	>	25000.0	nM	PMID[474080]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	10200.0	nM	PMID[474080]
NPT90	Cell Line	DU-145	Homo sapiens	IC50	>	25000.0	nM	PMID[474080]
NPT457	Cell Line	BT-549	Homo sapiens	IC50	=	10060.0	nM	PMID[474080]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	25000.0	nM	PMID[474080]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	IC50	=	10730.0	nM	PMID[474080]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	21390.0	nM	PMID[474080]

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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 NPC469943 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	133
0.1-0.2	1003
0.2-0.3	4779
0.3-0.4	16439
0.4-0.5	11023
0.5-0.6	6607
0.6-0.7	2360
0.7-0.8	338
0.8-0.85	13
0.85-0.9	1
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.8862	High Similarity	NPC139585
0.8235	Intermediate Similarity	NPC36463
0.8235	Intermediate Similarity	NPC298005
0.8214	Intermediate Similarity	NPC469942
0.8142	Intermediate Similarity	NPC470434

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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 NPC469943 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	114
0.1-0.2	624
0.2-0.3	3296
0.3-0.4	3608
0.4-0.5	1073
0.5-0.6	370
0.6-0.7	59
0.7-0.8	6
0.8-0.85	0
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
0.7731	Intermediate Similarity	NPD8174	Phase 2
0.7519	Intermediate Similarity	NPD8449	Approved
0.7463	Intermediate Similarity	NPD8450	Suspended
0.7043	Intermediate Similarity	NPD8522	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD6412	Phase 2

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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