NPASS Compound

Structure

CID247891 OpenBabel06191716052D 34 37 0 0 1 0 0 0 0 0999 V2000 5.8623 -1.6923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7619 -4.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2208 -2.9909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3967 -2.5384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5279 -4.0045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5279 -4.9820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9082 -1.6923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4548 -5.4710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9149 -4.0045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6084 -4.9820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0678 -3.5155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4656 -0.8461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9770 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6084 -6.9380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9149 -6.9380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3738 -2.5384 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.7619 -6.4490 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.4548 -6.4490 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3738 -3.5155 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.2208 -4.9820 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.9149 -4.9820 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0678 -6.4490 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9311 -1.6923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0678 -5.4710 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.7619 -5.4710 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.2208 -4.0045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4426 -0.8461 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 11.3209 -6.9490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2018 -6.9490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4426 -2.5384 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9770 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9770 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9770 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 7 1 0 0 0 0 4 16 1 0 0 0 0 5 6 1 0 0 0 0 5 19 1 0 0 0 0 6 20 1 0 0 0 0 7 23 1 0 0 0 0 8 10 1 0 0 0 0 8 18 1 0 0 0 0 9 11 1 0 0 0 0 9 21 1 0 0 0 0 10 25 1 0 0 0 0 11 26 1 0 0 0 0 12 13 1 0 0 0 0 12 27 1 0 0 0 0 13 34 1 0 0 0 0 14 17 1 0 0 0 0 14 18 1 0 0 0 0 15 17 1 0 0 0 0 15 22 1 0 0 0 0 16 1 1 1 0 0 0 16 19 1 0 0 0 0 17 25 1 1 0 0 0 18 28 1 1 0 0 0 19 26 1 6 0 0 0 20 24 1 0 0 0 0 20 26 1 6 0 0 0 21 24 1 0 0 0 0 21 25 1 6 0 0 0 22 24 1 0 0 0 0 22 29 1 6 0 0 0 23 27 2 3 0 0 0 23 30 1 0 0 0 0 31 34 1 0 0 0 0 32 34 2 0 0 0 0 33 34 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	499.3
Volume:	503.637
LogP:	1.256
LogD:	3.468
LogS:	-1.968
# Rotatable Bonds:	8
TPSA:	123.93
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.398
Synthetic Accessibility Score:	4.532
Fsp3:	0.962
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:	-5.493
MDCK Permeability:	2.083531035168562e-05
Pgp-inhibitor:	0.024
Pgp-substrate:	0.083
Human Intestinal Absorption (HIA):	0.934
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.183
Plasma Protein Binding (PPB):	76.8987045288086%
Volume Distribution (VD):	0.512
Pgp-substrate:	9.762907981872559%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.788
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.686
CYP2C9-inhibitor:	0.021
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.106
CYP3A4-inhibitor:	0.046
CYP3A4-substrate:	0.09

ADMET: Excretion

Clearance (CL):	5.697
Half-life (T1/2):	0.749

ADMET: Toxicity

hERG Blockers:	0.254
Human Hepatotoxicity (H-HT):	0.405
Drug-inuced Liver Injury (DILI):	0.034
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.036
Maximum Recommended Daily Dose:	0.526
Skin Sensitization:	0.962
Carcinogencity:	0.232
Eye Corrosion:	0.022
Eye Irritation:	0.055
Respiratory Toxicity:	0.966

Download Data

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

Natural Product: NPC247891

Natural Product ID:	NPC247891
*Common Name:**	Tauroursodeoxycholate
IUPAC Name:	2-[[(4R)-4-[(3R,5S,7S,8R,9S,10S,13R,14S,17R)-3,7-dihydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]ethanesulfonic acid
Synonyms:	Ursodeoxy Cholic Acid
Standard InCHIKey:	BHTRKEVKTKCXOH-LBSADWJPSA-N
Standard InCHI:	InChI=1S/C26H45NO6S/c1-16(4-7-23(30)27-12-13-34(31,32)33)19-5-6-20-24-21(9-11-26(19,20)3)25(2)10-8-18(28)14-17(25)15-22(24)29/h16-22,24,28-29H,4-15H2,1-3H3,(H,27,30)(H,31,32,33)/t16-,17+,18-,19-,20+,21+,22+,24+,25+,26-/m1/s1
SMILES:	O[C@@H]1CC[C@]2([C@@H](C1)C[C@@H]([C@@H]1[C@@H]2CC[C@]2([C@H]1CC[C@@H]2[C@@H](CCC(=NCCS(=O)(=O)O)O)C)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL272427
PubChem CID:	9848818
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:0001159] Taurinated bile acids 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
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9949311]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9892086]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9870205]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869364]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869358]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9861496]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9861478]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9857238]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9851755]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9818465]

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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
EC50	3
IC50	3
Kd	1
Ki	1
Others	29

Activity Type	# Activity
Individual Protein	28
ORGANISM	5
Others	3
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	PMID[458603]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	PMID[458603]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.14	%	PMID[458602]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	15.88	%	PMID[458601]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-21.08	%	PMID[458600]
NPT4418	Individual Protein	Autotaxin	Homo sapiens	IC50	=	10300.0	nM	PMID[458599]
NPT745	Individual Protein	G-protein coupled bile acid receptor 1	Homo sapiens	Activity	=	39.0	%	PMID[458597]
NPT745	Individual Protein	G-protein coupled bile acid receptor 1	Homo sapiens	EC50	=	105150.0	nM	PMID[458597]
NPT745	Individual Protein	G-protein coupled bile acid receptor 1	Homo sapiens	EC50	=	50500.0	nM	PMID[458597]
NPT754	Individual Protein	Ileal bile acid transporter	Homo sapiens	Ki	=	28000.0	nM	PMID[458595]

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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 NPC247891 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	106
0.1-0.2	3669
0.2-0.3	20584
0.3-0.4	9348
0.4-0.5	5939
0.5-0.6	2590
0.6-0.7	408
0.7-0.8	40
0.8-0.85	5
0.85-0.9	1
0.9-0.95	1
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC159390
1.0	High Similarity	NPC133995
0.9762	High Similarity	NPC283751
0.9643	High Similarity	NPC320478
0.9302	High Similarity	NPC317363

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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 NPC247891 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	78
0.1-0.2	2187
0.2-0.3	5162
0.3-0.4	1239
0.4-0.5	348
0.5-0.6	102
0.6-0.7	29
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	4

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD6700	Approved
1.0	High Similarity	NPD6701	Clinical (unspecified phase)
0.9651	High Similarity	NPD6702	Approved
0.9651	High Similarity	NPD6703	Approved
0.7087	Intermediate Similarity	NPD8418	Phase 2

Showing 1 to 5 of 44 entries

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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