NPASS Compound

Structure

CID278091 OpenBabel06191716082D 33 37 0 0 1 0 0 0 0 0999 V2000 -5.7159 -0.3462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1821 -0.9345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0245 -1.9126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4483 -1.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8707 1.4523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6436 -0.9495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8215 -1.4238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1090 1.4218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6427 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6441 -2.8458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8223 -2.3719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 0.4748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2883 1.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8223 1.4228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6444 1.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9561 -0.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4665 2.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7792 -0.1975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1087 0.4734 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6439 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6430 -0.9486 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -0.9491 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4653 -2.3710 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4660 0.4738 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8218 -1.4234 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4648 -1.4224 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8221 0.4743 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 -2.4662 1.4223 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9396 -0.5698 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1715 3.0053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3174 -2.8623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 2 0 0 0 0 2 19 1 0 0 0 0 5 28 1 0 0 0 0 7 8 1 0 0 0 0 7 21 1 0 0 0 0 8 23 1 0 0 0 0 9 14 1 0 0 0 0 9 20 1 0 0 0 0 10 13 1 0 0 0 0 10 22 1 0 0 0 0 11 12 1 0 0 0 0 11 24 1 0 0 0 0 12 26 1 0 0 0 0 13 29 1 0 0 0 0 14 30 1 0 0 0 0 15 16 1 0 0 0 0 15 28 1 0 0 0 0 16 30 1 0 0 0 0 17 27 1 0 0 0 0 17 31 1 0 0 0 0 18 32 1 0 0 0 0 20 19 1 6 0 0 0 20 25 1 0 0 0 0 21 25 1 0 0 0 0 21 28 1 6 0 0 0 22 26 1 1 0 0 0 22 27 1 0 0 0 0 23 26 1 1 0 0 0 23 29 1 0 0 0 0 24 27 1 1 0 0 0 24 33 1 0 0 0 0 25 30 1 1 0 0 0 26 3 1 1 0 0 0 27 4 1 1 0 0 0 28 29 1 1 0 0 0 29 6 1 1 0 0 0 30 18 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.38
Volume:	508.388
LogP:	4.508
LogD:	4.375
LogS:	-4.424
# Rotatable Bonds:	3
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.457
Synthetic Accessibility Score:	4.909
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.236
MDCK Permeability:	2.3989468900253996e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.894
30% Bioavailability (F30%):	0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.059
Plasma Protein Binding (PPB):	90.29637145996094%
Volume Distribution (VD):	0.871
Pgp-substrate:	1.796513557434082%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.259
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.933
CYP2C9-inhibitor:	0.129
CYP2C9-substrate:	0.088
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.612
CYP3A4-inhibitor:	0.848
CYP3A4-substrate:	0.352

ADMET: Excretion

Clearance (CL):	4.64
Half-life (T1/2):	0.403

ADMET: Toxicity

hERG Blockers:	0.093
Human Hepatotoxicity (H-HT):	0.251
Drug-inuced Liver Injury (DILI):	0.01
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.092
Maximum Recommended Daily Dose:	0.929
Skin Sensitization:	0.915
Carcinogencity:	0.012
Eye Corrosion:	0.353
Eye Irritation:	0.521
Respiratory Toxicity:	0.845

Download Data

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

Natural Product: NPC278091

Natural Product ID:	NPC278091
*Common Name:**	23-Hydroxybetulin
IUPAC Name:	(1R,3aS,5aR,5bR,7aR,8R,9S,11aR,11bR,13aR,13bR)-3a,8-bis(hydroxymethyl)-5a,5b,8,11a-tetramethyl-1-prop-1-en-2-yl-1,2,3,4,5,6,7,7a,9,10,11,11b,12,13,13a,13b-hexadecahydrocyclopenta[a]chrysen-9-ol
Synonyms:
Standard InCHIKey:	PHMKDBZGQWXPAZ-MZFJGDBOSA-N
Standard InCHI:	InChI=1S/C30H50O3/c1-19(2)20-9-14-30(18-32)16-15-28(5)21(25(20)30)7-8-23-26(3)12-11-24(33)27(4,17-31)22(26)10-13-29(23,28)6/h20-25,31-33H,1,7-18H2,2-6H3/t20-,21+,22+,23+,24-,25+,26-,27-,28+,29+,30+/m0/s1
SMILES:	OC[C@@]12CC[C@H]([C@@H]2[C@@H]2[C@](CC1)(C)[C@]1(C)CC[C@@H]3[C@]([C@H]1CC2)(C)CC[C@@H]([C@@]3(C)CO)O)C(=C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3815071
PubChem CID:	14605681
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26722868]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	roots	n.a.	n.a.	PMID[10346940]
NPO26828	Barbarea verna	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25482	Phyllogeiton zeyheri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2201	Orthocaulis attenuatus	Species	Anastrophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25532	Blitum virgatum	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23780	Psoroma crassum	Species	Pannariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26183	Scabiosa pyrenaica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19205	Buxus sempervirens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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	3
Others	3

Activity Type	# Activity
Cell Line	1
Organism	2
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	20000.0	nM	PMID[573625]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	3400.0	nM	PMID[573625]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	5200.0	nM	PMID[573625]
NPT2	Others	Unspecified	""	Ratio IC50	=	1.5	n.a.	PMID[573625]
NPT27	Others	Unspecified	""	Ratio IC50	>	5.9	n.a.	PMID[573625]
NPT27	Others	Unspecified	""	Ratio IC50	>	3.8	n.a.	PMID[573625]

Showing 1 to 6 of 6 entries

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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 NPC278091 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	177
0.1-0.2	2247
0.2-0.3	11060
0.3-0.4	14292
0.4-0.5	5568
0.5-0.6	4148
0.6-0.7	3639
0.7-0.8	1293
0.8-0.85	150
0.85-0.9	91
0.9-0.95	10
0.95-1	22

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC93662
1.0	High Similarity	NPC78067
0.9857	High Similarity	NPC104387
0.9857	High Similarity	NPC178383
0.9857	High Similarity	NPC240235

Showing 1 to 5 of 200 entries

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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 NPC278091 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	2565
0.2-0.3	4350
0.3-0.4	1440
0.4-0.5	261
0.5-0.6	147
0.6-0.7	174
0.7-0.8	41
0.8-0.85	2
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8701	High Similarity	NPD7525	Registered
0.8625	High Similarity	NPD7520	Clinical (unspecified phase)
0.8571	High Similarity	NPD7645	Phase 2
0.8289	Intermediate Similarity	NPD6942	Approved
0.8289	Intermediate Similarity	NPD7339	Approved

Showing 1 to 5 of 200 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