NPASS Compound

Structure

CID41481 OpenBabel06191715372D 38 41 0 0 1 0 0 0 0 0999 V2000 -0.4228 -1.5992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4362 3.5877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4791 1.9848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3610 -2.2954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7934 1.2712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.7698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9173 1.3338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1472 1.7784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9173 0.4446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3772 1.3338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1472 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0378 -2.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5620 1.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4289 -0.1587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4331 -1.4039 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2639 3.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9237 1.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6198 -1.4565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3772 0.4446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6952 1.4437 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9047 -1.8579 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9479 0.4446 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0345 0.4446 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1668 -1.0083 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6071 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.8892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5620 -0.3565 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6952 -0.5543 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3964 4.7916 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3683 1.2147 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4756 -1.2612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5018 -2.5014 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6071 -0.8892 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9590 3.3581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4791 0.4446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0226 -0.8129 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8371 0.4446 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 15 1 0 0 0 0 2 16 1 0 0 0 0 3 17 1 0 0 0 0 4 18 1 0 0 0 0 5 26 1 0 0 0 0 6 26 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 11 2 0 0 0 0 10 19 2 0 0 0 0 11 19 1 0 0 0 0 12 15 1 0 0 0 0 12 21 1 0 0 0 0 13 22 1 0 0 0 0 14 27 1 0 0 0 0 14 34 1 0 0 0 0 15 28 1 1 0 0 0 16 29 2 0 0 0 0 16 34 1 0 0 0 0 17 30 2 0 0 0 0 17 35 1 0 0 0 0 18 31 2 0 0 0 0 18 36 1 0 0 0 0 19 25 1 0 0 0 0 20 13 1 6 0 0 0 20 23 1 0 0 0 0 20 26 1 0 0 0 0 21 24 1 0 0 0 0 21 32 1 1 0 0 0 22 27 1 6 0 0 0 22 37 1 0 0 0 0 23 28 1 1 0 0 0 23 35 1 0 0 0 0 24 27 1 1 0 0 0 24 36 1 0 0 0 0 25 33 2 0 0 0 0 25 37 1 0 0 0 0 26 38 1 0 0 0 0 27 28 1 1 0 0 0 28 38 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	532.23
Volume:	528.065
LogP:	3.239
LogD:	2.068
LogS:	-4.228
# Rotatable Bonds:	10
TPSA:	134.66
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.43
Synthetic Accessibility Score:	5.825
Fsp3:	0.643
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:	-5.255
MDCK Permeability:	6.325425783870742e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.134
Human Intestinal Absorption (HIA):	0.088
20% Bioavailability (F20%):	0.964
30% Bioavailability (F30%):	0.941

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.54
Plasma Protein Binding (PPB):	56.11608123779297%
Volume Distribution (VD):	1.62
Pgp-substrate:	24.368091583251953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.037
CYP1A2-substrate:	0.032
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.079
CYP2C9-inhibitor:	0.255
CYP2C9-substrate:	0.037
CYP2D6-inhibitor:	0.204
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.504
CYP3A4-substrate:	0.285

ADMET: Excretion

Clearance (CL):	3.361
Half-life (T1/2):	0.881

ADMET: Toxicity

hERG Blockers:	0.235
Human Hepatotoxicity (H-HT):	0.945
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.041
Rat Oral Acute Toxicity:	0.075
Maximum Recommended Daily Dose:	0.058
Skin Sensitization:	0.492
Carcinogencity:	0.236
Eye Corrosion:	0.004
Eye Irritation:	0.157
Respiratory Toxicity:	0.564

Download Data

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

Natural Product: NPC41481

Natural Product ID:	NPC41481
*Common Name:**	Salasol A
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PBYYDTQGTBZJGB-OKPVOZINSA-N
Standard InCHI:	InChI=1S/C28H36O10/c1-15-12-21(32)24(36-18(4)31)27(14-34-16(2)29)22(37-25(33)19-10-8-7-9-11-19)13-20-23(35-17(3)30)28(15,27)38-26(20,5)6/h7-11,15,20-24,32H,12-14H2,1-6H3/t15-,20-,21+,22+,23-,24+,27-,28-/m1/s1
SMILES:	CC(=O)OC[C@@]12[C@@H](OC(=O)c3ccccc3)C[C@@H]3[C@H]([C@]2(OC3(C)C)[C@@H](C[C@@H]([C@@H]1OC(=O)C)O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL489050
PubChem CID:	11092680
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

*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
NPO9420	Aspergillus arenarius	Species	Aspergillaceae	Eukaryota	sclerotia	n.a.	n.a.	PMID[9599285]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24697288]
NPO12977	Solenopsis invicta	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21905650]
NPO22421	Microtropis japonica	Species	Celastraceae	Eukaryota	Stems	n.a.	n.a.	PMID[19534471]
NPO22421	Microtropis japonica	Species	Celastraceae	Eukaryota	n.a.	stem	n.a.	PMID[18471021]
NPO22421	Microtropis japonica	Species	Celastraceae	Eukaryota	stem	n.a.	n.a.	PMID[18471021]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14738381]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	Argentine	n.a.	PMID[14738381]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	stems	Thailand	n.a.	PMID[14510595]

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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
MIC	1

Activity Type	# Activity
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	28200.0	nM	PMID[541608]

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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 NPC41481 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	275
0.1-0.2	1021
0.2-0.3	2178
0.3-0.4	4075
0.4-0.5	7995
0.5-0.6	11908
0.6-0.7	12531
0.7-0.8	2124
0.8-0.85	253
0.85-0.9	155
0.9-0.95	88
0.95-1	94

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC118080
1.0	High Similarity	NPC27377
1.0	High Similarity	NPC291599
1.0	High Similarity	NPC472576
1.0	High Similarity	NPC97947

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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 NPC41481 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	227
0.1-0.2	665
0.2-0.3	1391
0.3-0.4	2712
0.4-0.5	2373
0.5-0.6	1283
0.6-0.7	447
0.7-0.8	50
0.8-0.85	2
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
0.8231	Intermediate Similarity	NPD7236	Approved
0.8143	Intermediate Similarity	NPD5952	Clinical (unspecified phase)
0.8079	Intermediate Similarity	NPD7239	Suspended
0.8012	Intermediate Similarity	NPD8470	Clinical (unspecified phase)
0.795	Intermediate Similarity	NPD7799	Discontinued

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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