NPASS Compound

Structure

NPC55668 OpenBabel06302215222D 33 37 0 0 1 0 0 0 0 0999 V2000 0.4868 -1.8169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9737 -0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8432 -1.4605 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8432 -2.4342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 -2.9211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5297 -2.4342 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5297 -4.3816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5297 -1.4605 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3729 -0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2162 -1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2162 -2.4342 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9398 -3.0857 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.5437 -3.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5754 -3.8735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3729 -2.9211 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4046 -3.0228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8922 -2.8833 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2800 -3.7764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8645 -2.8323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1165 -1.8918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2999 -1.3615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2490 -0.3892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6910 0.4784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2213 -0.3382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3814 0.0529 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5432 -1.9743 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 -0.9737 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5297 -0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8432 0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 0.4868 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 32 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 28 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 16 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 9 28 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 6 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 18 27 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 1 0 0 0 22 27 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 28 29 1 6 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.38
Volume:	508.388
LogP:	5.653
LogD:	4.943
LogS:	-5.288
# Rotatable Bonds:	2
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.487
Synthetic Accessibility Score:	4.755
Fsp3:	0.967
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:	-4.942
MDCK Permeability:	1.1474351595097687e-05
Pgp-inhibitor:	0.339
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.979
30% Bioavailability (F30%):	0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.207
Plasma Protein Binding (PPB):	92.3845443725586%
Volume Distribution (VD):	1.166
Pgp-substrate:	2.287417411804199%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.611
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.964
CYP2C9-inhibitor:	0.157
CYP2C9-substrate:	0.501
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.796
CYP3A4-inhibitor:	0.275
CYP3A4-substrate:	0.353

ADMET: Excretion

Clearance (CL):	5.034
Half-life (T1/2):	0.226

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.28
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.049
Maximum Recommended Daily Dose:	0.804
Skin Sensitization:	0.848
Carcinogencity:	0.06
Eye Corrosion:	0.818
Eye Irritation:	0.497
Respiratory Toxicity:	0.969

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

Natural Product: NPC55668

Natural Product ID:	NPC55668
*Common Name:**	XSQYWMLMQVUWSF-UOAUUATESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XSQYWMLMQVUWSF-UOAUUATESA-N
Standard InCHI:	InChI=1S/C30H50O3/c1-25(2)21-12-17-29(7)22(27(21,5)15-13-23(25)31)10-9-19-20(11-16-28(19,29)6)30(8)18-14-24(33-30)26(3,4)32/h19-22,24,32H,9-18H2,1-8H3/t19-,20+,21+,22+,24+,27+,28-,29-,30-/m1/s1
SMILES:	CC1(C)[C@@H]2CC[C@]3(C)[C@@H](CC[C@@H]4[C@H](CC[C@@]34C)[C@@]3(C)CC[C@@H](C(C)(C)O)O3)[C@@]2(C)CCC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO18521	Capparis flavicans	Species	Capparaceae	Eukaryota	aerial parts	Khon Kaen Province, Thailand	2006-Aug	PMID[19943620]
NPO3125	Scaphechinus mirabilis	Species	Scutellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16180820]
NPO17392	Ipomoea hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12652	Xylosalsola richteri	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6840	Cassia pudibunda	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15625	Umbilicaria spodochroa	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO829	Vaccaria hispanica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16834	Baccharis sarothroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16655	Rabdosia flexicaulis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15360	Stephania hispidula	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC55668 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	337
0.1-0.2	3103
0.2-0.3	12033
0.3-0.4	11948
0.4-0.5	5890
0.5-0.6	6102
0.6-0.7	2712
0.7-0.8	486
0.8-0.85	69
0.85-0.9	11
0.9-0.95	1
0.95-1	5

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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 NPC55668 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	372
0.1-0.2	3460
0.2-0.3	3707
0.3-0.4	971
0.4-0.5	251
0.5-0.6	269
0.6-0.7	90
0.7-0.8	18
0.8-0.85	12
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
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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