NPASS Compound

Structure

NPC232189 OpenBabel06302215372D 43 47 0 0 1 0 0 0 0 0999 V2000 -1.7321 3.0000 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.5263 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 O 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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 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 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 42 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 31 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 27 1 0 0 0 0 10 11 1 0 0 0 0 10 30 1 1 0 0 0 11 12 1 0 0 0 0 11 29 1 6 0 0 0 12 13 1 0 0 0 0 12 28 1 1 0 0 0 13 14 1 6 0 0 0 13 27 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 1 0 0 0 18 19 1 0 0 0 0 18 25 1 6 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 6 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 38 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 42 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 40 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 40 41 1 0 0 0 0 42 43 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	608.17
Volume:	560.823
LogP:	0.525
LogD:	-0.047
LogS:	-3.378
# Rotatable Bonds:	7
TPSA:	242.13
# H-Bond Aceptor:	15
# H-Bond Donor:	8
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.138
Synthetic Accessibility Score:	4.669
Fsp3:	0.5
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.342
MDCK Permeability:	2.927175592049025e-05
Pgp-inhibitor:	0.658
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.972
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.102
Plasma Protein Binding (PPB):	72.30196380615234%
Volume Distribution (VD):	0.611
Pgp-substrate:	9.232772827148438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.076
CYP1A2-substrate:	0.059
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.046
CYP2D6-substrate:	0.136
CYP3A4-inhibitor:	0.044
CYP3A4-substrate:	0.038

ADMET: Excretion

Clearance (CL):	1.285
Half-life (T1/2):	0.427

ADMET: Toxicity

hERG Blockers:	0.311
Human Hepatotoxicity (H-HT):	0.085
Drug-inuced Liver Injury (DILI):	0.952
AMES Toxicity:	0.865
Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.007
Skin Sensitization:	0.103
Carcinogencity:	0.565
Eye Corrosion:	0.003
Eye Irritation:	0.329
Respiratory Toxicity:	0.012

Download Data

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

Natural Product: NPC232189

Natural Product ID:	NPC232189
*Common Name:**	LHWONDXFTUKXDH-BFTLVBKUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LHWONDXFTUKXDH-BFTLVBKUSA-N
Standard InCHI:	InChI=1S/C28H32O15/c1-9-3-11-18(22(34)17-12(19(11)31)5-10(39-2)6-13(17)30)14(4-9)41-28-26(38)24(36)21(33)16(43-28)8-40-27-25(37)23(35)20(32)15(7-29)42-27/h3-6,15-16,20-21,23-30,32-33,35-38H,7-8H2,1-2H3/t15-,16-,20-,21-,23+,24+,25-,26-,27-,28-/m1/s1
SMILES:	Cc1cc2c(c(c1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O1)O)O)O)C(=O)c1c(cc(cc1O)OC)C2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5320543
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[9090870]
NPO23429	Lycium barbarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31397570]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	Root Bark	n.a.	n.a.	PMID[26982999]
NPO19996	Caulerpa peltata	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25593390]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	root bark	n.a.	n.a.	PMID[23282106]
NPO21244	Delphinium nuttallianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19012276]
NPO14304.1	Physalis alkekengi var. franchetii	Varieties	Solanaceae	Eukaryota	calyces	Yilan, Heilongjiang Province, China	2004-SEP	PMID[18348534]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	root	n.a.	PMID[16212233]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[12467621]
NPO21244	Delphinium nuttallianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10978210]

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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 NPC232189 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	440
0.1-0.2	1670
0.2-0.3	3482
0.3-0.4	8188
0.4-0.5	9299
0.5-0.6	5353
0.6-0.7	5382
0.7-0.8	6383
0.8-0.85	1849
0.85-0.9	573
0.9-0.95	63
0.95-1	15

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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 NPC232189 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	379
0.1-0.2	956
0.2-0.3	1820
0.3-0.4	2687
0.4-0.5	1905
0.5-0.6	912
0.6-0.7	332
0.7-0.8	105
0.8-0.85	36
0.85-0.9	18
0.9-0.95	0
0.95-1	0

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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