NPASS Compound

Structure

NPC183096 OpenBabel06302215342D 40 46 0 0 1 0 0 0 0 0999 V2000 1.2959 1.5712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3906 0.5757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5759 -0.0041 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5906 -0.1590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4638 -0.2493 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6021 -0.1445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5805 0.0276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4206 0.0950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2824 -0.0098 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2673 -0.1766 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3204 -0.9856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2673 -1.7946 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2064 -1.2523 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0779 -0.5438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5563 -0.2026 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5713 -0.0358 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5008 -0.2006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3222 -0.1846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4343 0.0606 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2184 -0.4856 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2184 -1.4856 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0274 -2.0734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9410 -1.6666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4626 0.7930 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2779 1.3720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1704 -1.5184 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8828 -0.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2962 1.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.1133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6101 -1.7611 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6101 -1.0567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2201 -0.7044 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.7044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6101 -1.0567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2201 -0.7044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2201 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6101 0.3522 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 0.6101 0.3522 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2201 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 19 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 5 29 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 28 1 0 0 0 0 9 18 1 0 0 0 0 9 19 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 20 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 21 1 0 0 0 0 13 14 1 0 0 0 0 13 26 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 29 30 1 0 0 0 0 30 31 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 35 36 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	555.32
Volume:	564.115
LogP:	3.553
LogD:	3.521
LogS:	-4.738
# Rotatable Bonds:	9
TPSA:	86.69
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.489
Synthetic Accessibility Score:	6.906
Fsp3:	0.781
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:	-5.383
MDCK Permeability:	6.587256939383224e-05
Pgp-inhibitor:	0.758
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.937

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.142
Plasma Protein Binding (PPB):	30.328460693359375%
Volume Distribution (VD):	1.289
Pgp-substrate:	26.383405685424805%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.981
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.887
CYP2C9-inhibitor:	0.017
CYP2C9-substrate:	0.031
CYP2D6-inhibitor:	0.549
CYP2D6-substrate:	0.639
CYP3A4-inhibitor:	0.862
CYP3A4-substrate:	0.787

ADMET: Excretion

Clearance (CL):	10.84
Half-life (T1/2):	0.465

ADMET: Toxicity

hERG Blockers:	0.965
Human Hepatotoxicity (H-HT):	0.365
Drug-inuced Liver Injury (DILI):	0.196
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.568
Maximum Recommended Daily Dose:	0.28
Skin Sensitization:	0.247
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC183096

Natural Product ID:	NPC183096
*Common Name:**	XHJDCLXGXWJUHK-DNZCMCMLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XHJDCLXGXWJUHK-DNZCMCMLSA-N
Standard InCHI:	InChI=1S/C32H45NO7/c1-6-33-16-30(17-40-29(35)18-9-7-8-10-22(18)36-2)12-11-25(34)32-20-13-19-23(37-3)15-31(39-5,26(20)27(19)38-4)21(28(32)33)14-24(30)32/h7-10,19-21,23-28,34H,6,11-17H2,1-5H3/t19-,20-,21+,23+,24-,25+,26-,27+,28-,30+,31+,32-/m1/s1
SMILES:	CCN1C[C@@]2(CC[C@@H]([C@@]34[C@@H]5C[C@@H]6[C@H](C[C@]([C@@H](C[C@H]23)[C@@H]14)([C@H]5[C@H]6OC)OC)OC)O)COC(=O)c1ccccc1OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101036081
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003788] Aconitane-type diterpenoid alkaloids

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[13160012]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14325279]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15853884]
NPO6971	Thapsia garganica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124763]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18313305]
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21648406]
NPO18732	Vetiveria zizanioides	Species	Poaceae	Eukaryota	Roots	n.a.	n.a.	PMID[27598828]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[783153]
NPO10896	Juliania adstringens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO17262	Polygala caudata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26987	Zanthoxylum dipetalum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6971	Thapsia garganica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO26987	Zanthoxylum dipetalum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10896	Juliania adstringens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO17262	Polygala caudata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6971	Thapsia garganica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18732	Vetiveria zizanioides	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26987	Zanthoxylum dipetalum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO18732	Vetiveria zizanioides	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26987	Zanthoxylum dipetalum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10896	Juliania adstringens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO590	Malus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6971	Thapsia garganica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17262	Polygala caudata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC183096 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	314
0.1-0.2	1315
0.2-0.3	2994
0.3-0.4	7505
0.4-0.5	11972
0.5-0.6	12839
0.6-0.7	5508
0.7-0.8	214
0.8-0.85	4
0.85-0.9	27
0.9-0.95	5
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC183096 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	203
0.1-0.2	645
0.2-0.3	1271
0.3-0.4	2355
0.4-0.5	2803
0.5-0.6	1474
0.6-0.7	381
0.7-0.8	17
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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