NPASS Compound

Structure

NPC144600 OpenBabel06302215362D 53 58 0 0 1 0 0 0 0 0999 V2000 -1.9870 -3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9870 -3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4870 -3.0258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4870 -4.7579 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5130 -4.7579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0130 -3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5130 -3.0258 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4870 -3.0258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0130 -2.1598 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0075 -2.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2154 -1.0771 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3494 -0.5771 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6063 -1.2463 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3448 -1.5553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3448 -0.9372 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5527 0.0409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1905 0.7100 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0175 1.6882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7606 1.0190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9685 1.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1764 2.9753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4333 3.6445 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5178 3.3355 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7257 2.3573 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6767 2.0483 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8847 1.0701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1415 0.4010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0926 0.0920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4199 2.7174 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2609 4.0046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6412 4.6226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1020 5.2918 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0530 4.9827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7962 5.6519 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5882 6.6300 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6372 6.9390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1060 6.2699 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3314 7.2991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1235 8.2773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7472 5.3428 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2609 4.0046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2120 3.6956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1290 -0.6704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9870 -5.6239 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9870 -5.6239 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5748 -4.8149 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5258 -5.1239 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5258 -6.1239 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3348 -6.7117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2303 -7.7062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5748 -6.4329 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3348 -4.5361 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2658 -3.8638 0.0000 O 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 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 44 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 1 0 0 0 9 7 1 6 0 0 0 9 10 1 0 0 0 0 9 13 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 43 1 0 0 0 0 12 13 1 0 0 0 0 12 27 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 27 1 0 0 0 0 18 24 1 0 0 0 0 18 19 1 0 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 0 0 0 0 22 31 1 6 0 0 0 23 24 1 0 0 0 0 23 30 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 29 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 32 37 1 0 0 0 0 33 34 1 0 0 0 0 33 41 1 0 0 0 0 34 35 1 0 0 0 0 34 40 1 0 0 0 0 35 36 1 0 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 38 39 1 0 0 0 0 41 42 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 0 0 0 0 45 51 1 0 0 0 0 46 47 1 0 0 0 0 46 53 1 0 0 0 0 47 48 1 0 0 0 0 47 52 1 0 0 0 0 48 49 1 0 0 0 0 48 51 1 0 0 0 0 49 50 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.38
Volume:	499.598
LogP:	6.096
LogD:	5.592
LogS:	-5.795
# Rotatable Bonds:	1
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.429
Synthetic Accessibility Score:	4.853
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.199
MDCK Permeability:	3.738842860911973e-05
Pgp-inhibitor:	0.098
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.415
30% Bioavailability (F30%):	0.808

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	95.24333953857422%
Volume Distribution (VD):	1.166
Pgp-substrate:	2.2092881202697754%

ADMET: Metabolism

CYP1A2-inhibitor:	0.03
CYP1A2-substrate:	0.654
CYP2C19-inhibitor:	0.065
CYP2C19-substrate:	0.941
CYP2C9-inhibitor:	0.146
CYP2C9-substrate:	0.632
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.831
CYP3A4-inhibitor:	0.266
CYP3A4-substrate:	0.435

ADMET: Excretion

Clearance (CL):	3.137
Half-life (T1/2):	0.185

ADMET: Toxicity

hERG Blockers:	0.079
Human Hepatotoxicity (H-HT):	0.102
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.091
Maximum Recommended Daily Dose:	0.693
Skin Sensitization:	0.34
Carcinogencity:	0.002
Eye Corrosion:	0.953
Eye Irritation:	0.878
Respiratory Toxicity:	0.541

Download Data

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

Natural Product: NPC144600

Natural Product ID:	NPC144600
*Common Name:**	XRPZNOLWSDIWHZ-GPYFSNQCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XRPZNOLWSDIWHZ-GPYFSNQCSA-N
Standard InCHI:	InChI=1S/C39H68O14/c1-18(2)23(51-35-32(46)30(44)25(16-40)53-35)9-8-19(3)20-14-21(41)34-37(20,4)13-11-27-38(5)12-10-24(29(43)28(38)22(42)15-39(27,34)47)52-36-33(49-7)31(45)26(48-6)17-50-36/h18-36,40-47H,8-17H2,1-7H3/t19-,20-,21+,22-,23+,24+,25-,26-,27-,28+,29+,30-,31+,32+,33-,34-,35+,36+,37-,38-,39+/m1/s1
SMILES:	CC(C)[C@H](CC[C@@H](C)[C@H]1C[C@@H]([C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@@H]([C@@H]([C@@H]3[C@@H](C[C@@]21O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)OC)O)OC)O)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O1)O)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:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

*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
NPO13814	Tupidanthus calyptratus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11421737]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18207	Radermachera sinica	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14510	Streptomyces acidiscabies	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO25557	Alternaria porri	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1488	Aphis spiraecola	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18207	Radermachera sinica	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14006	Halostachys caspica	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9076	Tiliacora dinklagei	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22644	Helichrysum argenteum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8371	Fagara rhoifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11691	Limnothrix rosea	Species	Pseudanabaenaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13088	Vicia pseudo-orobus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2159	Helipterum splendidum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13814	Tupidanthus calyptratus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2586	Alnus rubra	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14838	Myriocephalus stuartii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4309	Carapa procera	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9689	Pertusaria flavicans	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5467	Helenium campestre	Species	Asteraceae	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 NPC144600 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	555
0.1-0.2	4929
0.2-0.3	13111
0.3-0.4	10900
0.4-0.5	5722
0.5-0.6	3740
0.6-0.7	2384
0.7-0.8	967
0.8-0.85	175
0.85-0.9	65
0.9-0.95	133
0.95-1	16

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 NPC144600 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	539
0.1-0.2	4584
0.2-0.3	2831
0.3-0.4	618
0.4-0.5	305
0.5-0.6	209
0.6-0.7	46
0.7-0.8	15
0.8-0.85	1
0.85-0.9	1
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