NPASS Compound

Structure

NPC13237 OpenBabel06302215242D 51 55 0 0 1 0 0 0 0 0999 V2000 0.4722 -1.0176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2269 -0.5097 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6415 -0.8830 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2095 -1.6314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1721 -1.0554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0818 -1.9148 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7270 -0.9971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2102 -0.7181 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0900 0.0885 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6457 0.6854 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4588 0.6231 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2720 0.5608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9319 0.0816 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8467 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1017 -1.0613 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5066 -1.2088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6917 1.4668 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1772 2.1749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3029 2.2141 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8071 1.3063 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6541 0.2790 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5381 -0.2668 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3975 -0.1764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0460 -0.9659 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8833 0.6938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7270 1.5550 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3069 2.0188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1721 1.6133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6415 1.4409 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2269 1.0676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4722 1.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.5579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4832 0.8369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9663 0.5579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9663 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4832 -0.2790 0.0000 N 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 -3.2377 1.3844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3241 4.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7523 4.8032 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0317 5.0384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5203 2.8127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5529 1.6232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3769 1.3279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0445 1.8939 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5332 0.4668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3882 3.9052 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5339 4.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0060 3.3606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2195 4.8403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2646 0.3446 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 37 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 10 1 0 0 0 0 9 51 1 1 0 0 0 10 11 1 0 0 0 0 10 47 1 1 0 0 0 11 21 1 0 0 0 0 11 12 1 1 0 0 0 11 17 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 17 18 1 0 0 0 0 17 43 1 6 0 0 0 18 19 1 0 0 0 0 18 42 1 1 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 38 1 6 0 0 0 21 22 1 0 0 0 0 21 25 1 1 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 37 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 39 41 1 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 48 50 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	721.26
Volume:	681.75
LogP:	0.92
LogD:	0.514
LogS:	-3.868
# Rotatable Bonds:	9
TPSA:	240.61
# H-Bond Aceptor:	17
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.265
Synthetic Accessibility Score:	7.548
Fsp3:	0.676
Lipinski Rule-of-5:	Rejected
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:	-5.401
MDCK Permeability:	0.00013363092148210853
Pgp-inhibitor:	0.997
Pgp-substrate:	0.979
Human Intestinal Absorption (HIA):	0.908
20% Bioavailability (F20%):	0.983
30% Bioavailability (F30%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.055
Plasma Protein Binding (PPB):	31.623172760009766%
Volume Distribution (VD):	0.879
Pgp-substrate:	39.71028137207031%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.043
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.01
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.028
CYP3A4-inhibitor:	0.603
CYP3A4-substrate:	0.282

ADMET: Excretion

Clearance (CL):	2.297
Half-life (T1/2):	0.512

ADMET: Toxicity

hERG Blockers:	0.023
Human Hepatotoxicity (H-HT):	0.675
Drug-inuced Liver Injury (DILI):	0.957
AMES Toxicity:	0.046
Rat Oral Acute Toxicity:	0.024
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.074
Carcinogencity:	0.144
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.033

Download Data

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

Natural Product: NPC13237

Natural Product ID:	NPC13237
*Common Name:**	SHDBRMQJPSDFRT-KMPJZEJPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SHDBRMQJPSDFRT-KMPJZEJPSA-N
Standard InCHI:	InChI=1S/C34H43NO16/c1-14-15(2)29(42)50-26-24(41)28(49-19(6)39)33(13-45-16(3)36)27(48-18(5)38)23(40)21-25(47-17(4)37)34(33,32(26,8)44)51-31(21,7)12-46-30(43)20-10-9-11-35-22(14)20/h9-11,14-15,21,23-28,40-41,44H,12-13H2,1-8H3/t14-,15-,21+,23-,24-,25+,26-,27+,28-,31-,32-,33+,34-/m0/s1
SMILES:	C[C@H]1[C@H](C)C(=O)O[C@H]2[C@@H]([C@@H]([C@@]3(COC(=O)C)[C@@H]([C@H]([C@@H]4[C@H]([C@@]3([C@@]2(C)O)O[C@@]4(C)COC(=O)c2cccnc12)OC(=O)C)O)OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102317474
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives

*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
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2009.03.042]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.3136/fstr.15.499]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB10.140]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB2010.000-3252]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	root bark;leaves	Huayllabamba-Urquillos, Province of Urabamba, Cusco (Peru); Parque Nacional El Imposible, El Salvador	n.a.	PMID[16038541]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	Tongxiang, China	n.a.	PMID[24621197]
NPO11296	Arthrinium arundinis	Species	Apiosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25626143]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	root bark	Urubamba, Cusco, Peru	n.a.	PMID[25927586]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[28248102]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22409	Cyanostegia microphylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13457	Acacia pachyphloia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16652	Centipeda cunninghami	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19626	Lavandula dentata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21358	Pyrus ussuriensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22593	Graphis rikuzensis	Species	Aclididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20702	Discodermia dissoluta	Species	Theonellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11296	Arthrinium arundinis	Species	Apiosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9876	Isocoma pluriflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20567	Montipora mollis	Species	Acroporidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22006	Maytenus aquifolium	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2217	Valeriana wolgensis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1118	Elymus repens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22806	Euphorbia leuconeura	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22409	Cyanostegia microphylla	Species	Lamiaceae	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 NPC13237 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	328
0.1-0.2	1373
0.2-0.3	3213
0.3-0.4	10437
0.4-0.5	19083
0.5-0.6	5847
0.6-0.7	2056
0.7-0.8	189
0.8-0.85	37
0.85-0.9	41
0.9-0.95	60
0.95-1	33

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 NPC13237 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	222
0.1-0.2	515
0.2-0.3	632
0.3-0.4	1727
0.4-0.5	3200
0.5-0.6	2186
0.6-0.7	636
0.7-0.8	31
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
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