NPASS Compound

Structure

NPC250311 OpenBabel06302215342D 51 56 0 0 1 0 0 0 0 0999 V2000 1.8838 -4.1945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6270 -3.5254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4190 -2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4680 -2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2601 -1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0032 -0.5909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9543 -0.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1622 -1.8781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6974 -0.2308 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3090 -0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5000 -1.5388 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5000 -2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 -3.0388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2872 -1.1590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9563 -0.4158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9344 -0.6237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2435 -1.5748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2216 -1.7827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8907 -1.0396 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5306 -2.7338 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5088 -2.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8178 -3.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2300 -4.7017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8178 -5.5108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7688 -5.2017 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.6349 -5.7017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 -5.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 -4.2017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6349 -3.7017 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7688 -4.2017 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.6349 -2.7017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 -2.2017 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.3669 -2.7017 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.2329 -2.2017 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.2329 -1.2017 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.3669 -0.7017 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.3669 0.2983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 0.7983 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 -1.2017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.0990 -0.7017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.0990 -2.7017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3669 -3.7017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6349 -6.7017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5009 -7.2017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7688 -7.2017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6473 0.5352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6691 0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3601 1.6942 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 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 10 5 1 1 0 0 0 10 11 1 0 0 0 0 10 50 1 0 0 0 0 11 12 1 6 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 49 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 47 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 26 31 1 0 0 0 0 27 28 2 0 0 0 0 27 44 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 30 32 1 1 0 0 0 31 23 1 6 0 0 0 33 32 1 1 0 0 0 33 34 1 0 0 0 0 33 40 1 0 0 0 0 34 35 1 0 0 0 0 34 43 1 6 0 0 0 35 36 1 0 0 0 0 35 42 1 1 0 0 0 36 37 1 0 0 0 0 36 41 1 6 0 0 0 37 38 1 1 0 0 0 37 40 1 0 0 0 0 38 39 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 47 48 2 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:	714.22
Volume:	674.22
LogP:	1.146
LogD:	0.793
LogS:	-3.789
# Rotatable Bonds:	12
TPSA:	251.36
# H-Bond Aceptor:	16
# H-Bond Donor:	8
# Rings:	6
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.09
Synthetic Accessibility Score:	5.389
Fsp3:	0.429
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.293
MDCK Permeability:	3.230400398024358e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.76
20% Bioavailability (F20%):	0.031
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.105
Plasma Protein Binding (PPB):	75.82465362548828%
Volume Distribution (VD):	0.389
Pgp-substrate:	18.52806282043457%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.028
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.05
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.134
CYP2D6-inhibitor:	0.031
CYP2D6-substrate:	0.1
CYP3A4-inhibitor:	0.627
CYP3A4-substrate:	0.128

ADMET: Excretion

Clearance (CL):	1.453
Half-life (T1/2):	0.905

ADMET: Toxicity

hERG Blockers:	0.058
Human Hepatotoxicity (H-HT):	0.185
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.166
Rat Oral Acute Toxicity:	0.087
Maximum Recommended Daily Dose:	0.919
Skin Sensitization:	0.114
Carcinogencity:	0.942
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.735

Download Data

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

Natural Product: NPC250311

Natural Product ID:	NPC250311
*Common Name:**	WJIBQUKBEVAHAF-YIGWBOCFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WJIBQUKBEVAHAF-YIGWBOCFSA-N
Standard InCHI:	InChI=1S/C35H38O16/c1-46-19-9-17(8-18(38)10-19)31-22(11-36)21-6-15(7-24(39)32(21)50-31)2-5-26(40)47-13-16-3-4-20-23(33(44)45)14-48-34(27(16)20)51-35-30(43)29(42)28(41)25(12-37)49-35/h2-3,5-10,14,20,22,25,27-31,34-39,41-43H,4,11-13H2,1H3,(H,44,45)/b5-2+/t20-,22-,25-,27-,28-,29+,30-,31+,34+,35+/m1/s1
SMILES:	COc1cc(cc(c1)O)[C@H]1[C@H](CO)c2cc(/C=C/C(=O)OCC3=CC[C@@H]4C(=CO[C@H]([C@H]34)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)C(=O)O)cc(c2O1)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

*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
NPO17605	Adenaria floribunda	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043429]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22209460]
NPO4617	Tanacetum cinerariifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24253739]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29328	Genista tinctoria	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29328	Genista tinctoria	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4617	Tanacetum cinerariifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28860	Saprosma scortechinii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29122	Scyphiphora hydrophyllacea	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28580	Tetragonia tetragonioides	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29291	Diplopappus fruticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29328	Genista tinctoria	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29527	Stemonoporus affinis	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17605	Adenaria floribunda	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4617	Tanacetum cinerariifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28860	Saprosma scortechinii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29448	Centaurea thessala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12447	Plagiochila yokogurensis	Species	Plagiochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29077	Marsupella emarginata	Species	Gymnomitriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29197	Mimosa hostilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29342	Astraeus hygrometricus	Species	Astraeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22440	Arctanthemum arcticum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28914	Caragana sinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29186	Nardosmia laevigata	n.a.	n.a.	n.a.	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 NPC250311 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	368
0.1-0.2	1470
0.2-0.3	3215
0.3-0.4	7480
0.4-0.5	9914
0.5-0.6	5546
0.6-0.7	5844
0.7-0.8	7260
0.8-0.85	1439
0.85-0.9	154
0.9-0.95	7
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 NPC250311 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	317
0.1-0.2	872
0.2-0.3	1799
0.3-0.4	2680
0.4-0.5	1906
0.5-0.6	985
0.6-0.7	461
0.7-0.8	110
0.8-0.85	18
0.85-0.9	2
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