NPASS Compound

Structure

NPC93211 OpenBabel06302216212D 53 57 0 0 1 0 0 0 0 0999 V2000 8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 C 0 0 1 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 6.9282 -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 2 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 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 5.1962 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 4.5000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 2.5000 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 4.3301 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 6.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 O 0 0 0 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 3.4641 1.0000 0.0000 O 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 2.5981 2.5000 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 1.7321 -0.0000 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 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 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 53 1 6 0 0 0 4 5 1 0 0 0 0 4 52 1 1 0 0 0 5 6 1 0 0 0 0 5 51 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 36 1 0 0 0 0 10 11 1 0 0 0 0 10 50 1 6 0 0 0 11 12 1 1 0 0 0 11 23 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 24 36 1 0 0 0 0 25 26 1 0 0 0 0 27 26 1 6 0 0 0 27 28 1 0 0 0 0 27 32 1 0 0 0 0 28 29 1 0 0 0 0 28 35 1 1 0 0 0 29 30 1 0 0 0 0 29 34 1 6 0 0 0 30 31 1 0 0 0 0 30 33 1 1 0 0 0 31 32 1 0 0 0 0 36 37 1 6 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 47 2 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 49 1 0 0 0 0 46 47 1 0 0 0 0 46 48 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	756.25
Volume:	699.76
LogP:	-0.24
LogD:	-0.277
LogS:	-2.4
# Rotatable Bonds:	13
TPSA:	304.21
# H-Bond Aceptor:	19
# H-Bond Donor:	11
# Rings:	5
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.06
Synthetic Accessibility Score:	5.321
Fsp3:	0.559
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.682
MDCK Permeability:	4.481471114559099e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.994
20% Bioavailability (F20%):	0.882
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.119
Plasma Protein Binding (PPB):	92.80113983154297%
Volume Distribution (VD):	0.115
Pgp-substrate:	9.729077339172363%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.013
CYP2C19-inhibitor:	0.047
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.056
CYP2C9-substrate:	0.08
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.126
CYP3A4-inhibitor:	0.025
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	0.403
Half-life (T1/2):	0.696

ADMET: Toxicity

hERG Blockers:	0.245
Human Hepatotoxicity (H-HT):	0.505
Drug-inuced Liver Injury (DILI):	0.691
AMES Toxicity:	0.431
Rat Oral Acute Toxicity:	0.085
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.977
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.038
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC93211

Natural Product ID:	NPC93211
*Common Name:**	XPLMUADTACCMDJ-UVQMCPPLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XPLMUADTACCMDJ-UVQMCPPLSA-N
Standard InCHI:	InChI=1S/C34H44O19/c1-14-24(41)26(43)28(45)34(50-14)53-31-29(46)33(47-9-8-16-3-6-18(36)20(38)11-16)51-22(13-49-32-27(44)25(42)21(39)12-48-32)30(31)52-23(40)7-4-15-2-5-17(35)19(37)10-15/h2-7,10-11,14,21-22,24-39,41-46H,8-9,12-13H2,1H3/b7-4+/t14-,21+,22+,24-,25-,26+,27+,28+,29+,30+,31+,32-,33+,34-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](OCCc2ccc(c(c2)O)O)O[C@H](CO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)[C@H]1OC(=O)/C=C/c1ccc(c(c1)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6442994
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

*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
NPO1766	Hymenaea courbaril	Species	Fabaceae	Eukaryota	n.a.	Suriname rain forest	n.a.	PMID[11809056]
NPO19805	Forsythia viridissima	Species	Oleaceae	Eukaryota	n.a.	flower	n.a.	PMID[15481244]
NPO1939	Swartzia langsdorffii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124782]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17156960]
NPO6779	Sutherlandia frutescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18808182]
NPO5985	Klebsiella pneumoniae	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24572278]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26422318]
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26710212]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28218000]
NPO19805	Forsythia viridissima	Species	Oleaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30676026]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19805	Forsythia viridissima	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO77	Brandisia hancei	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19805	Forsythia viridissima	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19805	Forsythia viridissima	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1766	Hymenaea courbaril	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7812	Alhagi persarum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3944	Senecio variabilis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7601	Centaurea cana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO720	Badilloa salicina	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22995	Oophaga histrionica	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6779	Sutherlandia frutescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8175	Acacia kempeana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26373.1	Microbispora rosea subsp. aerata	Subspecies	Streptosporangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2011	Decaisnea fargesii	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2525	Castanopsis cuspidata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1009	Stentor coeruleus	Species	Stentoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1939	Swartzia langsdorffii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8476	Teucrium lanigerum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3828	Cereus pachanoi	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8312	Polygonatum stenophyllum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15817	Alternaria scirpicola	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12103	Salvia ballotiflora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5985	Klebsiella pneumoniae	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5039	Cryptomonas ovata	Species	Cryptomonadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2366	Diospyros buxifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5235	Laburnum watereri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6979	Baillonella toxisperma	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4644	Pteris pacifica	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO850	Metatrichia vesparium	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4096	Acanthias vulgaris	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2218	Aframomum sulcatum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25577	Samuela carnerosana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO77	Brandisia hancei	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3672	Montanoa guatemalensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21387	Forsythia suspensa	Species	Oleaceae	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 NPC93211 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	318
0.1-0.2	1362
0.2-0.3	3207
0.3-0.4	7796
0.4-0.5	9586
0.5-0.6	9041
0.6-0.7	8058
0.7-0.8	2958
0.8-0.85	216
0.85-0.9	86
0.9-0.95	35
0.95-1	34

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 NPC93211 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	270
0.1-0.2	794
0.2-0.3	1675
0.3-0.4	3046
0.4-0.5	1922
0.5-0.6	1111
0.6-0.7	299
0.7-0.8	32
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