NPASS Compound

Structure

NPC60709 OpenBabel06302215382D 68 76 0 0 1 0 0 0 0 0999 V2000 -3.2369 0.0308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9771 -0.4199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7375 -0.0043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7577 0.8621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0176 1.3128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2571 0.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5170 1.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0378 2.1792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5181 1.2778 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9366 -2.1527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6768 -2.6034 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4158 -2.9840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5449 -1.1812 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4829 -0.5510 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1665 -0.8146 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8943 -0.7302 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6768 -1.3248 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6768 -1.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4900 -2.0219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1665 -2.2087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3908 -3.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7929 -2.2087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7929 -2.5822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4694 -2.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1459 -2.5822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1459 -2.2087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4694 -2.0219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2827 -1.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2827 -1.3248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0408 -1.1381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3644 -1.3248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3644 -1.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0408 -1.8852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0408 -3.6184 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1149 -2.1317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1149 -0.8915 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4694 -1.0013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1433 -0.3885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7929 -0.8146 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3551 -1.3421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6046 -3.0155 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4694 -3.6356 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0763 -1.5255 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4995 -0.3173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8435 0.3296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6838 0.1177 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8475 1.0623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6091 1.3820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7132 2.2019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3560 2.4716 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0556 2.7017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2935 2.3821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1894 1.5622 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7698 1.7424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0077 1.4227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6499 1.9226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5458 2.7425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2158 3.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8738 2.5623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6359 2.8819 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3035 3.7537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1008 3.1643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1715 0.7123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0381 0.7170 0.0000 O 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 2.3813 3.0736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1434 3.3933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6984 2.9714 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 43 1 0 0 0 0 14 15 1 0 0 0 0 14 65 1 6 0 0 0 15 16 1 0 0 0 0 15 39 1 6 0 0 0 16 17 1 0 0 0 0 16 44 1 6 0 0 0 17 18 1 1 0 0 0 17 43 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 27 2 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 24 42 1 0 0 0 0 25 26 2 0 0 0 0 25 41 1 0 0 0 0 26 27 1 0 0 0 0 26 40 1 0 0 0 0 27 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 37 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 36 1 0 0 0 0 32 33 1 0 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 47 1 0 0 0 0 47 48 2 0 0 0 0 48 49 1 0 0 0 0 49 50 2 0 0 0 0 49 51 1 0 0 0 0 51 52 1 0 0 0 0 51 67 1 0 0 0 0 51 68 1 0 0 0 0 52 60 1 0 0 0 0 52 53 1 0 0 0 0 52 66 1 6 0 0 0 53 47 1 6 0 0 0 53 54 1 0 0 0 0 54 59 2 0 0 0 0 54 55 1 0 0 0 0 55 56 2 0 0 0 0 55 63 1 0 0 0 0 56 57 1 0 0 0 0 57 58 2 0 0 0 0 57 62 1 0 0 0 0 58 59 1 0 0 0 0 58 61 1 0 0 0 0 59 60 1 0 0 0 0 63 64 2 0 0 0 0 63 65 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	952.08
Volume:	827.927
LogP:	1.548
LogD:	0.305
LogS:	-1.993
# Rotatable Bonds:	3
TPSA:	450.25
# H-Bond Aceptor:	27
# H-Bond Donor:	14
# Rings:	9
# Heavy Atoms:	27

MedChem Properties

QED Drug-Likeness Score:	0.05
Synthetic Accessibility Score:	7.344
Fsp3:	0.22
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-7.095
MDCK Permeability:	1.1452891158114653e-05
Pgp-inhibitor:	0.184
Pgp-substrate:	0.033
Human Intestinal Absorption (HIA):	0.999
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	82.44171905517578%
Volume Distribution (VD):	0.393
Pgp-substrate:	39.436988830566406%

ADMET: Metabolism

CYP1A2-inhibitor:	0.044
CYP1A2-substrate:	0.004
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.023
CYP2C9-inhibitor:	0.476
CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.019
CYP3A4-substrate:	0.036

ADMET: Excretion

Clearance (CL):	4.088
Half-life (T1/2):	0.877

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.081
Drug-inuced Liver Injury (DILI):	0.996
AMES Toxicity:	0.179
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.847
Carcinogencity:	0.012
Eye Corrosion:	0.003
Eye Irritation:	0.864
Respiratory Toxicity:	0.005

Download Data

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

Natural Product: NPC60709

Natural Product ID:	NPC60709
*Common Name:**	WTKZYPVTAXZSEM-SDKOXTSWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WTKZYPVTAXZSEM-SDKOXTSWSA-N
Standard InCHI:	InChI=1S/C41H28O27/c42-13-1-8(2-14(43)24(13)48)34(54)67-39-33-32-30(64-38(58)12-6-19(47)40(59,60)41(61)23(12)22-11(37(57)66-33)5-17(46)27(51)31(22)68-41)18(63-39)7-62-35(55)9-3-15(44)25(49)28(52)20(9)21-10(36(56)65-32)4-16(45)26(50)29(21)53/h1-6,18,23,30,32-33,39,42-46,48-53,59-61H,7H2/t18-,23-,30-,32+,33-,39+,41-/m1/s1
SMILES:	c1c(cc(c(c1O)O)O)C(=O)O[C@H]1[C@H]2[C@@H]3[C@@H]([C@@H](COC(=O)c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O3)O)O)O)O1)OC(=O)C1=CC(=O)C([C@]3([C@H]1c1c(cc(c(c1O3)O)O)C(=O)O2)O)(O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO10810	Acridocarpus vivy	Species	Malpighiaceae	Eukaryota	n.a.	Madagascar rain forest	n.a.	PMID[15217279]
NPO16699	Agave utahensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19645463]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO995	Uncaria donisii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO995	Uncaria donisii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12475	Syneilesis palmata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11633	Kelletia kelletii	Species	Buccinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24896	Dinophysis acuminata	Species	Dinophysiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10884	Glycyrrhiza squamulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16699	Agave utahensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO995	Uncaria donisii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16775	Thermopsis lanceolata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16207	Acacia glaucescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11429	Matricaria parthenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14435	Mnium hornum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12765	Micromonospora inositola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7720	Cyathocline purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13047	Epipolasis kushimotoensis	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12393	Xanthoparmelia subincerta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8606	Mallotus repandus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16102	Senecio chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12218	Pulicaria wightiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15984	Blainvillea rhomboidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10810	Acridocarpus vivy	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13938	Plantago alpina	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11453	Centaurea cadmea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27015	Valeriana hardwickii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12475	Syneilesis palmata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4754	Yucca flexilis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO642	Artemisia bigelovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15300	Bipolaris zeicola	Species	Pleosporaceae	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 NPC60709 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	455
0.1-0.2	1866
0.2-0.3	3942
0.3-0.4	8841
0.4-0.5	9203
0.5-0.6	4795
0.6-0.7	6076
0.7-0.8	5985
0.8-0.85	1006
0.85-0.9	461
0.9-0.95	64
0.95-1	3

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 NPC60709 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	387
0.1-0.2	974
0.2-0.3	2064
0.3-0.4	2682
0.4-0.5	1835
0.5-0.6	803
0.6-0.7	277
0.7-0.8	106
0.8-0.85	15
0.85-0.9	7
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