NPASS Compound

Structure

NPC146122 OpenBabel06302215172D 51 55 0 0 1 0 0 0 0 0999 V2000 5.9099 -3.3481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9887 -3.0081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1723 -3.5535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1777 -4.5354 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4134 -5.1518 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4550 -4.9386 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7444 -5.8768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8782 -5.4481 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1203 -5.3148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7519 -4.6392 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0504 -3.9299 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8698 -2.9648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7318 -2.4947 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4452 -3.1693 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0241 -4.0563 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4013 -2.9456 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7412 -2.0244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7223 -2.0631 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3303 -1.2921 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9665 -0.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5745 0.3909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9948 -0.2391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5510 -3.4365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0600 -4.2868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0419 -4.2868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8503 -2.4547 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8503 -1.4728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7006 -0.9819 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8503 -1.4728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7006 -0.9819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7006 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8503 0.4909 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 0.1005 -4.1783 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5896 -3.4799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3299 -2.5331 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5395 -3.7284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2288 -4.6886 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1446 -6.3931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4594 -7.0964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5078 -6.8546 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7258 -8.0414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6372 -6.1078 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5770 -6.3920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2931 -5.7203 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8007 -7.3481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0646 -4.9565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8728 -4.3990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7941 -3.4203 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7598 -4.8201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 1 0 0 0 0 2 3 2 0 0 0 0 3 16 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 48 1 0 0 0 0 5 6 1 0 0 0 0 5 44 1 0 0 0 0 6 15 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 39 1 0 0 0 0 11 15 1 0 0 0 0 11 12 1 0 0 0 0 11 35 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 23 1 1 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 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 48 49 1 0 0 0 0 49 50 2 0 0 0 0 49 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	714.29
Volume:	702.424
LogP:	2.905
LogD:	1.744
LogS:	-4.506
# Rotatable Bonds:	14
TPSA:	187.26
# H-Bond Aceptor:	14
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.235
Synthetic Accessibility Score:	5.409
Fsp3:	0.622
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:	-5.346
MDCK Permeability:	0.0001329547812929377
Pgp-inhibitor:	1.0
Pgp-substrate:	0.974
Human Intestinal Absorption (HIA):	0.689
20% Bioavailability (F20%):	0.969
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.205
Plasma Protein Binding (PPB):	41.22148895263672%
Volume Distribution (VD):	1.673
Pgp-substrate:	25.79677391052246%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.011
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.052
CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.186
CYP2D6-substrate:	0.028
CYP3A4-inhibitor:	0.331
CYP3A4-substrate:	0.348

ADMET: Excretion

Clearance (CL):	2.976
Half-life (T1/2):	0.186

ADMET: Toxicity

hERG Blockers:	0.08
Human Hepatotoxicity (H-HT):	0.977
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.536
Rat Oral Acute Toxicity:	0.81
Maximum Recommended Daily Dose:	0.213
Skin Sensitization:	0.423
Carcinogencity:	0.06
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.952

Download Data

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

Natural Product: NPC146122

Natural Product ID:	NPC146122
*Common Name:**	GPIUIJXTLDGVBC-VSSVXZEDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GPIUIJXTLDGVBC-VSSVXZEDSA-N
Standard InCHI:	InChI=1S/C37H46O14/c1-18-25(46-19(2)38)16-36(34(7,8)51-33(44)24-13-11-10-12-14-24)28(18)29(48-21(4)40)31(49-22(5)41)35(9)27(47-20(3)39)15-26(43)37(50-23(6)42)17-45-32(36)30(35)37/h10-14,25-27,29-32,43H,15-17H2,1-9H3/t25-,26-,27-,29+,30-,31-,32+,35-,36+,37-/m1/s1
SMILES:	CC1=C2[C@@H]([C@H]([C@]3(C)[C@@H](C[C@H]([C@@]4(CO[C@@H]([C@H]34)[C@@]2(C[C@H]1OC(=O)C)C(C)(C)OC(=O)c1ccccc1)OC(=O)C)O)OC(=O)C)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002967] Hexacarboxylic acids 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
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[11473432]
NPO25366	Sapium indicum	Species	Euphorbiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[12713411]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124776]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	bark	n.a.	n.a.	PMID[17907781]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18804027]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	bark	n.a.	n.a.	PMID[19646881]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20233596]
NPO25054	Phaleria macrocarpa	Species	Thymelaeaceae	Eukaryota	nut shell	n.a.	n.a.	PMID[23044367]
NPO25252	Nannocystis exedens	Species	Nannocystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24460410]
NPO25311	Guettarda platypoda	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2553871]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32058711]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8557595]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[8991951]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9644081]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24852	Helicia nilagirica	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22283	Alhagi maurorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25492	Botryllus leachi	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22283	Alhagi maurorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18706	Anemone thalictroides	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24373	Lobelia inflata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23994	Ormosia macrophylla	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23894	Pulicaria insignis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25054	Phaleria macrocarpa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14189	Osmundaria spiralis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25311	Guettarda platypoda	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22618	Psolus eximius	Species	Psolidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25366	Sapium indicum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24461	Clusia sandiensis	Species	Clusiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24852	Helicia nilagirica	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24607	Goniothalamus dolichocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3721	Achyranthes obtusifolia	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24278	Pistacia chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24882	Erythrophleum chlorostachys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6645.1	Picea jezoensis var. jezoensis	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27390	Vernonia brevifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24802	Diploprion bifasciatum	Species	Serranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25252	Nannocystis exedens	Species	Nannocystaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO24730	Lactarius deliciosus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25277	Seiridium cupressi	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25441	Desmodium pulchellu	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20264	Moonia heterophylla	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23788	Beauveria bassiana	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28460	Achyrocline tomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22152	Tecoma undulata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15482	Vanderbylia fraxinea	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25389	Allium angulosum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25466	Lecanora sulphurella	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24566	Marasmiellus ramealis	Species	Omphalotaceae	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 NPC146122 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	280
0.1-0.2	1040
0.2-0.3	2302
0.3-0.4	4555
0.4-0.5	9314
0.5-0.6	12691
0.6-0.7	10813
0.7-0.8	1283
0.8-0.85	214
0.85-0.9	167
0.9-0.95	36
0.95-1	2

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 NPC146122 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	227
0.1-0.2	692
0.2-0.3	1514
0.3-0.4	2861
0.4-0.5	2313
0.5-0.6	1185
0.6-0.7	340
0.7-0.8	18
0.8-0.85	0
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