NPASS Compound

Structure

NPC306611 OpenBabel06302215132D 38 43 0 0 1 0 0 0 0 0999 V2000 -9.1804 1.0090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1806 1.0090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6805 0.1431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3707 0.5414 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.3707 -0.3938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5608 -0.8614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7509 -0.3938 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9589 -0.8502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1554 -0.3928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3516 0.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5417 -0.4029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7318 0.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7318 0.9998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5417 1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3516 0.9998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1435 1.4562 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9473 0.9987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7509 0.5414 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7509 1.5181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5608 1.0090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8290 2.0088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5608 1.9441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3707 2.4117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1806 1.9441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0465 2.4441 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8659 1.4998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9998 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8659 1.4998 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7318 0.9998 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7318 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8659 -0.4999 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8659 -1.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7318 -1.9997 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 2.5977 -0.4999 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4635 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5977 1.4998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8659 2.4996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 24 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 20 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 18 1 0 0 0 0 8 9 1 0 0 0 0 9 17 2 0 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 26 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 27 26 1 1 0 0 0 27 28 1 0 0 0 0 27 34 1 0 0 0 0 28 29 1 0 0 0 0 28 38 1 6 0 0 0 29 30 1 0 0 0 0 29 37 1 1 0 0 0 30 31 1 0 0 0 0 30 35 1 6 0 0 0 31 32 1 1 0 0 0 31 34 1 0 0 0 0 32 33 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	525.27
Volume:	532.807
LogP:	3.686
LogD:	2.906
LogS:	-5.48
# Rotatable Bonds:	4
TPSA:	121.24
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.484
Synthetic Accessibility Score:	4.962
Fsp3:	0.633
Lipinski Rule-of-5:	Accepted
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:	-5.485
MDCK Permeability:	9.561047590977978e-06
Pgp-inhibitor:	0.994
Pgp-substrate:	0.968
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.069

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.146
Plasma Protein Binding (PPB):	90.54268646240234%
Volume Distribution (VD):	1.548
Pgp-substrate:	5.856616497039795%

ADMET: Metabolism

CYP1A2-inhibitor:	0.081
CYP1A2-substrate:	0.759
CYP2C19-inhibitor:	0.028
CYP2C19-substrate:	0.638
CYP2C9-inhibitor:	0.118
CYP2C9-substrate:	0.102
CYP2D6-inhibitor:	0.444
CYP2D6-substrate:	0.09
CYP3A4-inhibitor:	0.842
CYP3A4-substrate:	0.46

ADMET: Excretion

Clearance (CL):	2.261
Half-life (T1/2):	0.132

ADMET: Toxicity

hERG Blockers:	0.862
Human Hepatotoxicity (H-HT):	0.351
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.113
Rat Oral Acute Toxicity:	0.944
Maximum Recommended Daily Dose:	0.934
Skin Sensitization:	0.545
Carcinogencity:	0.878
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC306611

Natural Product ID:	NPC306611
*Common Name:**	QGZCRYRTSBNQGS-FETZOIKWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QGZCRYRTSBNQGS-FETZOIKWSA-N
Standard InCHI:	InChI=1S/C30H39NO7/c1-28(2)21-9-6-15-12-18-17-8-7-16(37-27-24(35)23(34)25(36-5)20(14-32)38-27)13-19(17)31-26(18)30(15,4)29(21,3)11-10-22(28)33/h7-8,10-11,13,15,20-21,23-25,27,31-32,34-35H,6,9,12,14H2,1-5H3/t15-,20-,21-,23-,24-,25-,27-,29+,30-/m1/s1
SMILES:	CC1(C)[C@H]2CC[C@@H]3Cc4c5ccc(cc5[nH]c4[C@]3(C)[C@@]2(C)C=CC1=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	callus	n.a.	PMID[10552648]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18214349]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	seed	n.a.	PMID[21049975]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21800857]
NPO8234	Vernonia galamensis	Species	Asteraceae	Eukaryota	n.a.	seed	n.a.	PMID[9930408]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8620	Caesalpinia major	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24536	Senecio cylindricus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9330	Odinia antillensis	Species	Odiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2389	Pinus japonica	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3668	Kalanchoe delagoensis	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8234	Vernonia galamensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4875	Ugni molinae	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4072	Anacyclus radiatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8771	Heterodermia dissecta	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7188	Zieria granulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9072	Bolocera tuediae	Species	Actiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8009	Arctotis venusta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5540	Amorpha canescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6292	Teucrium brevifolium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5832	Acacia nelsonii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4321	Siphula ceratites	Species	Icmadophilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8620	Caesalpinia major	Species	Fabaceae	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 NPC306611 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	435
0.1-0.2	1729
0.2-0.3	4361
0.3-0.4	11827
0.4-0.5	12705
0.5-0.6	9471
0.6-0.7	1802
0.7-0.8	363
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
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 NPC306611 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	291
0.1-0.2	581
0.2-0.3	738
0.3-0.4	2004
0.4-0.5	2865
0.5-0.6	2078
0.6-0.7	554
0.7-0.8	39
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