NPASS Compound

Structure

NPC290315 OpenBabel06302215552D 39 42 0 0 1 0 0 0 0 0999 V2000 1.0312 -4.1883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0257 -4.0837 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4325 -3.1702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8447 -2.3612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2514 -1.4476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2460 -1.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8337 -2.1521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4270 -3.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0148 -3.8747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6637 -0.6386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6691 -0.7431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1691 -1.6092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -1.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 -0.4067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7796 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 -0.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7796 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 2.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 3.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 1.0933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1097 1.5933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9757 1.0933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9757 0.0933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1097 -0.4067 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1097 -1.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9757 -1.9067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 0.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8417 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8417 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1097 2.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 -1.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2079 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5352 1.6473 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 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 37 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 37 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 17 35 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 24 31 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 6 0 0 0 26 27 1 0 0 0 0 26 33 1 1 0 0 0 27 28 1 0 0 0 0 27 32 1 6 0 0 0 28 29 1 1 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 6 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	552.22
Volume:	530.986
LogP:	0.789
LogD:	0.974
LogS:	-2.897
# Rotatable Bonds:	10
TPSA:	176.76
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.235
Synthetic Accessibility Score:	4.411
Fsp3:	0.556
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:	-6.256
MDCK Permeability:	2.4945555196609348e-05
Pgp-inhibitor:	0.016
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.49
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.057

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.216
Plasma Protein Binding (PPB):	59.57222366333008%
Volume Distribution (VD):	0.433
Pgp-substrate:	27.782546997070312%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.348
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.786
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.431
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.31
CYP3A4-inhibitor:	0.082
CYP3A4-substrate:	0.294

ADMET: Excretion

Clearance (CL):	6.504
Half-life (T1/2):	0.826

ADMET: Toxicity

hERG Blockers:	0.259
Human Hepatotoxicity (H-HT):	0.179
Drug-inuced Liver Injury (DILI):	0.098
AMES Toxicity:	0.167
Rat Oral Acute Toxicity:	0.024
Maximum Recommended Daily Dose:	0.041
Skin Sensitization:	0.912
Carcinogencity:	0.107
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.034

Download Data

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

Natural Product: NPC290315

Natural Product ID:	NPC290315
*Common Name:**	QZZFPPFAVZPABT-XJPCFIILSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QZZFPPFAVZPABT-XJPCFIILSA-N
Standard InCHI:	InChI=1S/C27H36O12/c1-34-18-7-13(4-5-17(18)30)6-15-12-37-25(16(15)10-28)14-8-19(35-2)26(20(9-14)36-3)39-27-24(33)23(32)22(31)21(11-29)38-27/h4-5,7-9,15-16,21-25,27-33H,6,10-12H2,1-3H3/t15-,16-,21+,22+,23-,24+,25+,27-/m1/s1
SMILES:	COc1cc(ccc1O)C[C@@H]1CO[C@@H](c2cc(c(c(c2)OC)O[C@@H]2[C@H]([C@@H]([C@H]([C@H](CO)O2)O)O)O)OC)[C@@H]1CO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan 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
NPO683	Rosa canina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880322]
NPO7267	Glycosmis chlorosperma	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24798019]
NPO683	Rosa canina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7267	Glycosmis chlorosperma	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10398	Myrica gale	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO683	Rosa canina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8340	Stachys sylvatica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10398	Myrica gale	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO683	Rosa canina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6760	Saussurea conica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO683	Rosa canina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8340	Stachys sylvatica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7267	Glycosmis chlorosperma	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10398	Myrica gale	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19459	Dictyota kunthii	Species	Dictyotaceae	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 NPC290315 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	426
0.1-0.2	1437
0.2-0.3	3700
0.3-0.4	9606
0.4-0.5	9188
0.5-0.6	5200
0.6-0.7	7611
0.7-0.8	4123
0.8-0.85	889
0.85-0.9	399
0.9-0.95	99
0.95-1	19

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 NPC290315 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	332
0.1-0.2	781
0.2-0.3	1784
0.3-0.4	2857
0.4-0.5	1784
0.5-0.6	1026
0.6-0.7	489
0.7-0.8	88
0.8-0.85	9
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