NPASS Compound

Structure

NPC32368 OpenBabel06302215172D 43 47 0 0 1 0 0 0 0 0999 V2000 6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 5.5000 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 6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 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 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 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 1.0000 0.0000 C 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 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 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 1.0000 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 -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 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 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 3.4641 -3.0000 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 7.0000 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 3 4 1 0 0 0 0 3 43 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 42 1 1 0 0 0 15 16 1 0 0 0 0 15 41 1 0 0 0 0 16 17 1 0 0 0 0 16 40 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 6 0 0 0 19 20 1 0 0 0 0 20 30 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 39 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 38 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 36 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 34 35 2 0 0 0 0 34 37 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	594.14
Volume:	564.653
LogP:	2.894
LogD:	2.358
LogS:	-4.493
# Rotatable Bonds:	8
TPSA:	216.58
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.12
Synthetic Accessibility Score:	4.151
Fsp3:	0.2
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:	-6.173
MDCK Permeability:	1.1368038030923344e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.527
Human Intestinal Absorption (HIA):	0.129
20% Bioavailability (F20%):	0.12
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	99.71749114990234%
Volume Distribution (VD):	0.603
Pgp-substrate:	2.8302102088928223%

ADMET: Metabolism

CYP1A2-inhibitor:	0.382
CYP1A2-substrate:	0.024
CYP2C19-inhibitor:	0.276
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.689
CYP2C9-substrate:	0.924
CYP2D6-inhibitor:	0.734
CYP2D6-substrate:	0.234
CYP3A4-inhibitor:	0.575
CYP3A4-substrate:	0.046

ADMET: Excretion

Clearance (CL):	4.401
Half-life (T1/2):	0.818

ADMET: Toxicity

hERG Blockers:	0.136
Human Hepatotoxicity (H-HT):	0.12
Drug-inuced Liver Injury (DILI):	0.976
AMES Toxicity:	0.767
Rat Oral Acute Toxicity:	0.104
Maximum Recommended Daily Dose:	0.04
Skin Sensitization:	0.913
Carcinogencity:	0.258
Eye Corrosion:	0.003
Eye Irritation:	0.061
Respiratory Toxicity:	0.013

Download Data

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

Natural Product: NPC32368

Natural Product ID:	NPC32368
*Common Name:**	DVGGLGXQSFURLP-PGMOAVLWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DVGGLGXQSFURLP-PGMOAVLWSA-N
Standard InCHI:	InChI=1S/C30H26O13/c31-16-6-1-14(2-7-16)3-10-22(35)40-13-21-24(36)26(38)27(39)30(42-21)43-29-25(37)23-19(34)11-18(33)12-20(23)41-28(29)15-4-8-17(32)9-5-15/h1-12,21,24,26-27,30-34,36,38-39H,13H2/b10-3+/t21-,24-,26?,27?,30+/m1/s1
SMILES:	c1cc(ccc1/C=C/C(=O)OC[C@@H]1[C@H](C(C([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(cc1)O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44258863
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003678] Flavonoid 3-O-p-coumaroyl 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
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	Suwon, Korea	2012-Nov	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves	Suwon, Korea		DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Runners	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO25148	Helichrysum italicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11678669]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1453178]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[15568772]
NPO30707	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724855]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[21381697]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[22703163]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO25148	Helichrysum italicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24094434]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[24328283]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	Flowers	Muyang, China	n.a.	PMID[24621197]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[24704554]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32935986]
NPO19774	Rubus idaeus	Species	n.a.	n.a.		n.a.	n.a.	Database[FooDB]
NPO30072	Chamerion angustifolium	Species	n.a.	n.a.		n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruit	n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruits	n.a.		Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Leaf	n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Seed	n.a.	n.a.	Database[FooDB]
NPO31266	Fragaria ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO28301	Clerodendron cyrtophyllum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO25148	Helichrysum italicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30707	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30072	Chamerion angustifolium	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruits	n.a.		Database[Phenol-Explorer]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.		Database[Phenol-Explorer]
NPO8279	Chamerion angustifolium	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25148	Helichrysum italicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO28301	Clerodendron cyrtophyllum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30707	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23548	Leonurus heterophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8279	Chamerion angustifolium	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO25148	Helichrysum italicum	Species	Asteraceae	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 NPC32368 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	420
0.1-0.2	1733
0.2-0.3	4195
0.3-0.4	9315
0.4-0.5	8920
0.5-0.6	4708
0.6-0.7	5692
0.7-0.8	5242
0.8-0.85	1492
0.85-0.9	506
0.9-0.95	373
0.95-1	101

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 NPC32368 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	374
0.1-0.2	931
0.2-0.3	1921
0.3-0.4	2695
0.4-0.5	1895
0.5-0.6	908
0.6-0.7	271
0.7-0.8	116
0.8-0.85	22
0.85-0.9	11
0.9-0.95	6
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