NPASS Compound

Structure

NPC137780 OpenBabel06302215222D 42 47 0 0 1 0 0 0 0 0999 V2000 1.6960 -0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 -1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 -2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 -2.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9792 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8480 -1.4687 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6960 -0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6960 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5439 0.4896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5439 1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6960 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 2.4479 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8480 3.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 5.3854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 4.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 3.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 3.4271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 2.4479 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3919 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 0.4896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3919 0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 -0.4896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9359 0.4896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 1.9583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6960 0.9792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 6.3646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 3.4271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 0.4896 0.0000 C 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 -1.6960 2.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3919 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 -2.4479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 -3.9167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3919 -2.9375 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 42 1 0 0 0 0 4 5 2 0 0 0 0 4 41 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 37 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 1 0 0 0 9 10 1 0 0 0 0 10 36 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 39 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 38 1 0 0 0 0 14 36 1 0 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 15 32 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 32 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 6 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	578.14
Volume:	549.942
LogP:	2.298
LogD:	1.615
LogS:	-4.674
# Rotatable Bonds:	3
TPSA:	220.76
# H-Bond Aceptor:	12
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.159
Synthetic Accessibility Score:	4.519
Fsp3:	0.2
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.846
MDCK Permeability:	4.587209787132451e-06
Pgp-inhibitor:	0.057
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.932
20% Bioavailability (F20%):	0.988
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	89.0903091430664%
Volume Distribution (VD):	0.399
Pgp-substrate:	9.188642501831055%

ADMET: Metabolism

CYP1A2-inhibitor:	0.035
CYP1A2-substrate:	0.111
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.673
CYP2C9-substrate:	0.932
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.217
CYP3A4-inhibitor:	0.085
CYP3A4-substrate:	0.238

ADMET: Excretion

Clearance (CL):	14.334
Half-life (T1/2):	0.753

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.144
Drug-inuced Liver Injury (DILI):	0.816
AMES Toxicity:	0.337
Rat Oral Acute Toxicity:	0.462
Maximum Recommended Daily Dose:	0.793
Skin Sensitization:	0.965
Carcinogencity:	0.037
Eye Corrosion:	0.003
Eye Irritation:	0.91
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC137780

Natural Product ID:	NPC137780
*Common Name:**	XFZJEEAOWLFHDH-DQPHOHOGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XFZJEEAOWLFHDH-DQPHOHOGSA-N
Standard InCHI:	InChI=1S/C30H26O12/c31-13-7-20(37)24-23(8-13)41-29(12-2-4-16(33)19(36)6-12)27(40)26(24)25-21(38)10-17(34)14-9-22(39)28(42-30(14)25)11-1-3-15(32)18(35)5-11/h1-8,10,22,26-29,31-40H,9H2/t22-,26+,27+,28-,29+/m0/s1
SMILES:	c1cc(c(cc1[C@H]1[C@H](Cc2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4ccc(c(c4)O)O)[C@@H]3O)O)O)c2O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	442677
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	Nigeria(latitude 80°N and longitude 4°E)	2005; 2006	DOI[10.1002/ejlt.201000080]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11306-010-0259-y]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11306-014-0638-x]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytol.2008.07.007]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seeds	Plovdiv, Plovdiv region in South Bulgaria		DOI[10.1051/CTV/20163101031]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170689]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11312782]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11312782]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11408943]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12105962]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete	2007	PMID[19256538]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20826702]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23759170]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Stalks	n.a.	n.a.	PMID[24521157]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seeds	Benedictine Pannonhalma Archabbey, Hungary		PMID[29803478]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31433178]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Leaf Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8561	Liparis loeselii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9505	Magnolia pterocarpa	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27966	Stigmatella erecta	Species	Archangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6863	Dendrobates azureus	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17165	Teucrium heterophyllum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO870	Aglaia tsangii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8561	Liparis loeselii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16080	Cedrela fissilis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13761	Plexaurella nutans	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16781	Dorycnium suffruticosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17525	Baccharis sagittalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26159	Pseudocyphellaria faveolata	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17773	Senecio ambraceus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14281	Anaxagorea dolichocarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4024	Pedicularis procera	Species	Orobanchaceae	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 NPC137780 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	540
0.1-0.2	1744
0.2-0.3	4830
0.3-0.4	11566
0.4-0.5	6377
0.5-0.6	4254
0.6-0.7	6403
0.7-0.8	5525
0.8-0.85	875
0.85-0.9	446
0.9-0.95	101
0.95-1	36

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 NPC137780 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	441
0.1-0.2	880
0.2-0.3	2029
0.3-0.4	2681
0.4-0.5	1562
0.5-0.6	865
0.6-0.7	569
0.7-0.8	111
0.8-0.85	7
0.85-0.9	3
0.9-0.95	2
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