NPASS Compound

Structure

NPC226906 OpenBabel06302216022D 29 31 0 0 1 0 0 0 0 0999 V2000 4.3301 0.5000 0.0000 C 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 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -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 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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 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 2.0000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 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 1 2 2 0 0 0 0 1 11 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 7 9 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 1 0 0 0 21 22 1 0 0 0 0 21 28 1 6 0 0 0 22 23 1 0 0 0 0 22 27 1 1 0 0 0 23 24 1 6 0 0 0 23 26 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	406.13
Volume:	389.464
LogP:	0.685
LogD:	0.376
LogS:	-2.665
# Rotatable Bonds:	5
TPSA:	160.07
# H-Bond Aceptor:	9
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.343
Synthetic Accessibility Score:	3.828
Fsp3:	0.3
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.835
MDCK Permeability:	5.218726983002853e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.137
Human Intestinal Absorption (HIA):	0.615
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	92.1587142944336%
Volume Distribution (VD):	0.429
Pgp-substrate:	4.3622727394104%

ADMET: Metabolism

CYP1A2-inhibitor:	0.468
CYP1A2-substrate:	0.03
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.05
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.73
CYP2D6-inhibitor:	0.055
CYP2D6-substrate:	0.204
CYP3A4-inhibitor:	0.83
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	9.288
Half-life (T1/2):	0.839

ADMET: Toxicity

hERG Blockers:	0.228
Human Hepatotoxicity (H-HT):	0.037
Drug-inuced Liver Injury (DILI):	0.197
AMES Toxicity:	0.615
Rat Oral Acute Toxicity:	0.081
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.948
Carcinogencity:	0.116
Eye Corrosion:	0.004
Eye Irritation:	0.563
Respiratory Toxicity:	0.039

Download Data

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

Natural Product: NPC226906

Natural Product ID:	NPC226906
*Common Name:**	OLCVEOSSVCAFGR-FSONJKCJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OLCVEOSSVCAFGR-FSONJKCJSA-N
Standard InCHI:	InChI=1S/C20H22O9/c21-9-16-17(25)18(26)19(27)20(29-16)28-15-4-3-10(7-14(15)24)1-2-11-5-12(22)8-13(23)6-11/h1-8,16-27H,9H2/b2-1+/t16-,17-,18+,19-,20-/m0/s1
SMILES:	C(=Cc1cc(cc(c1)O)O)/c1ccc(c(c1)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes [CHEMONTID:0000142] Stilbene 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
NPO12079	Dysoxylum cumingianum	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1021/jo00051a050]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076555]
NPO14520	Bassia muricata	Species	Chenopodiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[11454355]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11459643]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1517743]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19719093]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22512738]
NPO13237	Teucrium yemense	Species	n.a.	n.a.	Aerial Parts	n.a.	n.a.	PMID[28581290]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8277318]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14014	Eriocheir sinensis	Species	Varunidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15297	Aconitum seravschanicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14014	Eriocheir sinensis	Species	Varunidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14014	Eriocheir sinensis	Species	Varunidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4345	Caulocystis cephalornithos	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2198	Rivularia firma	Species	Rivulariaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13403	Gadus morhua callarias	Species	Gadidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13523	Neobalanocarpus heimii	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11580	Onobrychis arenaria	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16590	Cytophaga hutchinsoni	Species	Cytophagaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13421	Sphaerella laricina	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3214	Lavandula vera	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2631	Aster sedifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14217	Adansonia grandidieri	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12252	Psychotria stachyoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9752	Miliusa velutina	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14014	Eriocheir sinensis	Species	Varunidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7819.1	Epichloe festucae var. lolii	Varieties	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO624	Isaria fumosorosea	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14412	Aphyllocladus denticulatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12079	Dysoxylum cumingianum	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8386	Enceliopsis argophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11749	Eria mollis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10688	Flacourtia jangomas	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO986	Rattus rattus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15297	Aconitum seravschanicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9448	Dictyopteris australis	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13716	Aconitum tasiromontanum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13237	Teucrium yemense	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1501	Senecio subdentatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14520	Bassia muricata	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22526	Justicia secunda	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14104	Dendriopoterium menendezii	Species	Rosaceae	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 NPC226906 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	443
0.1-0.2	1771
0.2-0.3	5465
0.3-0.4	11384
0.4-0.5	6275
0.5-0.6	5260
0.6-0.7	6656
0.7-0.8	4117
0.8-0.85	888
0.85-0.9	324
0.9-0.95	90
0.95-1	24

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 NPC226906 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	360
0.1-0.2	854
0.2-0.3	2098
0.3-0.4	2818
0.4-0.5	1538
0.5-0.6	918
0.6-0.7	480
0.7-0.8	78
0.8-0.85	3
0.85-0.9	3
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