NPASS Compound

Structure

NPC282298 OpenBabel06302215402D 24 25 0 0 1 0 0 0 0 0999 V2000 -1.7321 2.0000 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 2.0000 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 -2.5981 3.5000 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 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 O 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 -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 -0.8660 0.5000 0.0000 C 0 0 3 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 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 3 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 0.0000 -1.0000 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 0.5000 2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.8660 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 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 18 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 21 1 0 0 0 0 15 24 1 6 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 20 1 0 0 0 0 18 19 1 6 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.37
Volume:	537.758
LogP:	6.193
LogD:	5.305
LogS:	-5.597
# Rotatable Bonds:	6
TPSA:	63.6
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.339
Synthetic Accessibility Score:	4.839
Fsp3:	0.871
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.011
MDCK Permeability:	1.9433342458796687e-05
Pgp-inhibitor:	0.868
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.98
30% Bioavailability (F30%):	0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.426
Plasma Protein Binding (PPB):	92.45789337158203%
Volume Distribution (VD):	1.072
Pgp-substrate:	2.5057387351989746%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.439
CYP2C19-inhibitor:	0.204
CYP2C19-substrate:	0.945
CYP2C9-inhibitor:	0.315
CYP2C9-substrate:	0.705
CYP2D6-inhibitor:	0.06
CYP2D6-substrate:	0.704
CYP3A4-inhibitor:	0.693
CYP3A4-substrate:	0.278

ADMET: Excretion

Clearance (CL):	6.288
Half-life (T1/2):	0.089

ADMET: Toxicity

hERG Blockers:	0.071
Human Hepatotoxicity (H-HT):	0.6
Drug-inuced Liver Injury (DILI):	0.035
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.077
Maximum Recommended Daily Dose:	0.342
Skin Sensitization:	0.717
Carcinogencity:	0.135
Eye Corrosion:	0.141
Eye Irritation:	0.232
Respiratory Toxicity:	0.963

Download Data

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

Natural Product: NPC282298

Natural Product ID:	NPC282298
*Common Name:**	LDPLFHGGZNSKDS-HDOXWXFPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LDPLFHGGZNSKDS-HDOXWXFPSA-N
Standard InCHI:	InChI=1S/C14H16O10/c15-6-1-5(2-7(16)10(6)18)12(20)24-9-4-14(23,13(21)22)3-8(17)11(9)19/h1-2,8-9,11,15-19,23H,3-4H2,(H,21,22)/t8?,9?,11-,14+/m0/s1
SMILES:	c1c(cc(c(c1O)O)O)C(=O)OC1C[C@](CC([C@@H]1O)O)(C(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	460894
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001292] Cyclic alcohols and derivatives [CHEMONTID:0002509] Cyclitols and derivatives [CHEMONTID:0002512] Quinic acids and derivatives

*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
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Shanxi province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Anhui province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Gansu province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Henan province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Shandong province, China		DOI[10.1016/j.foodres.2020.109416]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	DOI[10.2174/092986712800229032]
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]
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]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19402674]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[19721258]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[19772486]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[20806783]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[21782011]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[22190295]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[26838074]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[27313650]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[27429639]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29741372]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	HeZe, ShanDong, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32951423]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Xinjiang,China		PMID[33063333]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	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
NPO10339	NPC282298	n.a.	Fruits	0.05	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]

☑ 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 NPC282298 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	339
0.1-0.2	1435
0.2-0.3	3732
0.3-0.4	8228
0.4-0.5	9887
0.5-0.6	4600
0.6-0.7	6894
0.7-0.8	6970
0.8-0.85	440
0.85-0.9	98
0.9-0.95	65
0.95-1	9

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 NPC282298 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	293
0.1-0.2	849
0.2-0.3	1929
0.3-0.4	2725
0.4-0.5	1902
0.5-0.6	956
0.6-0.7	400
0.7-0.8	90
0.8-0.85	4
0.85-0.9	1
0.9-0.95	1
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