NPASS Compound

Structure

NPC202154 OpenBabel06302215192D 33 36 0 0 1 0 0 0 0 0999 V2000 4.3301 -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 1 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 2 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 -1.5000 0.0000 O 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 1.7321 0.0000 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 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 -0.8660 2.5000 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 -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 -3.4641 -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 0 0 0 0 0 0 0 0 0 0 -4.3301 -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 -2.5981 -1.5000 0.0000 C 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 -0.8660 -0.5000 0.0000 O 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 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 2.5981 -0.5000 0.0000 O 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 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 33 1 6 0 0 0 4 5 1 0 0 0 0 4 32 1 1 0 0 0 5 6 1 0 0 0 0 5 31 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 27 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 30 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 29 1 0 0 0 0 13 27 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 2 0 0 0 0 16 28 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 25 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.15
Volume:	406.709
LogP:	2.19
LogD:	2.541
LogS:	-3.976
# Rotatable Bonds:	6
TPSA:	92.68
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.719
Synthetic Accessibility Score:	3.781
Fsp3:	0.409
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.844
MDCK Permeability:	4.3331587221473455e-05
Pgp-inhibitor:	0.875
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.127

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.694
Plasma Protein Binding (PPB):	73.31912994384766%
Volume Distribution (VD):	0.751
Pgp-substrate:	13.501514434814453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.027
CYP1A2-substrate:	0.958
CYP2C19-inhibitor:	0.241
CYP2C19-substrate:	0.848
CYP2C9-inhibitor:	0.096
CYP2C9-substrate:	0.64
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.911
CYP3A4-inhibitor:	0.718
CYP3A4-substrate:	0.771

ADMET: Excretion

Clearance (CL):	12.518
Half-life (T1/2):	0.338

ADMET: Toxicity

hERG Blockers:	0.252
Human Hepatotoxicity (H-HT):	0.165
Drug-inuced Liver Injury (DILI):	0.915
AMES Toxicity:	0.234
Rat Oral Acute Toxicity:	0.085
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.182
Carcinogencity:	0.072
Eye Corrosion:	0.004
Eye Irritation:	0.04
Respiratory Toxicity:	0.835

Download Data

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

Natural Product: NPC202154

Natural Product ID:	NPC202154
*Common Name:**	LXSRQKADIMPZPQ-GQJWHOGZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LXSRQKADIMPZPQ-GQJWHOGZSA-N
Standard InCHI:	InChI=1S/C21H20O12/c1-6-13(26)15(28)17(30)21(31-6)33-19-11(25)5-10(24)12-14(27)16(29)18(32-20(12)19)7-2-3-8(22)9(23)4-7/h2-6,13,15,17,21-26,28-30H,1H3/t6-,13-,15+,17+,21+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)Oc1c(cc(c2c(=O)c(c(c3ccc(c(c3)O)O)oc12)O)O)O)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:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003540] Flavonoid-8-O-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
NPO16932	Croton oblongifolius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10479328]
NPO6742	Knema elegans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16309311]
NPO16932	Croton oblongifolius	Species	Euphorbiaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17341114]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32031812]
NPO16353	Gynocardia odorata	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16353	Gynocardia odorata	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16932	Croton oblongifolius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16353	Gynocardia odorata	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3579	Lucilia sericata	Species	Calliphoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17768	Heliabravoa chende	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6742	Knema elegans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13825	Echinops dagestanicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17531	Rosa portlandica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9139	Madhuca neriifolia	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13579	Euthyroides episcopalis	Species	Euthyroididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5102	Ircinia wistarii	Species	Irciniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16932	Croton oblongifolius	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8167	Astragalus mucidus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16353	Gynocardia odorata	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13351	Buxus malayana	Species	Buxaceae	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 NPC202154 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	448
0.1-0.2	1851
0.2-0.3	4364
0.3-0.4	10007
0.4-0.5	8019
0.5-0.6	4264
0.6-0.7	5286
0.7-0.8	5173
0.8-0.85	1456
0.85-0.9	1147
0.9-0.95	499
0.95-1	183

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 NPC202154 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	407
0.1-0.2	961
0.2-0.3	2012
0.3-0.4	2688
0.4-0.5	1752
0.5-0.6	882
0.6-0.7	290
0.7-0.8	118
0.8-0.85	16
0.85-0.9	15
0.9-0.95	8
0.95-1	1

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