NPASS Compound

Structure

CID85162 OpenBabel06191715422D 31 33 0 0 1 0 0 0 0 0999 V2000 -5.1962 0.0000 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 -1.7321 3.0000 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 3.4641 1.0000 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 2.5981 1.5000 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 1.0000 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 -2.5981 -1.5000 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 -5.1962 1.0000 0.0000 C 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 -2.5981 1.5000 0.0000 C 0 0 2 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 1.7321 1.0000 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 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 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 -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 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 1.5000 0.0000 O 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 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 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 1 13 1 0 0 0 0 2 13 1 0 0 0 0 3 14 2 0 0 0 0 4 14 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 6 17 1 0 0 0 0 7 18 2 0 0 0 0 8 9 1 0 0 0 0 8 13 2 0 0 0 0 10 15 1 0 0 0 0 10 16 1 0 0 0 0 11 19 2 0 0 0 0 11 20 1 0 0 0 0 12 21 1 0 0 0 0 12 22 1 0 0 0 0 14 15 1 0 0 0 0 15 9 1 1 0 0 0 16 19 1 0 0 0 0 16 25 2 0 0 0 0 17 23 2 0 0 0 0 17 26 1 0 0 0 0 18 23 1 0 0 0 0 18 27 1 0 0 0 0 19 28 1 0 0 0 0 20 24 2 0 0 0 0 20 29 1 0 0 0 0 21 24 1 0 0 0 0 21 30 2 0 0 0 0 22 23 1 6 0 0 0 22 31 1 0 0 0 0 24 25 1 0 0 0 0 25 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	424.19
Volume:	444.3
LogP:	6.143
LogD:	3.775
LogS:	-3.619
# Rotatable Bonds:	6
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.468
Synthetic Accessibility Score:	4.005
Fsp3:	0.32
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.958
MDCK Permeability:	1.3492980542650912e-05
Pgp-inhibitor:	0.706
Pgp-substrate:	0.64
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.835
30% Bioavailability (F30%):	0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006
Plasma Protein Binding (PPB):	98.96395111083984%
Volume Distribution (VD):	0.438
Pgp-substrate:	1.8677743673324585%

ADMET: Metabolism

CYP1A2-inhibitor:	0.546
CYP1A2-substrate:	0.742
CYP2C19-inhibitor:	0.838
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.877
CYP2C9-substrate:	0.963
CYP2D6-inhibitor:	0.904
CYP2D6-substrate:	0.378
CYP3A4-inhibitor:	0.23
CYP3A4-substrate:	0.168

ADMET: Excretion

Clearance (CL):	12.631
Half-life (T1/2):	0.236

ADMET: Toxicity

hERG Blockers:	0.048
Human Hepatotoxicity (H-HT):	0.793
Drug-inuced Liver Injury (DILI):	0.929
AMES Toxicity:	0.072
Rat Oral Acute Toxicity:	0.877
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.91
Carcinogencity:	0.333
Eye Corrosion:	0.003
Eye Irritation:	0.914
Respiratory Toxicity:	0.911

Download Data

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

Natural Product: NPC85162

Natural Product ID:	NPC85162
*Common Name:**	Exiguaflavone A
IUPAC Name:	(2S)-2-(2,6-dihydroxyphenyl)-5,7-dihydroxy-8-[(2R)-5-methyl-2-prop-1-en-2-ylhex-4-enyl]-2,3-dihydrochromen-4-one
Synonyms:
Standard InCHIKey:	FPUREMWTZVLZBZ-QRQCRPRQSA-N
Standard InCHI:	InChI=1S/C25H28O6/c1-13(2)8-9-15(14(3)4)10-16-19(28)11-20(29)24-21(30)12-22(31-25(16)24)23-17(26)6-5-7-18(23)27/h5-8,11,15,22,26-29H,3,9-10,12H2,1-2,4H3/t15-,22+/m1/s1
SMILES:	CC(=CC[C@@H](C(=C)C)Cc1c(O)cc(c2c1O[C@@H](CC2=O)c1c(O)cccc1O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464368
PubChem CID:	15735861
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans [CHEMONTID:0003508] 8-prenylated flavanones

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO74	Artemisia indica	Species	Asteraceae	Eukaryota	n.a.	stem	n.a.	PMID[9748386]
NPO24630	Sophora exigua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10839220]
NPO24630	Sophora exigua	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1016/0031-9422(92)80056-K]
NPO74	Artemisia indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24630	Sophora exigua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 5 of 5 entries

Previous1Next

☑ 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

Show entries

Search:

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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

Activity Type	# Activity
EC50	1

Activity Type	# Activity
Organism	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	EC50	=	10800.0	nM	PMID[476036]

Showing 1 to 1 of 1 entries

Previous1Next

☑ 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 NPC85162 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	353
0.1-0.2	1404
0.2-0.3	3557
0.3-0.4	9330
0.4-0.5	9335
0.5-0.6	3493
0.6-0.7	5644
0.7-0.8	5432
0.8-0.85	2144
0.85-0.9	1191
0.9-0.95	582
0.95-1	232

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC223812
1.0	High Similarity	NPC81697
1.0	High Similarity	NPC107177
1.0	High Similarity	NPC77794
1.0	High Similarity	NPC125894

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC85162 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	316
0.1-0.2	910
0.2-0.3	1500
0.3-0.4	2523
0.4-0.5	1973
0.5-0.6	1192
0.6-0.7	505
0.7-0.8	168
0.8-0.85	39
0.85-0.9	16
0.9-0.95	6
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9562	High Similarity	NPD1552	Clinical (unspecified phase)
0.9562	High Similarity	NPD1550	Clinical (unspecified phase)
0.9493	High Similarity	NPD1549	Phase 2
0.9366	High Similarity	NPD4378	Clinical (unspecified phase)
0.932	High Similarity	NPD8443	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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