NPASS Compound

Structure

CID26238 OpenBabel06191715352D 36 39 0 0 0 0 0 0 0 0999 V2000 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 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 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 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 -3.0000 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 1.7321 -3.0000 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 -5.0000 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 2.5981 -1.5000 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 -0.0000 -3.0000 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 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 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 -0.0000 -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 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 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 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 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 -1.5000 0.0000 C 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 -0.0000 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 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 1.7321 -2.0000 0.0000 O 0 0 0 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 36 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 9 1 0 0 0 0 4 10 2 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 8 2 0 0 0 0 6 12 1 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 19 2 0 0 0 0 10 19 1 0 0 0 0 11 20 2 0 0 0 0 12 21 2 0 0 0 0 13 24 2 0 0 0 0 14 25 2 0 0 0 0 15 16 1 0 0 0 0 15 19 1 0 0 0 0 16 26 1 0 0 0 0 17 20 1 0 0 0 0 17 22 1 0 0 0 0 18 21 1 0 0 0 0 18 23 1 0 0 0 0 20 24 1 0 0 0 0 21 25 1 0 0 0 0 22 28 2 0 0 0 0 22 29 1 0 0 0 0 23 28 1 0 0 0 0 23 30 2 0 0 0 0 24 31 1 0 0 0 0 25 32 1 0 0 0 0 26 27 1 0 0 0 0 26 33 2 0 0 0 0 27 29 2 0 0 0 0 27 30 1 0 0 0 0 28 34 1 0 0 0 0 29 35 1 0 0 0 0 30 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	484.19
Volume:	511.678
LogP:	5.772
LogD:	3.611
LogS:	-4.408
# Rotatable Bonds:	9
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.233
Synthetic Accessibility Score:	2.653
Fsp3:	0.167
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:	-5.841
MDCK Permeability:	2.540954483265523e-05
Pgp-inhibitor:	0.678
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.445
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022
Plasma Protein Binding (PPB):	100.69974517822266%
Volume Distribution (VD):	0.407
Pgp-substrate:	0.9003977179527283%

ADMET: Metabolism

CYP1A2-inhibitor:	0.315
CYP1A2-substrate:	0.567
CYP2C19-inhibitor:	0.942
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.698
CYP2C9-substrate:	0.952
CYP2D6-inhibitor:	0.391
CYP2D6-substrate:	0.725
CYP3A4-inhibitor:	0.331
CYP3A4-substrate:	0.555

ADMET: Excretion

Clearance (CL):	10.001
Half-life (T1/2):	0.797

ADMET: Toxicity

hERG Blockers:	0.062
Human Hepatotoxicity (H-HT):	0.076
Drug-inuced Liver Injury (DILI):	0.884
AMES Toxicity:	0.263
Rat Oral Acute Toxicity:	0.219
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.948
Carcinogencity:	0.091
Eye Corrosion:	0.003
Eye Irritation:	0.902
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC26238

Natural Product ID:	NPC26238
*Common Name:**	Diuvaretin
IUPAC Name:	1-[2,4-dihydroxy-3,5-bis[(2-hydroxyphenyl)methyl]-6-methoxyphenyl]-3-phenylpropan-1-one
Synonyms:	Diuvaretin
Standard InCHIKey:	KDEMELRYKGOXDL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H28O6/c1-36-30-23(18-21-12-6-8-14-25(21)32)28(34)22(17-20-11-5-7-13-24(20)31)29(35)27(30)26(33)16-15-19-9-3-2-4-10-19/h2-14,31-32,34-35H,15-18H2,1H3
SMILES:	COc1c(C(=O)CCc2ccccc2)c(O)c(c(c1Cc1ccccc1O)O)Cc1ccccc1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464771
PubChem CID:	3085222
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO17534	Uvaria chamae	Species	Annonaceae	Eukaryota	n.a.	root	n.a.	PMID[845713]
NPO40206	Monanthotaxis trichocarpa	Species	Annonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31986029]
NPO7058	Australostichopus mollis	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22271309]
NPO7058	Australostichopus mollis	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974605]
NPO17534	Uvaria chamae	Species	Annonaceae	Eukaryota	roots	n.a.	n.a.	PMID[15217292]
NPO14915	Uvaria acuminata	Species	Annonaceae	Eukaryota	n.a.	root	n.a.	PMID[14709883]
NPO3250	Uvaria leptocladon	Species	Annonaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1016/S0031-9422(00)95109-4]
NPO20502	Swertia cincta	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1002/cbdv.200490123]
NPO22878	Libocedrus bidwillii	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19790	Cyclamen africanum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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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

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☑ 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

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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	=	4.2	ug.mL-1	PMID[517664]

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☑ 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 NPC26238 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	381
0.1-0.2	1706
0.2-0.3	4226
0.3-0.4	11787
0.4-0.5	6321
0.5-0.6	4184
0.6-0.7	5837
0.7-0.8	5361
0.8-0.85	1690
0.85-0.9	819
0.9-0.95	374
0.95-1	11

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Similarity Score	Similarity Level	Natural Product ID
0.9783	High Similarity	NPC282957
0.9783	High Similarity	NPC194949
0.9778	High Similarity	NPC251681
0.9778	High Similarity	NPC243528
0.9643	High Similarity	NPC475348

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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 NPC26238 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	353
0.1-0.2	984
0.2-0.3	1419
0.3-0.4	2735
0.4-0.5	1901
0.5-0.6	1212
0.6-0.7	371
0.7-0.8	132
0.8-0.85	31
0.85-0.9	9
0.9-0.95	3
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9225	High Similarity	NPD7410	Clinical (unspecified phase)
0.9118	High Similarity	NPD1240	Approved
0.9091	High Similarity	NPD4378	Clinical (unspecified phase)
0.8993	High Similarity	NPD1510	Phase 2
0.8986	High Similarity	NPD1607	Approved

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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