NPASS Compound

Structure

CID180340 OpenBabel06191715552D 29 33 0 0 0 0 0 0 0 0999 V2000 -1.8320 -0.7588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7355 0.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -6.0000 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 0.0000 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 -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 5.1962 -5.0000 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 0.8660 -1.5000 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 4.3301 -3.5000 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 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 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 -3.0000 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 1.7321 -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 4.3301 -1.5000 0.0000 O 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 6.9282 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -5.0000 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 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 23 1 0 0 0 0 3 25 1 0 0 0 0 4 26 1 0 0 0 0 5 6 2 0 0 0 0 5 13 1 0 0 0 0 6 15 1 0 0 0 0 7 8 2 0 0 0 0 7 12 1 0 0 0 0 8 23 1 0 0 0 0 9 14 2 0 0 0 0 9 17 1 0 0 0 0 10 16 2 0 0 0 0 10 18 1 0 0 0 0 11 19 1 0 0 0 0 11 27 1 0 0 0 0 12 15 2 0 0 0 0 12 22 1 0 0 0 0 13 21 1 0 0 0 0 13 22 2 0 0 0 0 14 16 1 0 0 0 0 14 20 1 0 0 0 0 15 29 1 0 0 0 0 16 27 1 0 0 0 0 17 18 2 0 0 0 0 17 25 1 0 0 0 0 18 26 1 0 0 0 0 19 20 2 0 0 0 0 19 28 1 0 0 0 0 20 21 1 0 0 0 0 21 24 2 0 0 0 0 22 28 1 0 0 0 0 23 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.13
Volume:	392.595
LogP:	3.966
LogD:	3.414
LogS:	-5.227
# Rotatable Bonds:	2
TPSA:	67.13
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.637
Synthetic Accessibility Score:	3.056
Fsp3:	0.261
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.869
MDCK Permeability:	2.8535794626805e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	89.6941909790039%
Volume Distribution (VD):	0.629
Pgp-substrate:	8.18327522277832%

ADMET: Metabolism

CYP1A2-inhibitor:	0.363
CYP1A2-substrate:	0.963
CYP2C19-inhibitor:	0.733
CYP2C19-substrate:	0.561
CYP2C9-inhibitor:	0.859
CYP2C9-substrate:	0.912
CYP2D6-inhibitor:	0.04
CYP2D6-substrate:	0.9
CYP3A4-inhibitor:	0.553
CYP3A4-substrate:	0.566

ADMET: Excretion

Clearance (CL):	2.561
Half-life (T1/2):	0.237

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.995
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.684
Rat Oral Acute Toxicity:	0.537
Maximum Recommended Daily Dose:	0.448
Skin Sensitization:	0.11
Carcinogencity:	0.883
Eye Corrosion:	0.003
Eye Irritation:	0.016
Respiratory Toxicity:	0.859

Download Data

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

Natural Product: NPC180340

Natural Product ID:	NPC180340
*Common Name:**	Dehydrodeguelin
IUPAC Name:	n.a.
Synonyms:	Dehydrodeguelin
Standard InCHIKey:	NGQVFILFHVPLFE-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H20O6/c1-23(2)8-7-12-15(29-23)6-5-13-21(24)20-14-9-17(25-3)18(26-4)10-16(14)27-11-19(20)28-22(12)13/h5-10H,11H2,1-4H3
SMILES:	COc1cc2c(cc1OC)OCc1c2c(=O)c2c(o1)c1C=CC(Oc1cc2)(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL465673
PubChem CID:	3083803
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001607] Rotenoids [CHEMONTID:0003528] Rotenones

*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
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9868158]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834152]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9584408]
NPO21911	Tephrosia purpurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322358]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8759159]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[8759159]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350086]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8326318]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28075580]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28068085]

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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
IC50	10
MIC	1
Others	1

Activity Type	# Activity
Cell Line	4
NON-MOLECULAR	5
Organism	1
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT319	Cell Line	B16	Mus musculus	IC50	=	560.0	nM	PMID[473667]
NPT4264	Cell Line	Lewis lung carcinoma cell line		IC50	=	560.0	nM	PMID[473667]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	560.0	nM	PMID[473667]
NPT2	Others	Unspecified		IC50	=	560.0	nM	PMID[473667]
NPT1864	Cell Line	L5178Y	Mus musculus	IC50	=	10200.0	nM	PMID[473666]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	1200.0	nM	PMID[473665]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	80000.0	nM	PMID[473665]
NPT27	Others	Unspecified		IC50	>	80000.0	nM	PMID[473665]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	40.0	%	PMID[473665]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	500000.0	nM	PMID[473664]

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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 NPC180340 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	536
0.1-0.2	2084
0.2-0.3	5243
0.3-0.4	11720
0.4-0.5	5874
0.5-0.6	4180
0.6-0.7	5950
0.7-0.8	4594
0.8-0.85	1756
0.85-0.9	702
0.9-0.95	53
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9865	High Similarity	NPC128961
0.9732	High Similarity	NPC472408
0.9664	High Similarity	NPC166201
0.9608	High Similarity	NPC40037
0.9539	High Similarity	NPC19097

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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 NPC180340 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	448
0.1-0.2	1047
0.2-0.3	1959
0.3-0.4	2705
0.4-0.5	1714
0.5-0.6	852
0.6-0.7	298
0.7-0.8	97
0.8-0.85	25
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9167	High Similarity	NPD5494	Approved
0.8846	High Similarity	NPD2801	Approved
0.8634	High Similarity	NPD1247	Approved
0.8608	High Similarity	NPD2393	Clinical (unspecified phase)
0.8553	High Similarity	NPD3817	Phase 2

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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