NPASS Compound

Natural Product: NPC320421

Natural Product ID	NPC320421
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Butyl-2,5-Dihydroxycyclohexa-2,5-Diene-1,4-Dione
IUPAC Name	3-butyl-2,5-dihydroxycyclohexa-2,5-diene-1,4-dione
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3416162
PubChem CID	72195591
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000118] Ketones [CHEMONTID:0003487] Cyclic ketones [CHEMONTID:0002495] Quinones [CHEMONTID:0002384] Benzoquinones [CHEMONTID:0002494] P-benzoquinones

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 26 26 0 0 0 0 0 0 0 0999 V2000 -3.9523 0.7105 0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8383 0.3605 -0.5532 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4999 0.2418 0.1651 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4800 -0.1153 -0.9062 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8778 -0.2690 -0.3763 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5277 -1.4233 -0.4891 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9653 -2.5308 -1.1058 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8785 -1.5725 0.0391 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5412 -2.6386 -0.0383 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5485 -0.4416 0.7095 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8686 0.6870 0.8007 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5146 0.8714 0.2830 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9202 1.9921 0.4080 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4739 1.7752 1.4288 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5927 -0.1980 0.5417 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5910 1.4676 -0.0929 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5646 1.0154 1.3734 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0622 -0.5979 -1.0648 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7684 1.1232 -1.3759 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5619 -0.6140 0.8529 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2352 1.1543 0.7011 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7718 -1.0037 -1.4718 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4944 0.7383 -1.6348 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5246 -2.4948 -2.0187 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5620 -0.5392 1.1107 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2099 2.3015 1.0032 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 6 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 11 14 1 0 12 5 1 0 1 15 1 0 1 16 1 0 1 17 1 0 2 18 1 0 2 19 1 0 3 20 1 0 3 21 1 0 4 22 1 0 4 23 1 0 7 24 1 0 10 25 1 0 14 26 1 0 M END

Standard InCHIKey	SXHSRMMHMDZHGC-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H12O4/c1-2-3-4-6-9(13)7(11)5-8(12)10(6)14/h5,11,14H,2-4H2,1H3
SMILES	CCCCC1=C(O)C(=O)C=C(C1=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	196.07	Volume:	197.575 ? Van der Waals volume.
Dense:	0.992	LogP:	2.085 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.092 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.358 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	8.0
TPSA:	74.6 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.672	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.754	Fsp³:	0.4
MCE-18:	8.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	1
Colloidal aggregators:	0.601	Fluc inhibitor:	0.638 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.017 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.104 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.99	Promiscuous compounds:	0.209

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.236	MDCK Permeability:	-4.567
Pgp-inhibitor:	0.202	Pgp-substrate:	0.143
PAMPA:	0.906 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.83
20% Bioavailability (F20%):	0.38	30% Bioavailability (F30%):	0.976
50% Bioavailability (F50%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003	MRP1:	0.849
Plasma Protein Binding (PPB):	93.516%	Volume Distribution (VD):	-0.294
Fu:	6.358% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.97
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.473
BSEP inhibitor:	0.393

ADMET: Metabolism

CYP1A2-inhibitor:	0.508	CYP1A2-substrate:	0.003
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.015
CYP2C9-inhibitor:	0.487	CYP2C9-substrate:	0.862
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.037
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.114
HLM stability:	0.49 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

2.914

Half-life (T1/2):

1.436

ADMET: Toxicity

hERG Blockers:	0.029	hERG Blockers (10um):	0.108
Human Hepatotoxicity (H-HT):	0.545	Drug-induced Liver Injury (DILI):	0.548
AMES Toxicity:	0.344	Rat Oral Acute Toxicity:	0.541
Maximum Recommended Daily Dose:	0.352	Skin Sensitization:	0.846
Carcinogencity:	0.395	Eye Corrosion:	0.967
Eye Irritation:	0.998	Respiratory Toxicity:	0.892
Drug-induced Neurotoxicity:	0.1	Ototoxicity:	0.228
Hematotoxicity:	0.459	Drug-induced Nephrotoxicity:	0.286
Genotoxicity:	0.209	RPMI-8226 Immunitoxicity:	0.048
A549 Cytotoxicity:	0.015	Hek293 Cytotoxicity:	0.08
BCF:	1.376 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.16 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.225 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.865 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3803	Ardisia japonica	Species	Primulaceae	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	Organism Name	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

Activity Type	# Activity
IC50	4
Activity	6

Activity Type	# Activity
Individual protein	10

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1119	Individual protein	Arachidonate 12-lipoxygenase	Homo sapiens	Activity	=	93.3	%	PMID[25765759]
NPT3167	Individual protein	Macrophage-expressed gene 1 protein	Homo sapiens	IC50	>	10000.0	nM	PMID[25765759]
NPT3167	Individual protein	Macrophage-expressed gene 1 protein	Homo sapiens	Activity	=	84.6	%	PMID[25765759]
NPT792	Individual protein	Arachidonate 15-lipoxygenase	Homo sapiens	Activity	=	82.3	%	PMID[25765759]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	>	10000.0	nM	PMID[25765759]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	65.4	%	PMID[25765759]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	93.5	%	PMID[25765759]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	92.8	%	PMID[25765759]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC320421 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	21599
0.1-0.2	26885
0.2-0.3	1349
0.3-0.4	14
0.4-0.5	8
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.871	High Similarity	NPC7029
0.871	High Similarity	NPC143168
0.7333	Intermediate Similarity	NPC137396

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC320421 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6740
0.1-0.2	2363
0.2-0.3	45
0.3-0.4	0
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.871	High Similarity	NPD2664	Clinical (unspecified phase)

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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