NPASS Compound

Natural Product: NPC152411

Natural Product ID	NPC152411
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SZWBRVPZWJYIHI-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	17132
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0004646] 1-hydroxy-2-unsubstituted benzenoids

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 31 31 0 0 0 0 0 0 0 0999 V2000 4.6689 -0.2289 -0.7507 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4330 0.0667 0.1081 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2825 -0.6510 -0.5629 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9834 -0.4327 0.2039 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6561 1.0411 0.2634 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6210 1.2616 1.0160 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7789 0.5853 0.4054 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5874 1.1754 -0.5445 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6660 0.5231 -1.1024 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9921 -0.7646 -0.7337 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1917 -1.3653 0.2148 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1124 -0.7116 0.7725 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0713 -1.4335 -1.2838 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3288 -0.2416 -1.7925 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3942 0.5877 -0.5668 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0505 -1.2214 -0.3973 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2728 1.1714 -0.0056 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5764 -0.2412 1.1518 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5406 -1.7158 -0.6001 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1532 -0.2151 -1.5721 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1828 -0.7529 1.2662 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1635 -1.0118 -0.2330 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6723 1.5184 -0.7312 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4719 1.5140 0.8858 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4439 0.9297 2.0722 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7734 2.3665 1.0845 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3534 2.1956 -0.8564 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2782 1.0118 -1.8423 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4388 -2.3941 0.5203 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5028 -1.2269 1.5234 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0197 -1.3398 -0.9551 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 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 10 13 1 0 12 7 1 0 1 14 1 0 1 15 1 0 1 16 1 0 2 17 1 0 2 18 1 0 3 19 1 0 3 20 1 0 4 21 1 0 4 22 1 0 5 23 1 0 5 24 1 0 6 25 1 0 6 26 1 0 8 27 1 0 9 28 1 0 11 29 1 0 12 30 1 0 13 31 1 0 M END

Standard InCHIKey	SZWBRVPZWJYIHI-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C12H18O/c1-2-3-4-5-6-11-7-9-12(13)10-8-11/h7-10,13H,2-6H2,1H3
SMILES	CCCCCCc1ccc(cc1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	178.14	Volume:	208.433 ? Van der Waals volume.
Dense:	0.855	LogP:	4.442 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.564 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.53 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	6.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	1.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.684	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.477	Fsp³:	0.5
MCE-18:	5.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.191	Fluc inhibitor:	0.212 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.013 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.994	Promiscuous compounds:	0.218

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.87	MDCK Permeability:	-4.726
Pgp-inhibitor:	0.135	Pgp-substrate:	0.312
PAMPA:	0.148 ? 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):	0.044
20% Bioavailability (F20%):	0.412	30% Bioavailability (F30%):	0.679
50% Bioavailability (F50%):	0.927

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.248	MRP1:	0.548
Plasma Protein Binding (PPB):	99.333%	Volume Distribution (VD):	0.888
Fu:	0.985% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.925
OATP1B3 inhibitor:	0.975	BCRP inhibitor:	0.718
BSEP inhibitor:	0.945

ADMET: Metabolism

CYP1A2-inhibitor:	0.121	CYP1A2-substrate:	0.994
CYP2C19-inhibitor:	0.641	CYP2C19-substrate:	0.323
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.959
CYP2D6-inhibitor:	0.992	CYP2D6-substrate:	0.914
CYP3A4-inhibitor:	0.029	CYP3A4-substrate:	0.976
CYP2B6-substrate:	0.009	CYP2C8-inhibitor:	1.0
HLM stability:	0.686 ? 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):

7.164

Half-life (T1/2):

0.45

ADMET: Toxicity

hERG Blockers:	0.715	hERG Blockers (10um):	0.897
Human Hepatotoxicity (H-HT):	0.431	Drug-induced Liver Injury (DILI):	0.064
AMES Toxicity:	0.129	Rat Oral Acute Toxicity:	0.2
Maximum Recommended Daily Dose:	0.2	Skin Sensitization:	0.817
Carcinogencity:	0.129	Eye Corrosion:	0.986
Eye Irritation:	0.997	Respiratory Toxicity:	0.797
Drug-induced Neurotoxicity:	0.264	Ototoxicity:	0.244
Hematotoxicity:	0.108	Drug-induced Nephrotoxicity:	0.289
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.047
A549 Cytotoxicity:	0.724	Hek293 Cytotoxicity:	0.647
BCF:	2.272 ? 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:	4.822 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.178 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.077 ? 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
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20824	Ecklonia kurome	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO20824	Ecklonia kurome	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20824	Ecklonia kurome	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20824	Ecklonia kurome	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20824	Ecklonia kurome	Species	Lessoniaceae	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

Molecular-level activity

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

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 NPC152411 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	26826
0.1-0.2	19602
0.2-0.3	2818
0.3-0.4	428
0.4-0.5	114
0.5-0.6	40
0.6-0.7	17
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.963	High Similarity	NPC123273
0.963	High Similarity	NPC318325
0.8889	High Similarity	NPC242240
0.8148	Intermediate Similarity	NPC23167
0.7059	Intermediate Similarity	NPC177420
0.6857	Remote Similarity	NPC55561
0.6786	Remote Similarity	NPC608485
0.6667	Remote Similarity	NPC25493
0.6571	Remote Similarity	NPC474839
0.6471	Remote Similarity	NPC3358
0.6471	Remote Similarity	NPC306884
0.6471	Remote Similarity	NPC603092
0.6111	Remote Similarity	NPC132078
0.6111	Remote Similarity	NPC600556
0.6061	Remote Similarity	NPC294186
0.6061	Remote Similarity	NPC147310
0.6061	Remote Similarity	NPC137415
0.6061	Remote Similarity	NPC166313
0.6061	Remote Similarity	NPC192032
0.6061	Remote Similarity	NPC24407
0.6061	Remote Similarity	NPC11280
0.6	Remote Similarity	NPC113460
0.5946	Remote Similarity	NPC280347
0.5946	Remote Similarity	NPC261573
0.5938	Remote Similarity	NPC138117
0.5938	Remote Similarity	NPC325292
0.5806	Remote Similarity	NPC210849
0.5758	Remote Similarity	NPC260000
0.575	Remote Similarity	NPC475018
0.5714	Remote Similarity	NPC197783
0.5556	Remote Similarity	NPC76938
0.5556	Remote Similarity	NPC32714
0.55	Remote Similarity	NPC94139
0.55	Remote Similarity	NPC147284
0.5476	Remote Similarity	NPC196976
0.5429	Remote Similarity	NPC37802
0.5429	Remote Similarity	NPC59506
0.5333	Remote Similarity	NPC599994
0.5294	Remote Similarity	NPC610566
0.5278	Remote Similarity	NPC488411
0.5278	Remote Similarity	NPC488410
0.5278	Remote Similarity	NPC488409
0.5263	Remote Similarity	NPC609578
0.525	Remote Similarity	NPC483454
0.525	Remote Similarity	NPC162314
0.5238	Remote Similarity	NPC226401
0.5238	Remote Similarity	NPC174096
0.5161	Remote Similarity	NPC258219
0.5152	Remote Similarity	NPC246056
0.5143	Remote Similarity	NPC91461
0.5143	Remote Similarity	NPC7686
0.5143	Remote Similarity	NPC40258
0.5135	Remote Similarity	NPC241891
0.5135	Remote Similarity	NPC134829
0.5128	Remote Similarity	NPC146798
0.5128	Remote Similarity	NPC222522
0.5128	Remote Similarity	NPC106396
0.5128	Remote Similarity	NPC94351
0.5128	Remote Similarity	NPC168303
0.5116	Remote Similarity	NPC317305
0.5106	Remote Similarity	NPC200988
0.5106	Remote Similarity	NPC145023

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC152411 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5232
0.1-0.2	3589
0.2-0.3	283
0.3-0.4	30
0.4-0.5	12
0.5-0.6	2
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6176	Remote Similarity	NPD846	Phase 4
0.5263	Remote Similarity	NPD3719	Phase 4
0.5128	Remote Similarity	NPD3718	Approved

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