NPASS Compound

Natural Product: NPC482802

Natural Product ID	NPC482802
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OLUQMFYBNOJBQQ-UVTDQMKNSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5283281
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002951] Long-chain fatty alcohols

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 41 40 0 0 0 0 0 0 0 0999 V2000 -6.0038 -1.1749 -1.4942 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0483 -0.6687 -0.7388 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0680 -0.0503 0.5769 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9967 -0.7099 1.4693 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6013 -0.3840 0.9935 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5558 -1.0822 1.8560 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2047 -0.5230 1.3448 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2222 0.9165 1.7016 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1664 1.9122 0.8451 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0876 1.8223 -0.5438 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3194 1.2102 -0.9199 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2284 0.8169 -1.1509 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5260 0.2365 -1.4826 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6275 -0.2532 -1.7732 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8028 -0.7631 -2.0822 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9976 -0.2490 -1.2910 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8231 0.6584 -0.3238 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2168 -0.3873 -3.4625 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0327 1.0965 -1.2973 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4495 -1.5814 -2.5049 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9963 -1.3029 -1.4414 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0303 -0.7457 -1.2321 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7945 1.0266 0.5089 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0591 -0.1930 1.0699 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1733 -1.8135 1.3470 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1003 -0.3556 2.4908 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4684 0.7035 0.9949 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5159 -0.7311 -0.0639 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6651 -0.7246 2.9097 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6084 -2.1861 1.7704 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1857 -0.7419 0.2764 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6279 -1.0603 1.8786 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3009 1.1877 2.7955 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1643 2.9341 1.3139 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0937 2.8158 -1.1099 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8771 -1.9056 -2.0688 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9754 -0.6054 -1.5552 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8190 0.9886 -0.1681 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6311 1.0054 0.2675 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7953 0.5266 -3.5170 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6747 0.3345 -1.8004 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 3 0 12 13 1 0 13 14 3 0 14 15 1 0 15 16 1 0 16 17 2 0 15 18 1 0 10 19 1 0 1 20 1 0 1 21 1 0 2 22 1 0 3 23 1 0 3 24 1 0 4 25 1 0 4 26 1 0 5 27 1 0 5 28 1 0 6 29 1 0 6 30 1 0 7 31 1 0 7 32 1 0 8 33 1 0 9 34 1 0 10 35 1 0 15 36 1 0 16 37 1 0 17 38 1 0 17 39 1 0 18 40 1 0 19 41 1 0 M END

Standard InCHIKey	OLUQMFYBNOJBQQ-UVTDQMKNSA-N
Standard InCHI	InChI=1S/C17H22O2/c1-3-5-6-7-8-9-10-14-17(19)15-12-11-13-16(18)4-2/h3-4,10,14,16-19H,1-2,5-9H2/b14-10-
SMILES	C=CCCCCC/C=CC(C#CC#CC(C=C)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	258.16	Volume:	301.713 ? Van der Waals volume.
Dense:	0.856	LogP:	3.585 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.925 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.301 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	5.0
TPSA:	40.46 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.399	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.354	Fsp³:	0.412
MCE-18:	2.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.004	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.051 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.784	Promiscuous compounds:	0.017

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.651	MDCK Permeability:	-4.713
Pgp-inhibitor:	0.264	Pgp-substrate:	0.0
PAMPA:	0.869 ? 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):	0.0
20% Bioavailability (F20%):	0.0	30% Bioavailability (F30%):	0.001
50% Bioavailability (F50%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	96.608%	Volume Distribution (VD):	-0.14
Fu:	3.177% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.002	BCRP inhibitor:	1.0
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	CYP1A2-substrate:	0.998
CYP2C19-inhibitor:	0.037	CYP2C19-substrate:	0.255
CYP2C9-inhibitor:	0.991	CYP2C9-substrate:	0.009
CYP2D6-inhibitor:	0.488	CYP2D6-substrate:	0.974
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.968
CYP2B6-substrate:	0.003	CYP2C8-inhibitor:	1.0
HLM stability:	0.372 ? 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):

4.577

Half-life (T1/2):

1.483

ADMET: Toxicity

hERG Blockers:	0.025	hERG Blockers (10um):	0.766
Human Hepatotoxicity (H-HT):	0.126	Drug-induced Liver Injury (DILI):	0.283
AMES Toxicity:	0.309	Rat Oral Acute Toxicity:	0.687
Maximum Recommended Daily Dose:	0.814	Skin Sensitization:	0.74
Carcinogencity:	0.201	Eye Corrosion:	0.977
Eye Irritation:	0.994	Respiratory Toxicity:	1.0
Drug-induced Neurotoxicity:	0.33	Ototoxicity:	0.618
Hematotoxicity:	0.001	Drug-induced Nephrotoxicity:	0.006
Genotoxicity:	0.039	RPMI-8226 Immunitoxicity:	0.058
A549 Cytotoxicity:	0.014	Hek293 Cytotoxicity:	0.388
BCF:	1.772 ? 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:	4.366 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.3 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.617 ? 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
NPO15816	Gymnaster koraiensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[12088435]
NPO15816	Gymnaster koraiensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15816	Gymnaster koraiensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO15816	Gymnaster koraiensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO15816	Gymnaster koraiensis	n.a.	n.a.	n.a.	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
ED50	1

Activity Type	# Activity
Cell line	1

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
NPT137	Cell line	L1210	Mus musculus	ED50	=	0.12	ug ml-1	PMID[12088435]

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 NPC482802 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	37657
0.1-0.2	11538
0.2-0.3	499
0.3-0.4	78
0.4-0.5	34
0.5-0.6	29
0.6-0.7	10
0.7-0.8	0
0.8-0.85	4
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC124183
0.8929	High Similarity	NPC243813
0.8333	Intermediate Similarity	NPC91226
0.8333	Intermediate Similarity	NPC243546
0.8333	Intermediate Similarity	NPC31194
0.8333	Intermediate Similarity	NPC248884
0.7812	Intermediate Similarity	NPC153538
0.7812	Intermediate Similarity	NPC93639
0.7353	Intermediate Similarity	NPC482801
0.7143	Intermediate Similarity	NPC142092
0.6944	Remote Similarity	NPC35141
0.6765	Remote Similarity	NPC321763
0.6765	Remote Similarity	NPC101616
0.6471	Remote Similarity	NPC72699
0.6471	Remote Similarity	NPC481854
0.641	Remote Similarity	NPC66460
0.641	Remote Similarity	NPC325929
0.641	Remote Similarity	NPC271282
0.6098	Remote Similarity	NPC212730
0.6	Remote Similarity	NPC481860
0.5946	Remote Similarity	NPC484320
0.5946	Remote Similarity	NPC168510
0.5946	Remote Similarity	NPC481848
0.5814	Remote Similarity	NPC265551
0.5676	Remote Similarity	NPC481855
0.5676	Remote Similarity	NPC55063
0.5676	Remote Similarity	NPC19834
0.5676	Remote Similarity	NPC166942
0.5667	Remote Similarity	NPC125122
0.5667	Remote Similarity	NPC471276
0.5667	Remote Similarity	NPC471280
0.5667	Remote Similarity	NPC471281
0.5641	Remote Similarity	NPC85079
0.5641	Remote Similarity	NPC151782
0.5556	Remote Similarity	NPC484322
0.5484	Remote Similarity	NPC170776
0.5484	Remote Similarity	NPC9273
0.5484	Remote Similarity	NPC165447
0.5484	Remote Similarity	NPC471959
0.5484	Remote Similarity	NPC199286
0.5484	Remote Similarity	NPC489046
0.5484	Remote Similarity	NPC76198
0.5484	Remote Similarity	NPC610719
0.5385	Remote Similarity	NPC48821
0.5385	Remote Similarity	NPC13418
0.5312	Remote Similarity	NPC607242
0.5152	Remote Similarity	NPC249670
0.5135	Remote Similarity	NPC55383
0.5116	Remote Similarity	NPC29697

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC482802 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8425
0.1-0.2	709
0.2-0.3	14
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
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
		NPD

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