NPASS Compound

Natural Product: NPC260809

Natural Product ID	NPC260809
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NTQOBLPQKXJXCZ-RKESYOIOSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL412361
PubChem CID	14446336
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0001789] Trichothecenes

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 70 73 0 0 0 0 0 0 0 0999 V2000 7.5761 -0.3469 -0.3832 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6792 -0.3691 0.8629 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6313 0.6697 0.6594 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6410 0.8181 1.7633 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8298 -0.4109 2.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0549 -0.8768 0.8949 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4344 -1.9259 0.3056 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9369 -0.2316 0.4067 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2670 -0.7442 -0.6948 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1929 -1.0368 -0.4495 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9894 0.1679 -0.0215 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0322 0.1338 1.4958 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6628 -1.0666 1.9368 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8591 -1.3766 3.2533 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4681 -0.5682 4.1338 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5276 -2.6530 3.6944 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2530 1.4049 -0.4182 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5111 1.2743 -1.7099 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2627 0.2125 -1.8471 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0655 -0.0674 -3.0308 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0216 2.5353 -0.5537 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2174 2.3376 -1.2194 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2801 2.2909 -0.1267 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4142 0.8179 0.1662 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3678 0.0848 -0.6215 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8508 -1.2864 -0.8921 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3318 0.9722 -1.8669 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0105 0.6709 -3.1475 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3556 0.8354 -2.8005 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6773 0.4337 -0.3615 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6968 -0.1051 0.4200 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4470 -0.2442 1.6434 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0163 -0.4890 -0.1954 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9480 3.0631 0.9547 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4544 0.6284 -0.9246 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6419 -0.4291 -0.1310 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3132 -1.1627 -1.0834 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2627 -1.3952 0.9155 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3692 -0.1362 1.7058 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1624 0.4751 -0.3308 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1519 1.6662 0.5707 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2247 1.0643 2.6857 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9420 1.6598 1.5962 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1961 -0.1901 2.9363 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5405 -1.2005 2.3720 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7477 -1.7011 -0.9912 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5994 -1.3351 -1.4555 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2605 -1.8348 0.2928 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0523 0.0579 1.8072 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4136 1.0354 1.9654 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9042 -3.2260 2.8408 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3083 -2.4165 4.4444 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7627 -3.2710 4.2228 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5197 1.6270 0.3753 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4671 2.0034 -2.5060 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4644 0.8340 -3.5374 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9127 -0.7489 -2.7189 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4799 -0.7021 -3.7535 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3798 3.1510 -1.9238 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1930 2.7238 -0.6036 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4459 0.5916 1.2423 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2170 -2.1013 -0.4953 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8627 -1.4707 -0.4660 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9984 -1.3978 -2.0084 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7901 -0.3567 -3.5214 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5299 1.4270 -3.8304 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7991 -1.0453 -1.1119 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6304 -1.0835 0.4762 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5339 0.4569 -0.5338 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5434 2.8786 1.7078 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 2 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 1 12 13 1 0 13 14 1 0 14 15 2 0 14 16 1 0 11 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 17 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 6 25 27 1 0 27 28 1 0 28 29 1 0 24 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 23 34 1 0 19 9 1 0 27 22 1 0 25 11 1 0 27 29 1 6 1 35 1 0 1 36 1 0 1 37 1 0 2 38 1 0 2 39 1 0 3 40 1 0 3 41 1 0 4 42 1 0 4 43 1 0 5 44 1 0 5 45 1 0 9 46 1 6 10 47 1 0 10 48 1 0 12 49 1 0 12 50 1 0 16 51 1 0 16 52 1 0 16 53 1 0 17 54 1 1 18 55 1 0 20 56 1 0 20 57 1 0 20 58 1 0 22 59 1 6 23 60 1 6 24 61 1 1 26 62 1 0 26 63 1 0 26 64 1 0 28 65 1 0 28 66 1 0 33 67 1 0 33 68 1 0 33 69 1 0 34 70 1 0 M END

Standard InCHIKey	NTQOBLPQKXJXCZ-RKESYOIOSA-N
Standard InCHI	InChI=1S/C25H36O9/c1-6-7-8-9-19(28)33-17-11-24(12-30-15(3)26)18(10-14(17)2)34-22-20(29)21(32-16(4)27)23(24,5)25(22)13-31-25/h10,17-18,20-22,29H,6-9,11-13H2,1-5H3/t17-,18+,20+,21+,22+,23+,24+,25-/m0/s1
SMILES	CCCCCC(=O)O[C@H]1C[C@@]2(COC(=O)C)[C@@H](C=C1C)O[C@@H]1[C@@H]([C@H]([C@@]2(C)[C@@]21CO2)OC(=O)C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	480.24	Volume:	475.296 ? Van der Waals volume.
Dense:	1.01	LogP:	2.558 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.55 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.739 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	20.0
TPSA:	120.89 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	1.0	Rings:	4.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.183	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.962	Fsp³:	0.8
MCE-18:	103.333 ? 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:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.782	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.014 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.188	Promiscuous compounds:	0.738

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.291	MDCK Permeability:	-4.909
Pgp-inhibitor:	0.82	Pgp-substrate:	0.995
PAMPA:	0.798 ? 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):	0.077
20% Bioavailability (F20%):	0.994	30% Bioavailability (F30%):	0.988
50% Bioavailability (F50%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025	MRP1:	0.99
Plasma Protein Binding (PPB):	77.876%	Volume Distribution (VD):	-0.25
Fu:	22.073% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.89
OATP1B3 inhibitor:	0.084	BCRP inhibitor:	0.04
BSEP inhibitor:	0.963

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.321
CYP2C19-inhibitor:	0.546	CYP2C19-substrate:	0.021
CYP2C9-inhibitor:	0.019	CYP2C9-substrate:	0.454
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.046	CYP3A4-substrate:	0.436
CYP2B6-substrate:	0.025	CYP2C8-inhibitor:	0.998
HLM stability:	0.981 ? 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):

4.491

Half-life (T1/2):

0.884

ADMET: Toxicity

hERG Blockers:	0.02	hERG Blockers (10um):	0.222
Human Hepatotoxicity (H-HT):	0.348	Drug-induced Liver Injury (DILI):	0.899
AMES Toxicity:	0.99	Rat Oral Acute Toxicity:	0.845
Maximum Recommended Daily Dose:	0.777	Skin Sensitization:	1.0
Carcinogencity:	0.382	Eye Corrosion:	0.005
Eye Irritation:	0.711	Respiratory Toxicity:	0.479
Drug-induced Neurotoxicity:	0.516	Ototoxicity:	0.585
Hematotoxicity:	0.685	Drug-induced Nephrotoxicity:	0.983
Genotoxicity:	0.918	RPMI-8226 Immunitoxicity:	0.563
A549 Cytotoxicity:	0.681	Hek293 Cytotoxicity:	0.178
BCF:	0.642 ? 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:	3.602 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.688 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.0 ? 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
NPO11220	Fusarium sporotrichioides	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1800633]
NPO11220	Fusarium sporotrichioides	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25475336]
NPO11220	Fusarium sporotrichioides	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8289061]
NPO10844	Lactarius pergamenus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11220	Fusarium sporotrichioides	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4524	Bosistoa pentacocca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10844	Lactarius pergamenus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4524	Bosistoa pentacocca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10844	Lactarius pergamenus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11220	Fusarium sporotrichioides	Species	Nectriaceae	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 NPC260809 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	20374
0.1-0.2	26630
0.2-0.3	2775
0.3-0.4	52
0.4-0.5	10
0.5-0.6	3
0.6-0.7	5
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC474783
0.9455	High Similarity	NPC252242
0.9455	High Similarity	NPC475956
0.9091	High Similarity	NPC26557
0.8393	Intermediate Similarity	NPC79449
0.8393	Intermediate Similarity	NPC474957
0.8364	Intermediate Similarity	NPC347923
0.8364	Intermediate Similarity	NPC608318
0.7966	Intermediate Similarity	NPC200672
0.6667	Remote Similarity	NPC274458
0.6393	Remote Similarity	NPC476057
0.629	Remote Similarity	NPC240838
0.629	Remote Similarity	NPC600295
0.619	Remote Similarity	NPC50223
0.5672	Remote Similarity	NPC232515
0.5588	Remote Similarity	NPC214714
0.5588	Remote Similarity	NPC607785

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC260809 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6789
0.1-0.2	2305
0.2-0.3	53
0.3-0.4	3
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