NPASS Compound

Natural Product: NPC22204

Natural Product ID	NPC22204
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JJDVTBGHKGLZLP-HMHWFSEDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	100982655
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 68 71 0 0 0 0 0 0 0 0999 V2000 -7.7122 1.4915 2.4033 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0878 0.8319 1.0808 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5056 1.5881 -0.0826 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5190 -0.5724 1.1132 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0454 -0.4863 1.2678 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4627 0.6072 1.3503 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3139 -1.6386 1.3205 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9246 -1.7189 1.4625 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1690 -1.0357 0.3415 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6003 -1.4762 -1.0087 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7936 -2.5656 -1.6238 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3536 -2.6072 -1.1703 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0552 -1.2186 -0.5774 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2558 -1.1243 -0.2161 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1922 -0.2201 -0.5954 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4776 -0.3850 -0.0450 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5478 0.4278 -0.3106 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3693 1.4845 -1.1747 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1362 1.6855 -1.7353 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0611 0.8391 -1.4458 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1388 1.1163 -2.0535 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9502 2.7540 -2.6106 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4541 2.2724 -1.4165 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3513 3.2476 -2.1935 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6843 1.9935 -0.7974 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8016 0.9408 0.0434 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0230 0.5446 0.7491 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9709 -0.5594 1.5841 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0681 -1.0121 2.2915 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2759 -0.3561 2.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3313 0.7393 1.3521 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2159 1.1982 0.6339 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5397 1.4359 1.2089 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3705 -0.8217 2.8961 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7132 0.2131 0.2382 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7587 2.8178 -1.0703 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8174 -1.1926 0.6077 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4975 -2.8801 -2.2235 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3754 -3.8242 -1.4926 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6296 -0.3579 -1.8593 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4275 0.7168 3.1589 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6257 1.9869 2.8413 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9073 2.2418 2.2672 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1964 0.7822 0.9851 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2726 2.1806 -0.6298 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9737 0.8785 -0.7517 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7318 2.2892 0.3391 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8100 -1.1461 0.2051 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9557 -1.1206 1.9820 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6466 -2.8028 1.5010 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5896 -1.2567 2.4124 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3824 0.0514 0.4475 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6840 -1.7854 -0.9222 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7562 -2.3728 -2.7365 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2275 -3.3180 -0.3205 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3740 -0.4492 -1.2657 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6634 -1.2164 0.6496 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5420 2.0304 -2.0809 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4919 3.5784 -2.1905 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0503 -1.1111 1.7094 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0290 -1.8735 2.9436 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3538 2.0602 0.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5583 2.4010 0.8922 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0241 -1.4161 2.3630 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6926 3.7522 -1.4078 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0504 -3.7651 -2.1275 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1429 -3.8530 -0.8991 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1142 0.3608 -1.3794 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 19 22 1 0 18 23 1 0 23 24 2 0 23 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 31 33 1 0 30 34 1 0 26 35 1 0 25 36 1 0 13 37 1 0 12 38 1 0 11 39 1 0 10 40 1 0 37 9 1 0 20 15 1 0 32 27 1 0 35 17 1 0 1 41 1 0 1 42 1 0 1 43 1 0 2 44 1 0 3 45 1 0 3 46 1 0 3 47 1 0 4 48 1 0 4 49 1 0 8 50 1 0 8 51 1 0 9 52 1 6 10 53 1 1 11 54 1 6 12 55 1 1 13 56 1 6 16 57 1 0 21 58 1 0 22 59 1 0 28 60 1 0 29 61 1 0 32 62 1 0 33 63 1 0 34 64 1 0 36 65 1 0 38 66 1 0 39 67 1 0 40 68 1 0 M END

Standard InCHIKey	JJDVTBGHKGLZLP-HMHWFSEDSA-N
Standard InCHI	InChI=1S/C26H28O14/c1-9(2)5-16(29)37-8-15-19(31)22(34)24(36)26(40-15)39-14-7-13-17(20(32)18(14)30)21(33)23(35)25(38-13)10-3-4-11(27)12(28)6-10/h3-4,6-7,9,15,19,22,24,26-28,30-32,34-36H,5,8H2,1-2H3/t15-,19-,22+,24-,26-/m1/s1
SMILES	CC(C)CC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2cc3c(c(c2O)O)c(=O)c(c(c2ccc(c(c2)O)O)o3)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	564.15	Volume:	523.361 ? Van der Waals volume.
Dense:	1.078	LogP:	1.163 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.567 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.985 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	25.0
TPSA:	236.81 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	8.0	Rings:	4.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.146	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.299	Fsp³:	0.385
MCE-18:	98.333 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.843	Fluc inhibitor:	0.305 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.903 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.839 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.073	Promiscuous compounds:	0.724

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.439	MDCK Permeability:	-5.067
Pgp-inhibitor:	0.0	Pgp-substrate:	0.013
PAMPA:	0.998 ? 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):	0.925
20% Bioavailability (F20%):	0.93	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.183
Plasma Protein Binding (PPB):	82.859%	Volume Distribution (VD):	-0.179
Fu:	14.257% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.457
BSEP inhibitor:	0.197

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.005
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.009
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.961
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.935 ? 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):

3.351

Half-life (T1/2):

3.316

ADMET: Toxicity

hERG Blockers:	0.025	hERG Blockers (10um):	0.387
Human Hepatotoxicity (H-HT):	0.432	Drug-induced Liver Injury (DILI):	0.948
AMES Toxicity:	0.673	Rat Oral Acute Toxicity:	0.104
Maximum Recommended Daily Dose:	0.112	Skin Sensitization:	0.991
Carcinogencity:	0.149	Eye Corrosion:	0.0
Eye Irritation:	0.767	Respiratory Toxicity:	0.023
Drug-induced Neurotoxicity:	0.002	Ototoxicity:	0.846
Hematotoxicity:	0.073	Drug-induced Nephrotoxicity:	0.33
Genotoxicity:	0.671	RPMI-8226 Immunitoxicity:	0.076
A549 Cytotoxicity:	0.739	Hek293 Cytotoxicity:	0.098
BCF:	0.687 ? 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:	3.432 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.012 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.46 ? 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
NPO3676	Fusarium sambucinum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8	Buphthalmum salicifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4578	Cystoseira fimbriata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8	Buphthalmum salicifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4578	Cystoseira fimbriata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3676	Fusarium sambucinum	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 NPC22204 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	8996
0.1-0.2	36834
0.2-0.3	3182
0.3-0.4	620
0.4-0.5	190
0.5-0.6	24
0.6-0.7	5
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	Natural Product ID
0.7857	Intermediate Similarity	NPC477848
0.7841	Intermediate Similarity	NPC211532
0.734	Intermediate Similarity	NPC603856
0.7143	Intermediate Similarity	NPC245014
0.6739	Remote Similarity	NPC233994
0.6735	Remote Similarity	NPC599948
0.6702	Remote Similarity	NPC488364
0.6364	Remote Similarity	NPC84265
0.6105	Remote Similarity	NPC67105
0.5859	Remote Similarity	NPC470443
0.5778	Remote Similarity	NPC238376
0.5729	Remote Similarity	NPC254540
0.5652	Remote Similarity	NPC58716
0.5625	Remote Similarity	NPC116864
0.5625	Remote Similarity	NPC244776
0.5543	Remote Similarity	NPC277205
0.5543	Remote Similarity	NPC37919
0.5534	Remote Similarity	NPC80068
0.5455	Remote Similarity	NPC227508
0.5426	Remote Similarity	NPC117260
0.53	Remote Similarity	NPC275454
0.5229	Remote Similarity	NPC480796
0.5213	Remote Similarity	NPC609879
0.5192	Remote Similarity	NPC229409
0.5152	Remote Similarity	NPC172807
0.5106	Remote Similarity	NPC108831
0.5106	Remote Similarity	NPC182634
0.5098	Remote Similarity	NPC210073
0.5053	Remote Similarity	NPC282987
0.5053	Remote Similarity	NPC146792
0.5052	Remote Similarity	NPC285197
0.505	Remote Similarity	NPC187379
0.5046	Remote Similarity	NPC121703

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC22204 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3441
0.1-0.2	5640
0.2-0.3	59
0.3-0.4	4
0.4-0.5	6
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