NPASS Compound

Natural Product: NPC125353

Natural Product ID	NPC125353
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	MSWZFWKMSRAUBD-RXRWUWDJSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	12302999
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0001540] Monosaccharides [CHEMONTID:0001498] Hexoses

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 25 25 0 0 0 0 0 0 0 0999 V2000 -2.3997 0.5679 0.3064 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2428 -0.1774 -0.3698 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5453 -0.9678 0.6896 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6428 -0.1591 1.1585 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5765 -0.0691 -0.0389 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8272 0.3789 -1.2587 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9503 -0.5860 -2.2570 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4776 0.7442 -1.0140 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6362 0.8587 0.3249 N 0 0 0 0 0 0 0 0 0 0 0 0 0.2543 1.1426 1.4638 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0589 -2.1417 0.0802 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1686 1.2438 -0.6592 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0833 -0.1188 0.8229 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0258 1.3533 0.9937 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7345 -0.9072 -1.0629 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2437 -1.2059 1.5161 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1743 -0.6429 2.0012 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0248 -1.0735 -0.1870 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3504 1.2864 -1.6445 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9003 -0.9217 -2.2007 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4271 0.8612 -0.3265 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8653 0.7197 1.3196 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0044 1.6007 1.9225 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7895 -2.4312 -0.5298 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8642 0.6448 -1.0505 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 6 8 1 0 5 9 1 0 4 10 1 0 3 11 1 0 1 12 1 0 8 2 1 0 1 13 1 0 1 14 1 0 2 15 1 6 3 16 1 1 4 17 1 1 5 18 1 6 6 19 1 6 7 20 1 0 9 21 1 0 9 22 1 0 10 23 1 0 11 24 1 0 12 25 1 0 M END

Standard InCHIKey	MSWZFWKMSRAUBD-RXRWUWDJSA-N
Standard InCHI	InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3+,4-,5-,6+/m1/s1
SMILES	C([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O)O1)N)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	179.08	Volume:	158.724 ? Van der Waals volume.
Dense:	1.128	LogP:	-1.677 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.252 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	0.297 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	6.0
TPSA:	116.17 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	6.0	Rings:	1.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.288	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.844	Fsp³:	1.0
MCE-18:	22.667 ? 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:	0
Colloidal aggregators:	0.173	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.07 ? 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:	0.271	Promiscuous compounds:	0.019

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.331	MDCK Permeability:	-5.148
Pgp-inhibitor:	0.001	Pgp-substrate:	0.791
PAMPA:	0.986 ? 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):	0.806
20% Bioavailability (F20%):	0.447	30% Bioavailability (F30%):	0.69
50% Bioavailability (F50%):	0.774

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.203	MRP1:	0.147
Plasma Protein Binding (PPB):	15.663%	Volume Distribution (VD):	-0.447
Fu:	85.166% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.844
OATP1B3 inhibitor:	0.934	BCRP inhibitor:	0.076
BSEP inhibitor:	0.006

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.881	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.002	CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.021	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.01	CYP3A4-substrate:	0.004
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.243
HLM stability:	0.01 ? 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):

2.91

Half-life (T1/2):

1.884

ADMET: Toxicity

hERG Blockers:	0.02	hERG Blockers (10um):	0.114
Human Hepatotoxicity (H-HT):	0.599	Drug-induced Liver Injury (DILI):	0.33
AMES Toxicity:	0.836	Rat Oral Acute Toxicity:	0.118
Maximum Recommended Daily Dose:	0.022	Skin Sensitization:	0.996
Carcinogencity:	0.355	Eye Corrosion:	0.051
Eye Irritation:	0.88	Respiratory Toxicity:	0.096
Drug-induced Neurotoxicity:	0.198	Ototoxicity:	0.743
Hematotoxicity:	0.318	Drug-induced Nephrotoxicity:	0.602
Genotoxicity:	0.36	RPMI-8226 Immunitoxicity:	0.083
A549 Cytotoxicity:	0.091	Hek293 Cytotoxicity:	0.026
BCF:	0.107 ? 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:	1.533 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	2.734 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	1.897 ? 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
NPO14148	Panax pseudoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20614	Aristotelia peduncularis	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19208	Chaetomium minutum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14148	Panax pseudoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19208	Chaetomium minutum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14148	Panax pseudoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20614	Aristotelia peduncularis	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13350	Dermocybe icterinoides	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20934	Genista januensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20053	Psilocybe subaeruginosa	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18106	Mitrephora vulpina	Species	Annonaceae	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 NPC125353 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	35496
0.1-0.2	13980
0.2-0.3	335
0.3-0.4	30
0.4-0.5	3
0.5-0.6	10
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	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC322801
1.0	High Similarity	NPC600826
1.0	High Similarity	NPC606475
0.9615	High Similarity	NPC600025
0.5161	Remote Similarity	NPC73906
0.5161	Remote Similarity	NPC285364
0.5161	Remote Similarity	NPC255377
0.5161	Remote Similarity	NPC92246
0.5161	Remote Similarity	NPC165846
0.5161	Remote Similarity	NPC176017
0.5161	Remote Similarity	NPC21209
0.5161	Remote Similarity	NPC69445
0.5161	Remote Similarity	NPC289758
0.5161	Remote Similarity	NPC605355

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC125353 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7752
0.1-0.2	1282
0.2-0.3	93
0.3-0.4	14
0.4-0.5	1
0.5-0.6	4
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	4

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD9031	Approved
1.0	High Similarity	NPD9032	Phase 4
1.0	High Similarity	NPD9033	Approved
0.9615	High Similarity	NPD9030	Approved
0.5161	Remote Similarity	NPD8997	Approved
0.5161	Remote Similarity	NPD8998	Phase 2
0.5161	Remote Similarity	NPD8999	Phase 4
0.5161	Remote Similarity	NPD9000	Phase 3

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