NPASS Compound

Natural Product: NPC511063

Natural Product ID	NPC511063
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	29781-81-5
IUPAC Name	(2~{S},3~{R},4~{S},5~{S},6~{R})-2-decoxy-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 54 54 0 0 0 0 0 0 0 0999 V2000 7.2298 0.4302 0.0648 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7096 0.2748 -0.0543 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3337 -1.0060 0.6316 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8529 -1.2303 0.5908 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3808 -1.3339 -0.8244 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8876 -1.5868 -0.9097 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0687 -0.4862 -0.2569 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3448 0.8057 -0.9306 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6422 2.0077 -0.4095 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8507 1.9255 -0.4729 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3083 0.8875 0.2816 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6955 0.8253 0.2119 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0194 -0.4166 -0.3269 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2350 -0.8992 0.0852 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8942 -1.7788 -0.9531 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1320 -2.8851 -1.2757 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1619 0.2657 0.3618 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.4939 -0.1403 0.4246 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7096 0.8557 1.7022 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3276 2.0707 1.9572 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2108 0.9683 1.6333 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5580 0.0380 2.4149 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6865 -0.3267 -0.6003 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5359 1.4682 -0.1855 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5022 0.2456 1.1184 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2096 1.1023 0.4650 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4271 0.3038 -1.1092 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7321 -1.0030 1.6744 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8622 -1.8205 0.0445 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3346 -0.4084 1.1387 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5634 -2.1820 1.1095 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6964 -0.4738 -1.3973 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8626 -2.2318 -1.2859 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6939 -2.5471 -0.3889 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6192 -1.7069 -1.9793 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0041 -0.8023 -0.4372 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2322 -0.5023 0.8238 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0441 0.6705 -2.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4476 1.0178 -0.8741 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9194 2.9225 -1.0139 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9696 2.2781 0.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3469 2.8951 -0.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1291 1.6850 -1.5435 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0527 1.6375 -0.4389 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0651 -1.4988 1.0070 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1168 -1.1723 -1.8554 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8441 -2.1476 -0.5159 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3233 -2.6092 -1.8042 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0002 1.0298 -0.4260 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0254 0.4516 -0.1695 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9796 0.1129 2.4651 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3545 2.6381 1.1490 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9374 1.9765 1.9778 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0125 -0.5948 1.8814 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 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 1 0 14 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 21 12 1 0 1 23 1 0 1 24 1 0 1 25 1 0 2 26 1 0 2 27 1 0 3 28 1 0 3 29 1 0 4 30 1 0 4 31 1 0 5 32 1 0 5 33 1 0 6 34 1 0 6 35 1 0 7 36 1 0 7 37 1 0 8 38 1 0 8 39 1 0 9 40 1 0 9 41 1 0 10 42 1 0 10 43 1 0 12 44 1 6 14 45 1 1 15 46 1 0 15 47 1 0 16 48 1 0 17 49 1 6 18 50 1 0 19 51 1 1 20 52 1 0 21 53 1 1 22 54 1 0 M END

Standard InCHIKey	JDRSMPFHFNXQRB-LJIZCISZSA-N
Standard InCHI	InChI=1S/C16H32O6/c1-2-3-4-5-6-7-8-9-10-21-16-15(20)14(19)13(18)12(11-17)22-16/h12-20H,2-11H2,1H3/t12-,13-,14+,15-,16+/m1/s1
SMILES	CCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	320.22	Volume:	329.477 ? Van der Waals volume.
Dense:	0.972	LogP:	2.355 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.369 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.672 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	6.0
TPSA:	99.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	1.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.423	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.39	Fsp³:	1.0
MCE-18:	18.5 ? 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:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.318	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.019 ? 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:	0.399	Promiscuous compounds:	0.026

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.218	MDCK Permeability:	-4.758
Pgp-inhibitor:	0.001	Pgp-substrate:	0.242
PAMPA:	0.179 ? 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):	0.845
20% Bioavailability (F20%):	0.5	30% Bioavailability (F30%):	0.972
50% Bioavailability (F50%):	0.828

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012	MRP1:	0.365
Plasma Protein Binding (PPB):	92.38%	Volume Distribution (VD):	-0.237
Fu:	8.423% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.963
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.306
BSEP inhibitor:	0.101

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.922
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.223	CYP2D6-substrate:	0.033
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.997
HLM stability:	0.163 ? 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):

2.961

Half-life (T1/2):

1.367

ADMET: Toxicity

hERG Blockers:	0.087	hERG Blockers (10um):	0.514
Human Hepatotoxicity (H-HT):	0.473	Drug-induced Liver Injury (DILI):	0.473
AMES Toxicity:	0.334	Rat Oral Acute Toxicity:	0.043
Maximum Recommended Daily Dose:	0.024	Skin Sensitization:	0.993
Carcinogencity:	0.135	Eye Corrosion:	0.059
Eye Irritation:	0.916	Respiratory Toxicity:	0.219
Drug-induced Neurotoxicity:	0.026	Ototoxicity:	0.843
Hematotoxicity:	0.245	Drug-induced Nephrotoxicity:	0.644
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.071
A549 Cytotoxicity:	0.217	Hek293 Cytotoxicity:	0.083
BCF:	1.894 ? 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:	4.268 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.266 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.652 ? 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
NPO20874	Tanacetum vulgare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25924515]
NPO20874	Tanacetum vulgare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37630407]
NPO20874	Tanacetum vulgare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20874	Tanacetum vulgare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20874	Tanacetum vulgare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20874	Tanacetum vulgare	Species	Asteraceae	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 NPC511063 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	21948
0.1-0.2	22277
0.2-0.3	4709
0.3-0.4	715
0.4-0.5	166
0.5-0.6	29
0.6-0.7	6
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC606861
1.0	High Similarity	NPC607126
0.8333	Intermediate Similarity	NPC233726
0.6585	Remote Similarity	NPC155457
0.6486	Remote Similarity	NPC124963
0.6279	Remote Similarity	NPC13143
0.6279	Remote Similarity	NPC294813
0.617	Remote Similarity	NPC277570
0.6042	Remote Similarity	NPC206601
0.5918	Remote Similarity	NPC601155
0.5897	Remote Similarity	NPC326533
0.5882	Remote Similarity	NPC488690
0.5686	Remote Similarity	NPC285003
0.5625	Remote Similarity	NPC147292
0.5593	Remote Similarity	NPC482018
0.5593	Remote Similarity	NPC482015
0.5526	Remote Similarity	NPC23134
0.549	Remote Similarity	NPC12040
0.537	Remote Similarity	NPC469469
0.5306	Remote Similarity	NPC477750
0.5306	Remote Similarity	NPC477763
0.5306	Remote Similarity	NPC477757
0.5306	Remote Similarity	NPC477762
0.5306	Remote Similarity	NPC477755
0.5306	Remote Similarity	NPC477753
0.5263	Remote Similarity	NPC42503
0.5263	Remote Similarity	NPC282143
0.5263	Remote Similarity	NPC107914
0.5263	Remote Similarity	NPC242073
0.5263	Remote Similarity	NPC299781
0.5263	Remote Similarity	NPC488689
0.5263	Remote Similarity	NPC157193
0.5263	Remote Similarity	NPC608193
0.5254	Remote Similarity	NPC603467
0.5192	Remote Similarity	NPC241265
0.5179	Remote Similarity	NPC163812
0.5111	Remote Similarity	NPC268243
0.5094	Remote Similarity	NPC280367

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC511063 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6714
0.1-0.2	2216
0.2-0.3	187
0.3-0.4	19
0.4-0.5	13
0.5-0.6	1
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
0.5349	Remote Similarity	NPD904	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