NPASS Compound

Natural Product: NPC573712

Natural Product ID	NPC573712
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(3S,4S,5S,6R)-6-(hydroxymethyl)thiane-2,3,4,5-tetrol
IUPAC Name	(3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)tetrahydrothiopyran-2,3,4,5-tetrol
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 24 24 0 0 0 0 0 0 0 0999 V2000 3.3461 0.3701 -0.5853 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5529 -0.3687 0.2592 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1096 -0.3808 -0.1013 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2369 -1.4130 1.1401 S 0 0 0 0 0 0 0 0 0 0 0 0 -1.5242 -1.3321 0.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7982 -2.5691 0.0295 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5895 -0.2912 -0.4728 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9628 -0.0599 -0.7037 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9836 1.0106 -0.0704 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6127 1.4231 1.1136 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4995 1.0111 0.0365 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1165 1.9324 -0.7939 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8948 -0.1799 -1.1992 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6454 -0.0189 1.3090 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9258 -1.4161 0.2467 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8884 -0.7975 -1.0867 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1828 -1.0963 1.4624 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9703 -2.7869 -0.4990 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1897 -0.6861 -1.4174 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1660 0.8842 -0.8007 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2687 1.7650 -0.8456 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2996 2.1232 0.9465 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7553 1.3300 1.0902 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5770 1.5468 -1.5621 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 5 7 1 0 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 11 3 1 0 1 13 1 0 2 14 1 0 2 15 1 0 3 16 1 6 5 17 1 0 6 18 1 0 7 19 1 6 8 20 1 0 9 21 1 6 10 22 1 0 11 23 1 1 12 24 1 0 M END

Standard InCHIKey	KNWYARBAEIMVMZ-QTVWNMPRSA-N
Standard InCHI	InChI=1S/C6H12O5S/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6?/m1/s1
SMILES	OC[C@H]1SC(O)[C@@H](O)[C@@H](O)[C@@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	196.04	Volume:	166.236 ? Van der Waals volume.
Dense:	1.179	LogP:	-1.16 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.748 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.085 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	6.0
TPSA:	101.15 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	5.0	Rings:	1.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.318	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.568	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:	0.015	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.054 ? 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:	0.531	Promiscuous compounds:	0.009

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.304	MDCK Permeability:	-5.095
Pgp-inhibitor:	0.001	Pgp-substrate:	0.863
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):	0.453
20% Bioavailability (F20%):	0.256	30% Bioavailability (F30%):	0.354
50% Bioavailability (F50%):	0.802

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.111
Plasma Protein Binding (PPB):	37.412%	Volume Distribution (VD):	-0.465
Fu:	63.428% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.568
OATP1B3 inhibitor:	0.702	BCRP inhibitor:	0.026
BSEP inhibitor:	0.09

ADMET: Metabolism

CYP1A2-inhibitor:	0.017	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.037	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.627	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.003	CYP3A4-substrate:	0.024
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.547
HLM stability:	0.083 ? 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):

2.259

Half-life (T1/2):

2.095

ADMET: Toxicity

hERG Blockers:	0.014	hERG Blockers (10um):	0.289
Human Hepatotoxicity (H-HT):	0.371	Drug-induced Liver Injury (DILI):	0.359
AMES Toxicity:	0.491	Rat Oral Acute Toxicity:	0.056
Maximum Recommended Daily Dose:	0.007	Skin Sensitization:	0.988
Carcinogencity:	0.15	Eye Corrosion:	0.019
Eye Irritation:	0.833	Respiratory Toxicity:	0.044
Drug-induced Neurotoxicity:	0.004	Ototoxicity:	0.61
Hematotoxicity:	0.244	Drug-induced Nephrotoxicity:	0.391
Genotoxicity:	0.01	RPMI-8226 Immunitoxicity:	0.02
A549 Cytotoxicity:	0.034	Hek293 Cytotoxicity:	0.033
BCF:	0.139 ? 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:	1.286 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	2.292 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	1.522 ? 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
NPO46391	Clathria (Dendrocia) pyramida	Genus	Microcionidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC573712 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	35100
0.1-0.2	13959
0.2-0.3	714
0.3-0.4	39
0.4-0.5	22
0.5-0.6	13
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	10

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC73906
1.0	High Similarity	NPC285364
1.0	High Similarity	NPC255377
1.0	High Similarity	NPC92246
1.0	High Similarity	NPC165846
1.0	High Similarity	NPC176017
1.0	High Similarity	NPC21209
1.0	High Similarity	NPC69445
1.0	High Similarity	NPC289758
1.0	High Similarity	NPC605355
0.6957	Remote Similarity	NPC320189
0.5926	Remote Similarity	NPC114208
0.5926	Remote Similarity	NPC4884
0.5926	Remote Similarity	NPC321087
0.5926	Remote Similarity	NPC277475
0.5926	Remote Similarity	NPC602568
0.5161	Remote Similarity	NPC322801
0.5161	Remote Similarity	NPC14144
0.5161	Remote Similarity	NPC600826
0.5161	Remote Similarity	NPC606475
0.5128	Remote Similarity	NPC89145
0.5128	Remote Similarity	NPC157514
0.5128	Remote Similarity	NPC322314
0.5128	Remote Similarity	NPC269166

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC573712 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8114
0.1-0.2	921
0.2-0.3	77
0.3-0.4	15
0.4-0.5	15
0.5-0.6	3
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	NPD8997	Approved
1.0	High Similarity	NPD8998	Phase 2
1.0	High Similarity	NPD8999	Phase 4
1.0	High Similarity	NPD9000	Phase 3
0.5161	Remote Similarity	NPD9031	Approved
0.5161	Remote Similarity	NPD9032	Phase 4
0.5161	Remote Similarity	NPD9033	Approved

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