NPASS Compound

Natural Product: NPC282143

Natural Product ID	NPC282143
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Methyl Alpha-D-Mannoside
IUPAC Name	(2R,3S,4S,5S,6S)-2-(hydroxymethyl)-6-methoxyoxane-3,4,5-triol
Synonyms	Methyl Alpha-D-Mannopyranoside; Methyl Alpha-D-Mannoside
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL195368
PubChem CID	101798
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl 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 27 27 0 0 0 0 0 0 0 0999 V2000 2.9582 0.9337 1.0740 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4623 0.0876 0.1013 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0851 0.0373 0.0544 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6637 -1.4047 0.2819 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7386 -1.6626 -0.1718 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5090 -0.3572 -0.3741 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7299 0.5613 -1.2763 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1565 1.9919 -1.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7732 2.4275 0.2379 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6268 0.4246 -1.1894 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7045 -0.7215 -0.9999 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4443 -2.5362 0.6142 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8549 -1.7253 1.6413 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0689 0.8860 1.0102 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6755 0.6364 2.1057 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6855 1.9945 0.9218 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6942 0.7072 0.8306 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3869 -2.0373 -0.2825 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6937 -2.1215 -1.2045 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7549 0.1279 0.5890 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0146 0.3448 -2.3480 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2535 2.0916 -1.1295 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7108 2.6742 -1.7873 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3701 2.1015 0.9394 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8308 -0.3144 -1.8713 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3485 -2.4187 1.5724 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8709 -2.7285 1.6895 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 7 10 1 0 6 11 1 0 5 12 1 0 4 13 1 0 10 3 1 0 1 14 1 0 1 15 1 0 1 16 1 0 3 17 1 1 4 18 1 6 5 19 1 6 6 20 1 1 7 21 1 6 8 22 1 0 8 23 1 0 9 24 1 0 11 25 1 0 12 26 1 0 13 27 1 0 M END

Standard InCHIKey	HOVAGTYPODGVJG-VEIUFWFVSA-N
Standard InCHI	InChI=1S/C7H14O6/c1-12-7-6(11)5(10)4(9)3(2-8)13-7/h3-11H,2H2,1H3/t3-,4-,5+,6+,7+/m1/s1
SMILES	CO[C@@H]1[C@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	194.08	Volume:	173.813 ? Van der Waals volume.
Dense:	1.117	LogP:	-1.765 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.277 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	0.004 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	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:	0.386	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.505	Fsp³:	1.0
MCE-18:	21.714 ? 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:	0.105	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.052 ? 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:	0.542	Promiscuous compounds:	0.063

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.427	MDCK Permeability:	-4.966
Pgp-inhibitor:	0.0	Pgp-substrate:	0.675
PAMPA:	0.972 ? 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):	0.99
20% Bioavailability (F20%):	0.671	30% Bioavailability (F30%):	0.983
50% Bioavailability (F50%):	0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.243	MRP1:	0.176
Plasma Protein Binding (PPB):	30.872%	Volume Distribution (VD):	-0.5
Fu:	72.701% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.987
OATP1B3 inhibitor:	0.992	BCRP inhibitor:	0.101
BSEP inhibitor:	0.001

ADMET: Metabolism

CYP1A2-inhibitor:	0.048	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.002	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.011	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.003	CYP3A4-substrate:	0.091
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.027
HLM stability:	0.111 ? 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):

2.026

Half-life (T1/2):

2.58

ADMET: Toxicity

hERG Blockers:	0.014	hERG Blockers (10um):	0.096
Human Hepatotoxicity (H-HT):	0.613	Drug-induced Liver Injury (DILI):	0.726
AMES Toxicity:	0.909	Rat Oral Acute Toxicity:	0.064
Maximum Recommended Daily Dose:	0.022	Skin Sensitization:	0.994
Carcinogencity:	0.283	Eye Corrosion:	0.029
Eye Irritation:	0.936	Respiratory Toxicity:	0.061
Drug-induced Neurotoxicity:	0.064	Ototoxicity:	0.838
Hematotoxicity:	0.472	Drug-induced Nephrotoxicity:	0.704
Genotoxicity:	0.2	RPMI-8226 Immunitoxicity:	0.119
A549 Cytotoxicity:	0.187	Hek293 Cytotoxicity:	0.063
BCF:	0.146 ? 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:	1.462 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	2.342 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	1.801 ? 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
NPO4414	Lilium lancifolium	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4414	Lilium lancifolium	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4414	Lilium lancifolium	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4414	Lilium lancifolium	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4414	Lilium lancifolium	Species	Liliaceae	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

Activity Type	# Activity
IC50	12
Ratio IC50	3
Kd	6
Ratio	1
EC50	1

Activity Type	# Activity
Individual protein	12
Single protein	5
Organism	1
Unchecked	1
Others	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	Ratio IC50	=	29.0	n.a.	PMID[21962988]
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	IC50	=	1900.0	nM	PMID[21962988]
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	IC50	=	450000.0	nM	DOI[10.1039/C4MD00093E]
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	Kd	=	2200.0	nM	DOI[10.1039/C4MD00093E]
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	Ratio	=	1.0	n.a.	PMID[35777073]
NPT2712	Individual protein	Adhesin protein fimH	Escherichia coli K-12	Kd	=	2200.0	nM	PMID[35777073]
NPT25502	Single protein	Fucose-binding lectin PA-IIL	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM14847 / LMG 12228 / 1C / PRS 101 / PAO1)	IC50	=	157000.0	nM	PMID[31449405]
NPT25502	Single protein	Fucose-binding lectin PA-IIL	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM14847 / LMG 12228 / 1C / PRS 101 / PAO1)	IC50	=	37000.0	nM	PMID[31553873]
NPT25502	Single protein	Fucose-binding lectin PA-IIL	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM14847 / LMG 12228 / 1C / PRS 101 / PAO1)	IC50	=	46800.0	nM	PMID[36201248]
NPT25502	Single protein	Fucose-binding lectin PA-IIL	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM14847 / LMG 12228 / 1C / PRS 101 / PAO1)	IC50	=	104000.0	nM	PMID[36201248]
NPT5686	Individual protein	Concanavalin-A	Canavalia ensiformis	IC50	=	350000.0	nM	PMID[18990567]
NPT5707	Individual protein	C-type lectin domain family 4 member M	Homo sapiens	IC50	=	1270000.0	nM	PMID[34524803]
NPT5647	Individual protein	Lectin	Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656/ NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315))	Kd	=	2700.0	nM	DOI[10.1039/C5MD00557D]
NPT5647	Individual protein	Lectin	Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656/ NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315))	IC50	=	7000.0	nM	DOI[10.1039/C5MD00557D]
NPT4774	Individual protein	PA-I galactophilic lectin	Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)	Kd	=	71.0	nM	PMID[35777073]
NPT4774	Individual protein	PA-I galactophilic lectin	Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)	Kd	=	71000.0	nM	PMID[26804741]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT28438	Unchecked	Unchecked	n.a.	Kd	=	71000.0	nM	PMID[36256875]
NPT610	Others	Molecular identity unknown	n.a.	IC50	=	1100000.0	nM	PMID[15878660]
NPT3638	Organism	BK polyomavirus	BK polyomavirus	EC50	>	100000.0	nM	PMID[17893158]
NPT2	Others	Unspecified	n.a.	IC50	=	1320000.0	nM	PMID[21481594]
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	1.0	n.a.	PMID[21481594]

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
Mus musculus	n.a.	T1/2	=	0.0125	hr	PMID[26804741]

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 NPC282143 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	33031
0.1-0.2	13487
0.2-0.3	2551
0.3-0.4	580
0.4-0.5	170
0.5-0.6	21
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	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC42503
1.0	High Similarity	NPC299781
1.0	High Similarity	NPC157193
1.0	High Similarity	NPC608193
0.8077	Intermediate Similarity	NPC23134
0.7692	Intermediate Similarity	NPC107914
0.7692	Intermediate Similarity	NPC242073
0.6897	Remote Similarity	NPC124963
0.6667	Remote Similarity	NPC326533
0.6452	Remote Similarity	NPC317501
0.6452	Remote Similarity	NPC605930
0.625	Remote Similarity	NPC143326
0.6061	Remote Similarity	NPC31496
0.5882	Remote Similarity	NPC233726
0.5714	Remote Similarity	NPC130683
0.5556	Remote Similarity	NPC155457
0.5556	Remote Similarity	NPC268243
0.5405	Remote Similarity	NPC246558
0.5405	Remote Similarity	NPC323361
0.5405	Remote Similarity	NPC67660
0.5405	Remote Similarity	NPC145112
0.5405	Remote Similarity	NPC165198
0.5405	Remote Similarity	NPC209753
0.5405	Remote Similarity	NPC58629
0.5263	Remote Similarity	NPC13143
0.5263	Remote Similarity	NPC290179
0.5263	Remote Similarity	NPC132938
0.5263	Remote Similarity	NPC294813
0.5263	Remote Similarity	NPC603514
0.5263	Remote Similarity	NPC606861
0.5263	Remote Similarity	NPC607126
0.5128	Remote Similarity	NPC32148
0.5128	Remote Similarity	NPC152384
0.5128	Remote Similarity	NPC83248

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC282143 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7973
0.1-0.2	1000
0.2-0.3	135
0.3-0.4	19
0.4-0.5	10
0.5-0.6	9
0.6-0.7	3
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
0.6429	Remote Similarity	NPD8994	Approved
0.6364	Remote Similarity	NPD904	Phase 3
0.625	Remote Similarity	NPD905	Phase 4
0.5714	Remote Similarity	NPD887	Approved
0.5714	Remote Similarity	NPD895	Phase 4
0.5405	Remote Similarity	NPD888	Phase 3
0.5405	Remote Similarity	NPD889	Approved
0.5405	Remote Similarity	NPD890	Clinical (unspecified phase)
0.5405	Remote Similarity	NPD891	Phase 3
0.5405	Remote Similarity	NPD892	Phase 3
0.5405	Remote Similarity	NPD893	Approved
0.5405	Remote Similarity	NPD894	Phase 4

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