NPASS Compound

Natural Product: NPC51055

Natural Product ID	NPC51055
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KZLMQHDECHRBBR-PHAHAWKESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1938694
PubChem CID	56951182 57392447
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000403] Organic sulfuric acids and derivatives [CHEMONTID:0003455] Sulfuric acid esters [CHEMONTID:0001185] Sulfuric acid monoesters

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 60 59 0 0 0 0 0 0 0 0999 V2000 6.0609 1.3101 2.4561 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1058 0.3067 2.0644 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2611 0.0332 0.6402 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3294 -0.6738 -0.2114 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9104 -0.3551 -0.3907 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0028 -0.6830 0.7171 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5799 -0.2239 0.3720 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1184 -0.9340 -0.8561 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6733 -0.4959 -1.1623 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5530 0.9716 -1.4008 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8602 1.3142 -1.6940 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7693 0.3511 -1.7052 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2208 0.6156 -1.9933 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9677 0.1500 -0.7307 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4240 0.4132 -1.0150 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3079 -0.1339 0.0581 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0687 0.5191 1.4013 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3959 1.8746 1.3802 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7207 0.0139 -0.2672 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.6124 1.7658 -1.2427 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7565 -1.1895 -0.5152 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9200 -1.5664 0.8653 S 0 0 0 0 0 0 0 0 0 0 0 0 -2.1710 -0.3510 1.3377 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8644 -2.6359 0.6228 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9082 -2.1499 2.0919 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3945 0.8969 3.2471 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5706 2.2394 2.8948 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4155 1.6344 1.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0829 0.6656 2.5080 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8858 -0.6913 2.5905 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4417 1.0725 0.1271 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2984 -0.4805 0.4923 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7662 -0.7514 -1.2964 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3946 -1.8244 0.0392 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8130 0.7469 -0.6360 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5197 -0.8609 -1.3248 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2073 -0.3802 1.7147 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8924 -1.8365 0.7383 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8756 -0.4404 1.1978 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5806 0.8902 0.2312 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0848 -2.0194 -0.7373 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6638 -0.6551 -1.7893 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3981 -1.0866 -2.0604 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0949 -0.7800 -0.2593 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2524 1.3202 -2.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8042 1.5370 -0.4558 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1788 2.3445 -1.9029 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5166 -0.6833 -1.5063 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4247 1.6675 -2.1888 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5192 -0.0624 -2.8030 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5772 0.7818 0.0977 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6488 -0.1105 -1.9692 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1106 -1.2150 0.1666 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0488 0.3283 1.7290 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7552 0.0364 2.1279 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0080 2.1205 0.6657 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1781 -0.8923 -0.4160 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9061 0.7428 -0.9639 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7305 1.9752 -2.2232 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4617 -2.8534 1.7112 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 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 16 19 1 0 15 20 1 0 14 21 1 0 21 22 1 0 22 23 2 0 22 24 2 0 22 25 1 0 1 26 1 0 1 27 1 0 1 28 1 0 2 29 1 0 2 30 1 0 3 31 1 0 3 32 1 0 4 33 1 0 4 34 1 0 5 35 1 0 5 36 1 0 6 37 1 0 6 38 1 0 7 39 1 0 7 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 9 44 1 0 10 45 1 0 10 46 1 0 11 47 1 0 12 48 1 0 13 49 1 0 13 50 1 0 14 51 1 1 15 52 1 6 16 53 1 1 17 54 1 0 17 55 1 0 18 56 1 0 19 57 1 0 19 58 1 0 20 59 1 0 25 60 1 0 M END

Standard InCHIKey	KZLMQHDECHRBBR-PHAHAWKESA-N
Standard InCHI	InChI=1S/C17H35NO6S/c1-2-3-4-5-6-7-8-9-10-11-12-13-16(24-25(21,22)23)17(20)15(18)14-19/h11-12,15-17,19-20H,2-10,13-14,18H2,1H3,(H,21,22,23)/b12-11+/t15-,16+,17-/m1/s1
SMILES	CCCCCCCCCC/C=C/C[C@@H]([C@@H]([C@@H](CO)N)O)OS(=O)(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	381.22	Volume:	382.199 ? Van der Waals volume.
Dense:	0.997	LogP:	1.618 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.429 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.835 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	16.0	Rigid Bonds:	3.0
TPSA:	130.08 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	5.0	Rings:	0.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.183	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.783	Fsp³:	0.882
MCE-18:	6.0 ? 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:	0.557	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.007 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.089	Promiscuous compounds:	0.592

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.277	MDCK Permeability:	-4.823
Pgp-inhibitor:	0.0	Pgp-substrate:	0.018
PAMPA:	0.246 ? 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):	0.98
20% Bioavailability (F20%):	0.998	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.521
Plasma Protein Binding (PPB):	97.236%	Volume Distribution (VD):	-0.601
Fu:	2.572% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.459
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.282
BSEP inhibitor:	0.651

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.002	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.348
HLM stability:	0.002 ? 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):

2.476

Half-life (T1/2):

1.154

ADMET: Toxicity

hERG Blockers:	0.106	hERG Blockers (10um):	0.309
Human Hepatotoxicity (H-HT):	0.81	Drug-induced Liver Injury (DILI):	0.286
AMES Toxicity:	0.121	Rat Oral Acute Toxicity:	0.119
Maximum Recommended Daily Dose:	0.592	Skin Sensitization:	1.0
Carcinogencity:	0.121	Eye Corrosion:	0.253
Eye Irritation:	0.568	Respiratory Toxicity:	0.896
Drug-induced Neurotoxicity:	0.052	Ototoxicity:	0.719
Hematotoxicity:	0.431	Drug-induced Nephrotoxicity:	0.369
Genotoxicity:	0.051	RPMI-8226 Immunitoxicity:	0.065
A549 Cytotoxicity:	0.519	Hek293 Cytotoxicity:	0.184
BCF:	1.009 ? 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:	4.387 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.813 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.726 ? 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
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10579872]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11325244]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088447]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22182501]
NPO85	Spirastrella abata	Species	Spirastrellidae	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

Activity Type	# Activity
MIC	10
IC50	2

Activity Type	# Activity
Organism	10
Others	2

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
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>	100.0	ug.mL-1	PMID[19307359]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	=	100.0	ug.mL-1	PMID[18024584]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	100.0	ug.mL-1	PMID[3959031]
NPT330	Organism	Trichophyton mentagrophytes	Trichophyton mentagrophytes	MIC	>	100.0	ug.mL-1	PMID[3959031]
NPT329	Organism	Trichophyton rubrum	Trichophyton rubrum	MIC	>	100.0	ug.mL-1	PMID[19093848]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	12.0	ug.mL-1	PMID[15043431]
NPT87	Organism	Aspergillus fumigatus	Aspergillus fumigatus	MIC	>	100.0	ug.mL-1	PMID[19093848]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100.0	ug.mL-1	PMID[17958396]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	=	25.0	ug.mL-1	PMID[17958396]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	100.0	ug.mL-1	PMID[18442909]
NPT2	Others	Unspecified	n.a.	IC50	=	20000.0	nM	PMID[18442909]
NPT2	Others	Unspecified	n.a.	IC50	=	21000.0	nM	PMID[20805391]

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 NPC51055 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	21416
0.1-0.2	26621
0.2-0.3	1646
0.3-0.4	167
0.4-0.5	3
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC212008
1.0	High Similarity	NPC140327
1.0	High Similarity	NPC62293
0.8478	Intermediate Similarity	NPC207657
0.5111	Remote Similarity	NPC47333

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC51055 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5666
0.1-0.2	3304
0.2-0.3	162
0.3-0.4	14
0.4-0.5	4
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