NPASS Compound

Natural Product: NPC489511

Natural Product ID	NPC489511
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PRIVBYDFWSFUFP-RJLJEYQFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	16130477
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0003297] Organic Polymers [CHEMONTID:0003298] Polypeptides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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182436 1 0 183437 1 0 183438 1 0 186439 1 1 187440 1 0 187441 1 0 188442 1 0 191443 1 1 192444 1 0 192445 1 0 193446 1 0 194447 1 0 194448 1 0 194449 1 0 195450 1 0 195451 1 0 195452 1 0 198453 1 6 199454 1 0 199455 1 0 201456 1 0 202457 1 0 204458 1 0 205459 1 0 206460 1 0 207461 1 0 211462 1 6 212463 1 0 212464 1 0 213465 1 0 214466 1 0 214467 1 0 215468 1 0 216469 1 0 217470 1 0 218471 1 0 219472 1 0 220473 1 0 221474 1 0 222475 1 0 223476 1 0 224477 1 0 225478 1 0 226479 1 0 227480 1 0 228481 1 0 229482 1 0 230483 1 0 231484 1 0 232485 1 0 233486 1 0 234487 1 0 235488 1 0 M END

Standard InCHIKey	PRIVBYDFWSFUFP-RJLJEYQFSA-N
Standard InCHI	InChI=1S/C147H253N45O43/c1-18-75(9)113(140(229)167-81(15)120(209)188-114(76(10)19-2)141(230)168-82(16)121(210)189-115(77(11)20-3)142(231)178-94(47-50-106(154)198)123(212)164-66-108(200)163-68-110(202)192-60-36-46-105(192)139(228)179-97(145(234)235)45-35-59-161-147(158)159)187-109(201)67-165-124(213)95(48-51-111(203)204)176-138(227)104(72-196)186-143(232)116(78(12)21-4)190-130(219)93(44-34-58-160-146(156)157)174-127(216)90(41-26-31-55-150)172-125(214)88(39-24-29-53-148)170-118(207)79(13)166-136(225)102(70-194)184-135(224)101(64-107(155)199)183-129(218)96(49-52-112(205)206)177-132(221)98(61-73(5)6)181-128(217)91(42-27-32-56-151)173-126(215)89(40-25-30-54-149)171-119(208)80(14)169-144(233)117(83(17)197)191-131(220)92(43-28-33-57-152)175-137(226)103(71-195)185-133(222)99(62-74(7)8)182-134(223)100(180-122(211)86(153)69-193)63-84-65-162-87-38-23-22-37-85(84)87/h22-23,37-38,65,73-83,86,88-105,113-117,162,193-197H,18-21,24-36,39-64,66-72,148-153H2,1-17H3,(H2,154,198)(H2,155,199)(H,163,200)(H,164,212)(H,165,213)(H,166,225)(H,167,229)(H,168,230)(H,169,233)(H,170,207)(H,171,208)(H,172,214)(H,173,215)(H,174,216)(H,175,226)(H,176,227)(H,177,221)(H,178,231)(H,179,228)(H,180,211)(H,181,217)(H,182,223)(H,183,218)(H,184,224)(H,185,222)(H,186,232)(H,187,201)(H,188,209)(H,189,210)(H,190,219)(H,191,220)(H,203,204)(H,205,206)(H,234,235)(H4,156,157,160)(H4,158,159,161)/t75-,76-,77-,78-,79-,80-,81-,82-,83+,86-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,113-,114-,115-,116-,117-/m0/s1
SMILES	CC[C@H](C)[C@@H](C(=N[C@@H](C)C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](C)C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](CCC(=N)O)C(=NCC(=NCC(=O)N1CCC[C@H]1C(=N[C@@H](CCCNC(=N)N)C(=O)O)O)O)O)O)O)O)O)O)N=C(CN=C([C@H](CCC(=O)O)N=C([C@H](CO)N=C([C@H]([C@@H](C)CC)N=C([C@H](CCCNC(=N)N)N=C([C@H](CCCCN)N=C([C@H](CCCCN)N=C([C@H](C)N=C([C@H](CO)N=C([C@H](CC(=N)O)N=C([C@H](CCC(=O)O)N=C([C@H](CC(C)C)N=C([C@H](CCCCN)N=C([C@H](CCCCN)N=C([C@H](C)N=C([C@H]([C@@H](C)O)N=C([C@H](CCCCN)N=C([C@H](CO)N=C([C@H](CC(C)C)N=C([C@H](Cc1c[nH]c2ccccc12)N=C([C@H](CO)N)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	3336.9	Volume:	3290.136 ? Van der Waals volume.
Dense:	1.014	LogP:	1.057 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.439 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.824 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	121.0	Rigid Bonds:	52.0
TPSA:	1562.34 ? Topological Polar Surface Area.	H-Bond Acceptor:	88.0
H-Bond Donor:	62.0	Rings:	3.0
Heavy Atoms:	88.0

MedChem Properties

QED Drug-Likeness Score:	0.017	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	9.785	Fsp³:	0.694
MCE-18:	257.731 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.333	Fluc inhibitor:	0.369 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.348 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.7 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.336	Promiscuous compounds:	0.3

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.781	MDCK Permeability:	-5.205
Pgp-inhibitor:	0.0	Pgp-substrate:	1.0
PAMPA:	1.0 ? 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):	1.0
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	-30.139%	Volume Distribution (VD):	-0.916
Fu:	205.82% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.0 ? 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):

-5.038

Half-life (T1/2):

9.78

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	1.0	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.1
Maximum Recommended Daily Dose:	0.997	Skin Sensitization:	1.0
Carcinogencity:	0.984	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	1.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.994
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.043
BCF:	-0.769 ? 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:	2.867 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.302 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.983 ? 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
NPO26155	Paralithodes camtschaticus	Species	Lithodidae	Eukaryota	n.a.	n.a.	n.a.	PMID[29338238]
NPO26155	Paralithodes camtschaticus	Species	Lithodidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26155	Paralithodes camtschaticus	Species	Lithodidae	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
MIC	11

Activity Type	# Activity
Organism	11

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
NPT15806	Organism	Carnobacterium mobile	Carnobacterium mobile	MIC	=	6300.0	nM	PMID[29338238]
NPT1311	Organism	Listonella anguillarum	Listonella anguillarum	MIC	=	1600.0	nM	PMID[29338238]
NPT15807	Organism	Carnobacterium maltaromaticum	Carnobacterium maltaromaticum	MIC	=	50000.0	nM	PMID[29338238]
NPT1382	Organism	Corynebacterium glutamicum	Corynebacterium glutamicum	MIC	=	1600.0	nM	PMID[29338238]
NPT15809	Organism	Aeromonas salmonicida	Aeromonas salmonicida	MIC	=	3100.0	nM	PMID[29338238]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	100000.0	nM	PMID[29338238]
NPT15810	Organism	Yersinia ruckeri	Yersinia ruckeri	MIC	=	800.0	nM	PMID[29338238]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	1600.0	nM	PMID[29338238]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	1600.0	nM	PMID[29338238]
NPT15805	Organism	Carnobacterium funditum	Carnobacterium funditum	MIC	=	25000.0	nM	PMID[29338238]
NPT6514	Organism	Carnobacterium divergens	Carnobacterium divergens	MIC	=	25000.0	nM	PMID[29338238]

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 NPC489511 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	31139
0.1-0.2	17664
0.2-0.3	784
0.3-0.4	143
0.4-0.5	68
0.5-0.6	35
0.6-0.7	17
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	Natural Product ID
0.6825	Remote Similarity	NPC486517
0.6802	Remote Similarity	NPC320968
0.6598	Remote Similarity	NPC479082
0.6576	Remote Similarity	NPC486506
0.6576	Remote Similarity	NPC485247
0.6576	Remote Similarity	NPC486514
0.6561	Remote Similarity	NPC329843
0.6557	Remote Similarity	NPC477635
0.6378	Remote Similarity	NPC486515
0.6374	Remote Similarity	NPC479141
0.6327	Remote Similarity	NPC479083
0.623	Remote Similarity	NPC479128
0.6162	Remote Similarity	NPC486503
0.6111	Remote Similarity	NPC489512
0.6094	Remote Similarity	NPC329855
0.6022	Remote Similarity	NPC485125
0.6	Remote Similarity	NPC489217
0.599	Remote Similarity	NPC480533
0.5952	Remote Similarity	NPC480594
0.5938	Remote Similarity	NPC329847
0.5902	Remote Similarity	NPC486505
0.5806	Remote Similarity	NPC486508
0.5769	Remote Similarity	NPC486513
0.5761	Remote Similarity	NPC486507
0.5736	Remote Similarity	NPC485244
0.5687	Remote Similarity	NPC478504
0.5654	Remote Similarity	NPC484363
0.5645	Remote Similarity	NPC477632
0.5608	Remote Similarity	NPC484964
0.56	Remote Similarity	NPC477634
0.555	Remote Similarity	NPC477633
0.5479	Remote Similarity	NPC485246
0.5431	Remote Similarity	NPC484965
0.5424	Remote Similarity	NPC485116
0.5394	Remote Similarity	NPC483985
0.5389	Remote Similarity	NPC479574
0.5368	Remote Similarity	NPC485245
0.5363	Remote Similarity	NPC75634
0.5344	Remote Similarity	NPC485115
0.5312	Remote Similarity	NPC484365
0.5286	Remote Similarity	NPC480529
0.5286	Remote Similarity	NPC480528
0.5285	Remote Similarity	NPC485243
0.5263	Remote Similarity	NPC484963
0.5238	Remote Similarity	NPC486504
0.5227	Remote Similarity	NPC486283
0.5202	Remote Similarity	NPC480595
0.519	Remote Similarity	NPC480530
0.5139	Remote Similarity	NPC480596
0.513	Remote Similarity	NPC484078
0.5073	Remote Similarity	NPC489216
0.5027	Remote Similarity	NPC485114

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC489511 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4899
0.1-0.2	4104
0.2-0.3	124
0.3-0.4	19
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