NPASS Compound

Natural Product: NPC479574

Natural Product ID	NPC479574
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	YPRHSVNHBIVLHS-ZBPOMXMDSA-N
IUPAC Name	n.a.
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

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2 0 32 43 1 0 43 44 2 3 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 45 51 1 0 51 52 2 3 52 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 53 59 1 0 59 60 2 0 59 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 66 67 2 3 67 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 71 72 1 0 72 73 1 0 68 74 1 0 74 75 2 3 75 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 79 80 1 0 80 81 1 0 76 82 1 0 82 83 2 3 83 84 1 0 84 85 1 0 85 86 1 0 85 87 1 0 87 88 1 0 84 89 1 0 89 90 2 3 90 91 1 0 91 92 1 0 92 93 1 0 92 94 1 0 94 95 1 0 91 96 1 0 96 97 2 3 97 98 1 0 98 99 1 0 98100 1 0 100101 2 3 101102 1 0 102103 1 0 103104 1 0 104105 1 0 105106 1 0 106107 1 0 102108 1 0 108109 2 3 108110 1 0 100111 1 0 96112 1 0 89113 1 0 82114 1 0 74115 1 0 66116 1 0 51117 1 0 43118 1 0 30119 1 0 23120 1 0 18121 1 0 13122 1 0 6123 1 0 5124 1 0 124125 2 3 125126 1 0 126127 1 0 125128 1 0 42 34 1 0 65 61 1 0 42 37 1 0 1129 1 0 1130 1 0 1131 1 0 2132 1 0 2133 1 0 3134 1 1 4135 1 0 4136 1 0 4137 1 0 5138 1 6 8139 1 1 9140 1 0 9141 1 0 10142 1 0 11143 1 0 11144 1 0 11145 1 0 12146 1 0 12147 1 0 12148 1 0 15149 1 6 16150 1 0 16151 1 0 17152 1 0 20153 1 1 21154 1 0 21155 1 0 22156 1 0 25157 1 6 26158 1 0 26159 1 0 27160 1 0 28161 1 0 28162 1 0 28163 1 0 29164 1 0 29165 1 0 29166 1 0 32167 1 6 33168 1 0 33169 1 0 35170 1 0 36171 1 0 38172 1 0 39173 1 0 40174 1 0 41175 1 0 45176 1 1 46177 1 0 46178 1 0 47179 1 0 47180 1 0 48181 1 0 48182 1 0 49183 1 0 49184 1 0 50185 1 0 50186 1 0 53187 1 1 54188 1 0 54189 1 0 55190 1 0 55191 1 0 56192 1 0 56193 1 0 57194 1 0 57195 1 0 58196 1 0 58197 1 0 62198 1 0 62199 1 0 63200 1 0 63201 1 0 64202 1 0 64203 1 0 65204 1 6 68205 1 1 69206 1 0 69207 1 0 70208 1 0 70209 1 0 71210 1 0 71211 1 0 72212 1 0 72213 1 0 73214 1 0 73215 1 0 76216 1 1 77217 1 0 77218 1 0 78219 1 0 78220 1 0 79221 1 0 79222 1 0 80223 1 0 80224 1 0 81225 1 0 81226 1 0 84227 1 1 85228 1 1 86229 1 0 86230 1 0 86231 1 0 87232 1 0 87233 1 0 88234 1 0 88235 1 0 88236 1 0 91237 1 1 92238 1 1 93239 1 0 93240 1 0 93241 1 0 94242 1 0 94243 1 0 95244 1 0 95245 1 0 95246 1 0 98247 1 1 99248 1 0 99249 1 0 99250 1 0 102251 1 1 103252 1 0 103253 1 0 104254 1 0 104255 1 0 105256 1 0 105257 1 0 106258 1 0 106259 1 0 107260 1 0 107261 1 0 109262 1 0 110263 1 0 111264 1 0 112265 1 0 113266 1 0 114267 1 0 115268 1 0 116269 1 0 117270 1 0 118271 1 0 119272 1 0 120273 1 0 121274 1 0 122275 1 0 123276 1 0 126277 1 0 126278 1 0 127279 1 0 127280 1 0 128281 1 0 M END

Standard InCHIKey	YPRHSVNHBIVLHS-ZBPOMXMDSA-N
Standard InCHI	InChI=1S/C87H153N23O18/c1-12-51(8)70(107-69(113)45-93)85(126)104-64(43-50(6)7)79(120)105-67(48-112)82(123)106-66(47-111)81(122)102-63(42-49(4)5)78(119)103-65(44-55-46-95-57-29-16-15-28-56(55)57)80(121)99-59(31-18-23-37-89)76(117)101-62(34-21-26-40-92)87(128)110-41-27-35-68(110)83(124)100-60(32-19-24-38-90)75(116)98-61(33-20-25-39-91)77(118)108-72(53(10)14-3)86(127)109-71(52(9)13-2)84(125)96-54(11)74(115)97-58(73(94)114)30-17-22-36-88/h15-16,28-29,46,49-54,58-68,70-72,95,111-112H,12-14,17-27,30-45,47-48,88-93H2,1-11H3,(H2,94,114)(H,96,125)(H,97,115)(H,98,116)(H,99,121)(H,100,124)(H,101,117)(H,102,122)(H,103,119)(H,104,126)(H,105,120)(H,106,123)(H,107,113)(H,108,118)(H,109,127)/t51-,52-,53-,54-,58-,59-,60-,61-,62-,63-,64-,65-,66-,67-,68-,70-,71-,72-/m0/s1
SMILES	CC[C@H](C)[C@@H](C(=N[C@@H](CC(C)C)C(=N[C@@H](CO)C(=N[C@@H](CO)C(=N[C@@H](CC(C)C)C(=N[C@@H](Cc1c[nH]c2ccccc12)C(=N[C@@H](CCCCN)C(=N[C@@H](CCCCN)C(=O)N1CCC[C@H]1C(=N[C@@H](CCCCN)C(=N[C@@H](CCCCN)C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](C)C(=N[C@@H](CCCCN)C(=N)O)O)O)O)O)O)O)O)O)O)O)O)O)O)N=C(CN)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1808.18	Volume:	1846.058 ? Van der Waals volume.
Dense:	0.979	LogP:	3.754 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.937 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.251 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	65.0	Rigid Bonds:	31.0
TPSA:	733.02 ? Topological Polar Surface Area.	H-Bond Acceptor:	41.0
H-Bond Donor:	31.0	Rings:	3.0
Heavy Atoms:	41.0

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:	8.003	Fsp³:	0.724
MCE-18:	149.613 ? 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:	0.336	Fluc inhibitor:	0.021 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.245 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.759 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.006	Promiscuous compounds:	0.226

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.856	MDCK Permeability:	-5.208
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:	0.001
Plasma Protein Binding (PPB):	19.345%	Volume Distribution (VD):	-0.252
Fu:	80.779% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.001

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.953	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.975	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):

-0.663

Half-life (T1/2):

3.778

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:	0.989	Rat Oral Acute Toxicity:	0.785
Maximum Recommended Daily Dose:	0.147	Skin Sensitization:	1.0
Carcinogencity:	0.001	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.983
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.988
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.013
BCF:	-0.029 ? 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:	3.565 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.903 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.043 ? 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
NPO40163	Hylaeus signatus	Species	Colletidae	Eukaryota	Venom	n.a.	n.a.	PMID[26998557]

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

Activity Type	# Activity
Organism	10

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
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	=	5800.0	nM	PMID[26998557]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	100000.0	nM	PMID[26998557]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	49000.0	nM	PMID[26998557]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	100000.0	nM	PMID[26998557]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	>	100000.0	nM	PMID[26998557]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100000.0	nM	PMID[26998557]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	98000.0	nM	PMID[26998557]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	100000.0	nM	PMID[26998557]

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 NPC479574 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	26650
0.1-0.2	21708
0.2-0.3	1121
0.3-0.4	227
0.4-0.5	82
0.5-0.6	52
0.6-0.7	8
0.7-0.8	0
0.8-0.85	8
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8381	Intermediate Similarity	NPC479572
0.8381	Intermediate Similarity	NPC479568
0.8381	Intermediate Similarity	NPC479573
0.8381	Intermediate Similarity	NPC479566
0.8381	Intermediate Similarity	NPC479567
0.8381	Intermediate Similarity	NPC479569
0.8381	Intermediate Similarity	NPC479571
0.8302	Intermediate Similarity	NPC479570
0.7042	Intermediate Similarity	NPC320968
0.641	Remote Similarity	NPC110602
0.641	Remote Similarity	NPC479071
0.6241	Remote Similarity	NPC484874
0.617	Remote Similarity	NPC75634
0.6066	Remote Similarity	NPC479065
0.6048	Remote Similarity	NPC479066
0.6	Remote Similarity	NPC54420
0.6	Remote Similarity	NPC75726
0.5987	Remote Similarity	NPC479141
0.5966	Remote Similarity	NPC31385
0.5882	Remote Similarity	NPC223791
0.5802	Remote Similarity	NPC486515
0.5763	Remote Similarity	NPC107077
0.5746	Remote Similarity	NPC486282
0.5736	Remote Similarity	NPC100321
0.5714	Remote Similarity	NPC325976
0.5714	Remote Similarity	NPC326363
0.5682	Remote Similarity	NPC483985
0.5672	Remote Similarity	NPC489555
0.5645	Remote Similarity	NPC155143
0.5645	Remote Similarity	NPC479075
0.5635	Remote Similarity	NPC479073
0.5619	Remote Similarity	NPC479563
0.5619	Remote Similarity	NPC479561
0.5619	Remote Similarity	NPC479560
0.5619	Remote Similarity	NPC479564
0.5591	Remote Similarity	NPC479076
0.5546	Remote Similarity	NPC293917
0.5515	Remote Similarity	NPC477635
0.547	Remote Similarity	NPC489625
0.5455	Remote Similarity	NPC486283
0.5449	Remote Similarity	NPC486506
0.5449	Remote Similarity	NPC485247
0.5449	Remote Similarity	NPC486514
0.5389	Remote Similarity	NPC489511
0.5389	Remote Similarity	NPC484965
0.5376	Remote Similarity	NPC329843
0.5354	Remote Similarity	NPC482001
0.5225	Remote Similarity	NPC486517
0.5221	Remote Similarity	NPC479557
0.5221	Remote Similarity	NPC479554
0.5221	Remote Similarity	NPC479556
0.5221	Remote Similarity	NPC479558
0.5221	Remote Similarity	NPC479555
0.521	Remote Similarity	NPC213629
0.5167	Remote Similarity	NPC479083
0.5122	Remote Similarity	NPC483341
0.511	Remote Similarity	NPC479082
0.5078	Remote Similarity	NPC479553
0.5078	Remote Similarity	NPC479552
0.5078	Remote Similarity	NPC479551
0.5078	Remote Similarity	NPC479548
0.5078	Remote Similarity	NPC479549
0.5078	Remote Similarity	NPC479550
0.5057	Remote Similarity	NPC477634
0.5041	Remote Similarity	NPC171317
0.5039	Remote Similarity	NPC162860
0.5033	Remote Similarity	NPC485785
0.5029	Remote Similarity	NPC485244
0.5028	Remote Similarity	NPC489512

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC479574 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4122
0.1-0.2	4802
0.2-0.3	190
0.3-0.4	27
0.4-0.5	5
0.5-0.6	4
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
0.5546	Remote Similarity	NPD7621	Clinical (unspecified phase)
0.5203	Remote Similarity	NPD8431	Pre-clinical
0.5156	Remote Similarity	NPD8405	Pre-clinical
0.5108	Remote Similarity	NPD8493	Clinical (unspecified phase)

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