NPASS Compound

Natural Product: NPC486515

Natural Product ID	NPC486515
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DAHMCDJZHARGID-ZRILWKSDSA-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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155378 1 0 156379 1 0 157380 1 0 160381 1 6 161382 1 1 162383 1 0 162384 1 0 162385 1 0 163386 1 0 166387 1 1 167388 1 0 167389 1 0 168390 1 0 169391 1 0 169392 1 0 169393 1 0 170394 1 0 170395 1 0 170396 1 0 173397 1 1 174398 1 0 174399 1 0 176400 1 0 177401 1 0 180402 1 0 180403 1 0 183404 1 1 184405 1 0 184406 1 0 186407 1 0 187408 1 0 191409 1 0 191410 1 0 192411 1 0 192412 1 0 193413 1 0 193414 1 0 194415 1 1 197416 1 0 197417 1 0 200418 1 1 201419 1 0 201420 1 0 201421 1 0 204422 1 0 205423 1 0 206424 1 0 207425 1 0 208426 1 0 209427 1 0 210428 1 0 211429 1 0 212430 1 0 213431 1 0 214432 1 0 215433 1 0 216434 1 0 217435 1 0 220436 1 1 221437 1 0 221438 1 0 222439 1 0 225440 1 0 226441 1 0 227442 1 0 228443 1 0 229444 1 0 230445 1 0 231446 1 0 232447 1 0 M END

Standard InCHIKey	DAHMCDJZHARGID-ZRILWKSDSA-N
Standard InCHI	InChI=1S/C142H215N39O45S6/c1-13-68(7)111-137(221)153-55-108(196)159-96-61-228-227-60-95-119(203)151-53-106(194)157-84(38-39-109(197)198)123(207)179-114(73(12)187)141(225)175-99-64-231-230-63-98(173-129(213)93(58-184)169-131(96)215)133(217)170-92(57-183)128(212)161-82(27-18-21-41-144)121(205)162-86(45-74-30-34-77(188)35-31-74)125(209)160-83(28-19-22-42-145)122(206)176-110(67(5)6)138(222)174-100(135(219)180-113(72(11)186)140(224)165-85(44-66(3)4)124(208)164-89(48-102(146)190)118(202)150-54-107(195)158-90(49-103(147)191)142(226)181-43-23-29-101(181)136(220)152-51-104(192)154-70(9)115(199)171-95)65-232-229-62-97(132(216)163-87(46-75-32-36-78(189)37-33-75)126(210)168-91(56-182)127(211)155-71(10)116(200)167-94(59-185)130(214)177-111)172-120(204)81(26-17-20-40-143)156-105(193)52-149-117(201)88(47-76-50-148-80-25-16-15-24-79(76)80)166-139(223)112(69(8)14-2)178-134(99)218/h15-16,24-25,30-37,50,66-73,81-101,110-114,148,182-189H,13-14,17-23,26-29,38-49,51-65,143-145H2,1-12H3,(H2,146,190)(H2,147,191)(H,149,201)(H,150,202)(H,151,203)(H,152,220)(H,153,221)(H,154,192)(H,155,211)(H,156,193)(H,157,194)(H,158,195)(H,159,196)(H,160,209)(H,161,212)(H,162,205)(H,163,216)(H,164,208)(H,165,224)(H,166,223)(H,167,200)(H,168,210)(H,169,215)(H,170,217)(H,171,199)(H,172,204)(H,173,213)(H,174,222)(H,175,225)(H,176,206)(H,177,214)(H,178,218)(H,179,207)(H,180,219)(H,197,198)/t68-,69-,70-,71-,72+,73?,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,110-,111-,112-,113-,114-/m0/s1
SMILES	CC[C@H](C)[C@H]1C(=NCC(=N[C@H]2CSSC[C@H]3C(=NCC(=N[C@@H](CCC(=O)O)C(=N[C@@H](C(C)O)C(=N[C@H]4CSSC[C@@H](C(=N[C@@H](CO)C(=N[C@@H](CCCCN)C(=N[C@@H](Cc5ccc(cc5)O)C(=N[C@@H](CCCCN)C(=N[C@@H](C(C)C)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](Cc5ccc(cc5)O)C(=N[C@@H](CO)C(=N[C@@H](C)C(=N[C@@H](CO)C(=N1)O)O)O)O)O)N=C([C@H](CCCCN)N=C(CN=C([C@H](Cc1c[nH]c5ccccc15)N=C([C@H]([C@@H](C)CC)N=C4O)O)O)O)O)C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CC(C)C)C(=N[C@@H](CC(=N)O)C(=NCC(=N[C@@H](CC(=N)O)C(=O)N1CCC[C@H]1C(=NCC(=N[C@@H](C)C(=N3)O)O)O)O)O)O)O)O)O)O)O)O)O)O)N=C([C@H](CO)N=C2O)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	3378.41	Volume:	3201.789 ? Van der Waals volume.
Dense:	1.055	LogP:	-9.979 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-4.24 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.999 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	38.0	Rigid Bonds:	144.0
TPSA:	1444.34 ? Topological Polar Surface Area.	H-Bond Acceptor:	84.0
H-Bond Donor:	52.0	Rings:	9.0
Heavy Atoms:	90.0

MedChem Properties

QED Drug-Likeness Score:	0.007	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	10.0	Fsp³:	0.606
MCE-18:	353.684 ? 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:	0.343 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.335 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.651 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.822	Promiscuous compounds:	0.272

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.452	MDCK Permeability:	-5.317
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:	1.0
Plasma Protein Binding (PPB):	-14.039%	Volume Distribution (VD):	-0.754
Fu:	185.245% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.002

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.012	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	1.0	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):

-5.167

Half-life (T1/2):

11.413

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:	0.0	Rat Oral Acute Toxicity:	0.998
Maximum Recommended Daily Dose:	0.013	Skin Sensitization:	1.0
Carcinogencity:	0.646	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.264
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.997	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.0
BCF:	-0.476 ? 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:	2.917 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.667 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.114 ? 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
NPO40393	Viola inconspicua	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31464123]
NPO40393	Viola inconspicua	Species	Violaceae	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
Activity	1

Activity Type	# Activity
Organism	1

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
NPT19	Organism	Escherichia coli	Escherichia coli	Activity	=	50.0	%	PMID[31464123]

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 NPC486515 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	26737
0.1-0.2	21869
0.2-0.3	881
0.3-0.4	211
0.4-0.5	82
0.5-0.6	35
0.6-0.7	24
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
0.7988	Intermediate Similarity	NPC486506
0.7988	Intermediate Similarity	NPC485247
0.7988	Intermediate Similarity	NPC486514
0.7987	Intermediate Similarity	NPC486513
0.7976	Intermediate Similarity	NPC477635
0.7965	Intermediate Similarity	NPC485244
0.7709	Intermediate Similarity	NPC486517
0.767	Intermediate Similarity	NPC477634
0.7616	Intermediate Similarity	NPC484965
0.7614	Intermediate Similarity	NPC477633
0.7532	Intermediate Similarity	NPC485114
0.743	Intermediate Similarity	NPC329843
0.7267	Intermediate Similarity	NPC479141
0.716	Intermediate Similarity	NPC485246
0.716	Intermediate Similarity	NPC486505
0.7059	Intermediate Similarity	NPC479083
0.7018	Intermediate Similarity	NPC485245
0.6994	Remote Similarity	NPC485243
0.6984	Remote Similarity	NPC479082
0.6959	Remote Similarity	NPC477632
0.6932	Remote Similarity	NPC486503
0.6901	Remote Similarity	NPC486507
0.6894	Remote Similarity	NPC485116
0.6875	Remote Similarity	NPC485125
0.686	Remote Similarity	NPC482981
0.6648	Remote Similarity	NPC486508
0.661	Remote Similarity	NPC484964
0.6559	Remote Similarity	NPC329855
0.6484	Remote Similarity	NPC484362
0.6477	Remote Similarity	NPC489512
0.642	Remote Similarity	NPC484963
0.642	Remote Similarity	NPC485115
0.6398	Remote Similarity	NPC329847
0.6378	Remote Similarity	NPC489511
0.6369	Remote Similarity	NPC484365
0.6364	Remote Similarity	NPC320968
0.6257	Remote Similarity	NPC484078
0.6256	Remote Similarity	NPC479872
0.6178	Remote Similarity	NPC479128
0.608	Remote Similarity	NPC480529
0.6056	Remote Similarity	NPC484364
0.5981	Remote Similarity	NPC480594
0.595	Remote Similarity	NPC486504
0.593	Remote Similarity	NPC75634
0.592	Remote Similarity	NPC480528
0.5866	Remote Similarity	NPC481408
0.5821	Remote Similarity	NPC480530
0.5813	Remote Similarity	NPC483985
0.5802	Remote Similarity	NPC479574
0.5767	Remote Similarity	NPC484363
0.5714	Remote Similarity	NPC489216
0.561	Remote Similarity	NPC489555
0.5608	Remote Similarity	NPC489217
0.5576	Remote Similarity	NPC480595
0.5566	Remote Similarity	NPC480533
0.5528	Remote Similarity	NPC489215
0.5525	Remote Similarity	NPC485113
0.5484	Remote Similarity	NPC155143
0.5464	Remote Similarity	NPC153400
0.5455	Remote Similarity	NPC325976
0.5455	Remote Similarity	NPC326363
0.5278	Remote Similarity	NPC478504
0.5127	Remote Similarity	NPC479572
0.5127	Remote Similarity	NPC479568
0.5127	Remote Similarity	NPC479573
0.5127	Remote Similarity	NPC479566
0.5127	Remote Similarity	NPC479567
0.5127	Remote Similarity	NPC479569
0.5127	Remote Similarity	NPC479571
0.5118	Remote Similarity	NPC479140
0.5094	Remote Similarity	NPC479570
0.5085	Remote Similarity	NPC486283
0.503	Remote Similarity	NPC484877
0.5027	Remote Similarity	NPC484874
0.5026	Remote Similarity	NPC479121
0.5025	Remote Similarity	NPC480440

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486515 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4328
0.1-0.2	4644
0.2-0.3	147
0.3-0.4	26
0.4-0.5	5
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