NPASS Compound

Natural Product: NPC486513

Natural Product ID	NPC486513
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	IXNJUPHEHRRQGX-DWDQKXESSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44566284
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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M END

Standard InCHIKey	IXNJUPHEHRRQGX-DWDQKXESSA-N
Standard InCHI	InChI=1S/C149H211N37O48S6/c1-11-73(6)119-145(230)173-95(49-79-26-16-13-17-27-79)135(220)172-99(54-118(207)208)137(222)177-102-65-235-237-67-104-141(226)176-101(64-188)139(224)178-103-66-236-238-69-106(180-140(225)100(63-187)175-132(217)90(41-43-117(205)206)162-111(198)59-159-128(102)213)143(228)169-94(48-78-24-14-12-15-25-78)134(219)166-91(46-71(2)3)125(210)157-61-114(201)184-121(75(8)190)147(232)181-107(144(229)170-96(51-81-34-38-84(194)39-35-81)138(223)186-123(77(10)192)148(233)165-87(30-20-22-44-150)124(209)156-60-112(199)163-104)70-240-239-68-105(179-133(218)92(47-72(4)5)167-130(215)88(31-21-23-45-151)164-136(221)97(52-82-55-153-86-29-19-18-28-85(82)86)171-131(216)89(40-42-116(203)204)161-110(197)58-160-129(103)214)142(227)168-93(50-80-32-36-83(193)37-33-80)126(211)158-62-115(202)183-120(74(7)189)146(231)174-98(53-108(152)195)127(212)155-56-109(196)154-57-113(200)182-122(76(9)191)149(234)185-119/h12-19,24-29,32-39,55,71-77,87-107,119-123,153,187-194H,11,20-23,30-31,40-54,56-70,150-151H2,1-10H3,(H2,152,195)(H,154,196)(H,155,212)(H,156,209)(H,157,210)(H,158,211)(H,159,213)(H,160,214)(H,161,197)(H,162,198)(H,163,199)(H,164,221)(H,165,233)(H,166,219)(H,167,215)(H,168,227)(H,169,228)(H,170,229)(H,171,216)(H,172,220)(H,173,230)(H,174,231)(H,175,217)(H,176,226)(H,177,222)(H,178,224)(H,179,218)(H,180,225)(H,181,232)(H,182,200)(H,183,202)(H,184,201)(H,185,234)(H,186,223)(H,203,204)(H,205,206)(H,207,208)/t73-,74+,75+,76+,77+,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98+,99-,100-,101-,102-,103-,104-,105-,106-,107-,119-,120-,121-,122-,123-/m0/s1
SMILES	CC[C@H](C)[C@H]1C(=N[C@@H](Cc2ccccc2)C(=N[C@@H](CC(=O)O)C(=N[C@H]2CSSC[C@H]3C(=N[C@@H](CO)C(=N[C@H]4CSSC[C@@H](C(=N[C@@H](Cc5ccccc5)C(=N[C@@H](CC(C)C)C(=NCC(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](Cc5ccc(cc5)O)C(=NCC(=N[C@@H]([C@@H](C)O)C(=N[C@H](CC(=N)O)C(=NCC(=NCC(=N[C@@H]([C@@H](C)O)C(=N1)O)O)O)O)O)O)O)O)N=C([C@H](CC(C)C)N=C([C@H](CCCCN)N=C([C@H](Cc1c[nH]c5ccccc15)N=C([C@H](CCC(=O)O)N=C(CN=C4O)O)O)O)O)O)C(=N[C@@H](Cc1ccc(cc1)O)C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CCCCN)C(=NCC(=N3)O)O)O)O)O)O)O)O)O)O)N=C([C@H](CO)N=C([C@H](CCC(=O)O)N=C(CN=C2O)O)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	3478.35	Volume:	3300.227 ? Van der Waals volume.
Dense:	1.054	LogP:	-10.403 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-4.534 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.967 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	40.0	Rigid Bonds:	152.0
TPSA:	1461.12 ? Topological Polar Surface Area.	H-Bond Acceptor:	85.0
H-Bond Donor:	51.0	Rings:	10.0
Heavy Atoms:	91.0

MedChem Properties

QED Drug-Likeness Score:	0.006	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	10.0	Fsp³:	0.537
MCE-18:	364.127 ? 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:	0.35 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.333 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.637 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.825	Promiscuous compounds:	0.262

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.709	MDCK Permeability:	-5.127
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:	0.363
Plasma Protein Binding (PPB):	-14.618%	Volume Distribution (VD):	-0.845
Fu:	169.599% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.45

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.974	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):

-5.751

Half-life (T1/2):

11.899

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:	0.99
Maximum Recommended Daily Dose:	0.005	Skin Sensitization:	1.0
Carcinogencity:	0.061	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.015
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.625	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.0
BCF:	-0.528 ? 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:	2.844 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.547 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.931 ? 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
NPO40952	Viola hederaceae	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16441062]
NPO40952	Viola hederaceae	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
Others	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
NPT27	Others	Unspecified	n.a.	Activity	=	2.0	%	PMID[16441062]

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 NPC486513 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	26666
0.1-0.2	22044
0.2-0.3	823
0.3-0.4	194
0.4-0.5	63
0.5-0.6	42
0.6-0.7	21
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
0.7987	Intermediate Similarity	NPC486515
0.7665	Intermediate Similarity	NPC477634
0.7605	Intermediate Similarity	NPC477633
0.6936	Remote Similarity	NPC485244
0.6842	Remote Similarity	NPC486506
0.6842	Remote Similarity	NPC485247
0.6842	Remote Similarity	NPC486514
0.6839	Remote Similarity	NPC479128
0.6824	Remote Similarity	NPC477635
0.663	Remote Similarity	NPC486517
0.6494	Remote Similarity	NPC484965
0.6486	Remote Similarity	NPC479082
0.6446	Remote Similarity	NPC486507
0.6415	Remote Similarity	NPC485114
0.6378	Remote Similarity	NPC479083
0.6354	Remote Similarity	NPC329843
0.6347	Remote Similarity	NPC485115
0.6243	Remote Similarity	NPC479141
0.6163	Remote Similarity	NPC484964
0.6163	Remote Similarity	NPC485243
0.6118	Remote Similarity	NPC477632
0.6118	Remote Similarity	NPC485246
0.6118	Remote Similarity	NPC486505
0.6	Remote Similarity	NPC485116
0.5988	Remote Similarity	NPC485245
0.5966	Remote Similarity	NPC485125
0.5895	Remote Similarity	NPC489512
0.5859	Remote Similarity	NPC479872
0.5843	Remote Similarity	NPC486503
0.5838	Remote Similarity	NPC482981
0.5829	Remote Similarity	NPC484365
0.578	Remote Similarity	NPC484963
0.5779	Remote Similarity	NPC478504
0.5769	Remote Similarity	NPC489511
0.5739	Remote Similarity	NPC486508
0.5699	Remote Similarity	NPC329855
0.5679	Remote Similarity	NPC484347
0.5625	Remote Similarity	NPC484078
0.5538	Remote Similarity	NPC329847
0.5519	Remote Similarity	NPC484362
0.5512	Remote Similarity	NPC480594
0.5484	Remote Similarity	NPC489555
0.5449	Remote Similarity	NPC75634
0.5424	Remote Similarity	NPC484364
0.539	Remote Similarity	NPC483985
0.5381	Remote Similarity	NPC486504
0.5376	Remote Similarity	NPC481409
0.5366	Remote Similarity	NPC479133
0.5311	Remote Similarity	NPC479121
0.5274	Remote Similarity	NPC479572
0.5274	Remote Similarity	NPC479568
0.5274	Remote Similarity	NPC479573
0.5274	Remote Similarity	NPC479566
0.5274	Remote Similarity	NPC479567
0.5274	Remote Similarity	NPC479569
0.5274	Remote Similarity	NPC479571
0.5257	Remote Similarity	NPC153400
0.5243	Remote Similarity	NPC480533
0.5238	Remote Similarity	NPC479570
0.52	Remote Similarity	NPC480529
0.5189	Remote Similarity	NPC480595
0.5176	Remote Similarity	NPC480530
0.5163	Remote Similarity	NPC489217
0.5111	Remote Similarity	NPC320968
0.5052	Remote Similarity	NPC489216
0.505	Remote Similarity	NPC480528

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486513 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4044
0.1-0.2	4912
0.2-0.3	161
0.3-0.4	26
0.4-0.5	6
0.5-0.6	1
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
0.5034	Remote Similarity	NPD8405	Pre-clinical

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