NPASS Compound

Natural Product: NPC485116

Natural Product ID	NPC485116
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	QKBBIVYYGFGSBZ-OQSUNEHQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44559665
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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216443 1 0 217444 1 0 218445 1 0 219446 1 0 220447 1 0 221448 1 0 M END

Standard InCHIKey	QKBBIVYYGFGSBZ-OQSUNEHQSA-N
Standard InCHI	InChI=1S/C139H227N35O41S6/c1-18-71(13)107-134(210)156-86(51-76-31-21-20-22-32-76)121(197)166-105(69(9)10)132(208)164-94(62-218)127(203)158-89(57-176)123(199)151-82(42-43-103(185)186)112(188)144-55-102(184)148-96(64-220)138(214)173-47-29-36-98(173)129(205)170-108(72(14)19-2)135(211)160-91(59-178)124(200)155-87(53-100(143)182)120(196)149-79(33-23-26-44-140)114(190)154-85(52-77-38-40-78(181)41-39-77)119(195)163-95(63-219)128(204)167-104(68(7)8)131(207)152-81(35-25-28-46-142)115(191)157-88(56-175)122(198)150-80(34-24-27-45-141)116(192)162-93(61-217)126(202)159-90(58-177)125(201)161-92(60-216)113(189)145-54-101(183)147-83(49-66(3)4)118(194)153-84(50-67(5)6)117(193)146-73(15)111(187)171-110(75(17)180)137(213)168-106(70(11)12)133(209)172-109(74(16)179)136(212)165-97(65-221)139(215)174-48-30-37-99(174)130(206)169-107/h20-22,31-32,38-41,66-75,79-99,104-110,175-181,216-221H,18-19,23-30,33-37,42-65,140-142H2,1-17H3,(H2,143,182)(H,144,188)(H,145,189)(H,146,193)(H,147,183)(H,148,184)(H,149,196)(H,150,198)(H,151,199)(H,152,207)(H,153,194)(H,154,190)(H,155,200)(H,156,210)(H,157,191)(H,158,203)(H,159,202)(H,160,211)(H,161,201)(H,162,192)(H,163,195)(H,164,208)(H,165,212)(H,166,197)(H,167,204)(H,168,213)(H,169,206)(H,170,205)(H,171,187)(H,172,209)(H,185,186)/t71-,72-,73-,74-,75-,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,104-,105-,106-,107-,108-,109-,110-/m0/s1
SMILES	CC[C@H](C)[C@H]1C(=N[C@@H](Cc2ccccc2)C(=N[C@@H](C(C)C)C(=N[C@@H](CS)C(=N[C@@H](CO)C(=N[C@@H](CCC(=O)O)C(=NCC(=N[C@@H](CS)C(=O)N2CCC[C@H]2C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](CO)C(=N[C@@H](CC(=N)O)C(=N[C@@H](CCCCN)C(=N[C@@H](Cc2ccc(cc2)O)C(=N[C@@H](CS)C(=N[C@@H](C(C)C)C(=N[C@@H](CCCCN)C(=N[C@@H](CO)C(=N[C@@H](CCCCN)C(=N[C@@H](CS)C(=N[C@@H](CO)C(=N[C@@H](CS)C(=NCC(=N[C@@H](CC(C)C)C(=N[C@@H](CC(C)C)C(=N[C@@H](C)C(=N[C@@H]([C@H](C)O)C(=N[C@@H](C(C)C)C(=N[C@@H]([C@H](C)O)C(=N[C@@H](CS)C(=O)N2CCC[C@H]2C(=N1)O)O)O)O)O)O)O)O)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:	3234.51	Volume:	3123.434 ? Van der Waals volume.
Dense:	1.036	LogP:	-7.44 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-3.191 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.204 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	44.0	Rigid Bonds:	117.0
TPSA:	1286.78 ? Topological Polar Surface Area.	H-Bond Acceptor:	76.0
H-Bond Donor:	45.0	Rings:	5.0
Heavy Atoms:	82.0

MedChem Properties

QED Drug-Likeness Score:	0.013	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	9.768	Fsp³:	0.676
MCE-18:	301.901 ? 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:	0.32 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.307 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.739 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.606	Promiscuous compounds:	0.0

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.823	MDCK Permeability:	-5.859
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:	0.002
Plasma Protein Binding (PPB):	3.283%	Volume Distribution (VD):	-0.537
Fu:	101.28% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.269

ADMET: Metabolism

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

-4.312

Half-life (T1/2):

10.004

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:	0.137
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.01
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.992	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.0
BCF:	-0.401 ? 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:	3.186 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.756 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.065 ? 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
NPO40307	Psychotria longipes	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7714530]
NPO40307	Psychotria longipes	Species	Rubiaceae	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
IC50	1
MIC	7

Activity Type	# Activity
Organism	7
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
NPT3153	Organism	Kluyveromyces marxianus	Kluyveromyces marxianus	MIC	=	14000.0	nM	PMID[20718473]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	1550.0	nM	PMID[20718473]
NPT4997	Organism	Klebsiella oxytoca	Klebsiella oxytoca	MIC	=	5800.0	nM	PMID[20718473]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	13500.0	nM	PMID[20718473]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	=	13200.0	nM	PMID[20718473]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	39000.0	nM	PMID[20718473]
NPT2	Others	Unspecified	n.a.	IC50	=	3000.0	nM	PMID[7714530]
NPT186	Organism	Candida tropicalis	Candida tropicalis	MIC	=	56500.0	nM	PMID[20718473]

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 NPC485116 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	20654
0.1-0.2	27961
0.2-0.3	760
0.3-0.4	269
0.4-0.5	145
0.5-0.6	35
0.6-0.7	23
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
0.777	Intermediate Similarity	NPC485114
0.745	Intermediate Similarity	NPC486505
0.7383	Intermediate Similarity	NPC486507
0.7333	Intermediate Similarity	NPC477632
0.7179	Intermediate Similarity	NPC484363
0.7143	Intermediate Similarity	NPC484964
0.7105	Intermediate Similarity	NPC485246
0.7105	Intermediate Similarity	NPC482981
0.7032	Intermediate Similarity	NPC485243
0.6948	Remote Similarity	NPC485245
0.6894	Remote Similarity	NPC486515
0.6818	Remote Similarity	NPC485115
0.6772	Remote Similarity	NPC489217
0.6733	Remote Similarity	NPC485113
0.671	Remote Similarity	NPC484963
0.6646	Remote Similarity	NPC484365
0.6463	Remote Similarity	NPC484362
0.6369	Remote Similarity	NPC480440
0.6353	Remote Similarity	NPC489216
0.6312	Remote Similarity	NPC484078
0.6289	Remote Similarity	NPC484364
0.6221	Remote Similarity	NPC489215
0.6149	Remote Similarity	NPC477634
0.6115	Remote Similarity	NPC484877
0.6099	Remote Similarity	NPC479140
0.6092	Remote Similarity	NPC477633
0.6034	Remote Similarity	NPC485244
0.6023	Remote Similarity	NPC486506
0.6023	Remote Similarity	NPC485247
0.6023	Remote Similarity	NPC486514
0.6	Remote Similarity	NPC477635
0.6	Remote Similarity	NPC486513
0.5988	Remote Similarity	NPC479141
0.5944	Remote Similarity	NPC486517
0.5915	Remote Similarity	NPC489549
0.5875	Remote Similarity	NPC481408
0.5795	Remote Similarity	NPC480595
0.5767	Remote Similarity	NPC479121
0.5762	Remote Similarity	NPC479133
0.5704	Remote Similarity	NPC484348
0.569	Remote Similarity	NPC484965
0.5667	Remote Similarity	NPC329843
0.55	Remote Similarity	NPC479128
0.5455	Remote Similarity	NPC328649
0.5424	Remote Similarity	NPC489511
0.5405	Remote Similarity	NPC485124
0.539	Remote Similarity	NPC61004
0.5359	Remote Similarity	NPC484875
0.535	Remote Similarity	NPC479132
0.5316	Remote Similarity	NPC479135
0.5316	Remote Similarity	NPC479082
0.5312	Remote Similarity	NPC479131
0.5211	Remote Similarity	NPC479083
0.5203	Remote Similarity	NPC486271
0.5183	Remote Similarity	NPC479130
0.5183	Remote Similarity	NPC479129
0.5179	Remote Similarity	NPC480596
0.5176	Remote Similarity	NPC320968
0.5159	Remote Similarity	NPC484882
0.5141	Remote Similarity	NPC326349
0.5141	Remote Similarity	NPC323336
0.5079	Remote Similarity	NPC489512
0.5072	Remote Similarity	NPC244336
0.5062	Remote Similarity	NPC75634
0.505	Remote Similarity	NPC480594
0.5036	Remote Similarity	NPC489823
0.5032	Remote Similarity	NPC77905

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC485116 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3073
0.1-0.2	5809
0.2-0.3	240
0.3-0.4	25
0.4-0.5	3
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