NPASS Compound

Structure

CID178919 OpenBabel06191715552D 46 46 0 0 1 0 0 0 0 0999 V2000 3.2964 -0.4187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3293 0.5924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0024 1.7057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5349 -6.6172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1625 -6.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0133 -3.8191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3141 -2.1133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1668 2.2057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4608 1.6133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6276 -5.0039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3008 -6.1172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6124 -2.2981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3445 -5.1775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1777 1.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9696 -2.8794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3116 -0.5924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3445 0.7660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1777 -5.8512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6713 -2.8794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5240 1.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6428 -5.1775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9696 -1.5321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7017 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8356 -4.9115 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9848 -1.7057 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6865 -2.7057 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -4.4115 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3445 -3.6454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 0.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6428 -3.6454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3445 -0.7660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 -5.0851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6428 -0.7660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7017 -4.4115 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8356 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9848 -2.7057 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.2105 -4.1454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 1.6736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5088 -4.1454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2105 -0.2660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 -6.0851 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5088 -0.2660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6865 -1.7057 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.9115 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 0 2 17 1 0 0 0 0 3 17 1 0 0 0 0 4 18 1 0 0 0 0 5 18 1 0 0 0 0 6 19 1 0 0 0 0 7 19 1 0 0 0 0 8 20 1 0 0 0 0 9 20 1 0 0 0 0 10 21 1 0 0 0 0 11 21 1 0 0 0 0 13 35 1 0 0 0 0 14 36 1 0 0 0 0 15 37 1 0 0 0 0 16 22 1 0 0 0 0 22 12 1 6 0 0 0 23 17 1 6 0 0 0 23 32 1 0 0 0 0 23 36 1 0 0 0 0 24 18 1 6 0 0 0 24 33 1 0 0 0 0 24 35 1 0 0 0 0 25 22 1 6 0 0 0 25 34 1 0 0 0 0 25 37 1 0 0 0 0 26 19 1 1 0 0 0 26 29 1 0 0 0 0 26 44 1 0 0 0 0 27 20 1 1 0 0 0 27 30 1 0 0 0 0 27 46 1 0 0 0 0 28 21 1 1 0 0 0 28 31 1 0 0 0 0 28 45 1 0 0 0 0 29 35 1 0 0 0 0 29 38 2 0 0 0 0 30 36 1 0 0 0 0 30 39 2 0 0 0 0 31 37 1 0 0 0 0 31 40 2 0 0 0 0 32 41 2 0 0 0 0 32 44 1 0 0 0 0 33 42 2 0 0 0 0 33 45 1 0 0 0 0 34 43 2 0 0 0 0 34 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	653.43
Volume:	684.347
LogP:	4.049
LogD:	2.223
LogS:	-3.698
# Rotatable Bonds:	7
TPSA:	139.83
# H-Bond Aceptor:	12
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.298
Synthetic Accessibility Score:	5.199
Fsp3:	0.824
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.18
MDCK Permeability:	3.790035771089606e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.051
Human Intestinal Absorption (HIA):	0.908
20% Bioavailability (F20%):	0.089
30% Bioavailability (F30%):	0.396

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.038
Plasma Protein Binding (PPB):	90.32715606689453%
Volume Distribution (VD):	1.26
Pgp-substrate:	3.017411470413208%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.052
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.928
CYP2C9-inhibitor:	0.058
CYP2C9-substrate:	0.041
CYP2D6-inhibitor:	0.068
CYP2D6-substrate:	0.076
CYP3A4-inhibitor:	0.443
CYP3A4-substrate:	0.914

ADMET: Excretion

Clearance (CL):	5.968
Half-life (T1/2):	0.047

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.981
Drug-inuced Liver Injury (DILI):	0.988
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.018
Carcinogencity:	0.002
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.012

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC178919

Natural Product ID:	NPC178919
*Common Name:**	Enniatin B1
IUPAC Name:	(3S,6R,9S,12R,15S,18R)-3-[(2S)-butan-2-yl]-4,10,16-trimethyl-6,9,12,15,18-penta(propan-2-yl)-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
Synonyms:	Enniatin B1
Standard InCHIKey:	UQCSETXJXJTMKO-UMURLBKASA-N
Standard InCHI:	InChI=1S/C34H59N3O9/c1-16-22(12)25-34(43)46-27(20(8)9)30(39)36(14)23(17(2)3)32(41)44-26(19(6)7)29(38)35(13)24(18(4)5)33(42)45-28(21(10)11)31(40)37(25)15/h17-28H,16H2,1-15H3/t22-,23-,24-,25-,26+,27+,28+/m0/s1
SMILES:	CC[C@@H]([C@H]1C(=O)O[C@H](C(C)C)C(=O)N(C)[C@@H](C(C)C)C(=O)O[C@@H](C(=O)N([C@H](C(=O)O[C@@H](C(=O)N1C)C(C)C)C(C)C)C)C(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL446318
PubChem CID:	11262300
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461664]
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014349]
NPO41427	Fusarium tricinctum + Streptomyces lividans/Bacillus subtilis	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[35518011]
NPO2697	Monodora tenuifolia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3509958]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	seed	n.a.	PMID[24225786]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24175613]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21090694]
NPO422	Euphorbia cornigera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19376614]
NPO422	Euphorbia cornigera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17512094]
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17286429]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	3
MIC	10
Others	1

Activity Type	# Activity
Organism	14

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	64.0	ug.mL-1	PMID[538417]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	64.0	ug.mL-1	PMID[538417]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	8.0	ug.mL-1	PMID[538417]
NPT1118	Organism	Streptococcus pneumoniae	Streptococcus pneumoniae	MIC	=	4.0	ug.mL-1	PMID[538417]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	8.0	ug.mL-1	PMID[538417]
NPT2709	Organism	Bacillus subtilis subsp. subtilis str. 168	Bacillus subtilis subsp. subtilis str. 168	MIC	=	16.0	ug.mL-1	PMID[538417]
NPT20	Organism	Candida albicans	Candida albicans	IC50	=	2.0	ug.mL-1	PMID[538416]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	6.25	ug.mL-1	PMID[538416]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	IC50	=	9.0	ug.mL-1	PMID[538416]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	MIC	=	25.0	ug.mL-1	PMID[538416]

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC178919 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	310
0.1-0.2	16035
0.2-0.3	19575
0.3-0.4	5656
0.4-0.5	818
0.5-0.6	231
0.6-0.7	52
0.7-0.8	13
0.8-0.85	0
0.85-0.9	0
0.9-0.95	5
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9706	High Similarity	NPC263281
0.9437	High Similarity	NPC477145
0.9437	High Similarity	NPC473741
0.9403	High Similarity	NPC212866
0.9403	High Similarity	NPC29598

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC178919 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	3497
0.2-0.3	3982
0.3-0.4	1101
0.4-0.5	319
0.5-0.6	79
0.6-0.7	2
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9403	High Similarity	NPD7840	Approved
0.6429	Remote Similarity	NPD8144	Approved
0.6429	Remote Similarity	NPD8143	Approved
0.6375	Remote Similarity	NPD2697	Approved
0.6375	Remote Similarity	NPD2695	Approved

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Bioactivity similarity: Similar Natural Products in NPASS

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