NPASS Compound

Structure

NPC475286 OpenBabel07101719252D 36 40 0 0 1 0 0 0 0 0999 V2000 4.2112 -2.6668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1092 -5.5507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6021 -8.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1931 -4.0681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7079 -6.3597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1409 -7.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8112 -5.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5893 -4.1211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1067 -3.6613 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7024 -6.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5531 -8.5417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9157 -4.2491 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.1247 -2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -4.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6021 -7.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6382 -4.4302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8292 -3.8424 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.9338 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4706 -3.8870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7931 -6.6449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5893 -5.7392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4338 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2024 -7.3302 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 5.8622 -9.4928 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 7.8983 -6.6902 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.0215 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -5.3815 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5531 -6.9237 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.3841 -3.4803 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8976 -5.6504 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.1771 -4.9302 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.4338 -1.3090 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.6382 -5.4302 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.7428 -2.2601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.6615 -3.2992 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8795 -7.0516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 9 1 0 0 0 0 1 13 1 0 0 0 0 2 10 1 0 0 0 0 2 14 2 0 0 0 0 3 11 1 0 0 0 0 3 15 2 0 0 0 0 4 9 1 0 0 0 0 4 29 1 0 0 0 0 5 10 2 0 0 0 0 5 27 1 0 0 0 0 6 11 2 0 0 0 0 6 28 1 0 0 0 0 7 12 1 0 0 0 0 7 30 1 0 0 0 0 8 16 2 0 0 0 0 8 31 1 0 0 0 0 9 12 1 0 0 0 0 10 23 1 0 0 0 0 11 24 1 0 0 0 0 12 17 1 0 0 0 0 13 18 2 0 0 0 0 13 32 1 0 0 0 0 14 19 1 0 0 0 0 14 27 1 0 0 0 0 15 20 1 0 0 0 0 15 28 1 0 0 0 0 16 17 1 0 0 0 0 16 33 1 0 0 0 0 17 18 1 0 0 0 0 18 34 1 0 0 0 0 19 29 1 0 0 0 0 19 35 2 0 0 0 0 20 30 1 0 0 0 0 20 36 2 0 0 0 0 21 25 2 0 0 0 0 21 31 1 0 0 0 0 21 33 1 0 0 0 0 22 26 2 0 0 0 0 22 32 1 0 0 0 0 22 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	618.05
Volume:	486.037
LogP:	0.588
LogD:	1.479
LogS:	-3.627
# Rotatable Bonds:	9
TPSA:	200.64
# H-Bond Aceptor:	12
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.151
Synthetic Accessibility Score:	4.983
Fsp3:	0.273
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:	-5.817
MDCK Permeability:	4.176297352387337e-06
Pgp-inhibitor:	0.989
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.98
20% Bioavailability (F20%):	0.032
30% Bioavailability (F30%):	0.277

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.488
Plasma Protein Binding (PPB):	90.80856323242188%
Volume Distribution (VD):	0.6
Pgp-substrate:	24.035167694091797%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.355
CYP2C19-inhibitor:	0.645
CYP2C19-substrate:	0.019
CYP2C9-inhibitor:	0.215
CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.013
CYP3A4-inhibitor:	0.812
CYP3A4-substrate:	0.098

ADMET: Excretion

Clearance (CL):	2.646
Half-life (T1/2):	0.938

ADMET: Toxicity

hERG Blockers:	0.945
Human Hepatotoxicity (H-HT):	0.996
Drug-inuced Liver Injury (DILI):	0.96
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.804
Maximum Recommended Daily Dose:	0.989
Skin Sensitization:	0.554
Carcinogencity:	0.174
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC475286

Natural Product ID:	NPC475286
*Common Name:**	Ageliferin
IUPAC Name:	n.a.
Synonyms:	Ageliferin
Standard InCHIKey:	DNQPQSFZLPZAIA-HHJICFAHSA-N
Standard InCHI:	InChI=1S/C22H24Br2N10O2.2C2HF3O2/c23-10-2-14(27-5-10)19(35)29-4-9-1-13-18(34-22(26)32-13)17(16-8-31-21(25)33-16)12(9)7-30-20(36)15-3-11(24)6-28-15;23-2(4,5)1(6)7/h2-3,5-6,8-9,12,17,27-28H,1,4,7H2,(H,29,35)(H,30,36)(H3,25,31,33)(H3,26,32,34);2(H,6,7)/t9-,12-,17-;;/m1../s1
SMILES:	OC(=O)C(F)(F)F.OC(=O)C(F)(F)F.Brc1c[nH]c(c1)C(=O)NC[C@H]1Cc2[nH]c(=N)[nH]c2[C@H]([C@@H]1CNC(=O)c1[nH]cc(c1)Br)c1c[nH]c(=N)[nH]1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL502866
PubChem CID:	44575311 11513454
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001093] Carboxylic acid derivatives [CHEMONTID:0000475] Carboxylic acid amides [CHEMONTID:0004817] 2-heteroaryl carboxamides

*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
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	papua new guinean	n.a.	PMID[9784179]
NPO32675	agelas sp.	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9584409]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[26083682]
NPO32675	agelas sp.	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19209898]
NPO32675	agelas sp.	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562840]
NPO32675	agelas sp.	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15332839]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[14677933]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	at a depth of 14 m near the island of Ambon (Seram Seilale), Indonesia	1997-AUG	PMID[10514317]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 9 of 9 entries

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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	1
MIC	3
Others	4

Activity Type	# Activity
Organism	7
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2709	Organism	Bacillus subtilis subsp. subtilis str. 168	Bacillus subtilis subsp. subtilis str. 168	IZ	=	14.0	mm	PMID[509514]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	11.0	mm	PMID[509514]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	8.0	mm	PMID[509514]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	11.0	mm	PMID[509514]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	=	4.17	ug.mL-1	PMID[509513]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	8.33	ug.mL-1	PMID[509513]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	33.3	ug.mL-1	PMID[509513]
NPT2	Others	Unspecified	""	IC50	>	50000.0	nM	PMID[509513]

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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 NPC475286 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	721
0.1-0.2	12760
0.2-0.3	21391
0.3-0.4	3303
0.4-0.5	2675
0.5-0.6	1509
0.6-0.7	300
0.7-0.8	20
0.8-0.85	4
0.85-0.9	8
0.9-0.95	5
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC174281
0.9886	High Similarity	NPC136957
0.9886	High Similarity	NPC19696
0.9716	High Similarity	NPC48117
0.9716	High Similarity	NPC476526

Showing 1 to 5 of 200 entries

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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 NPC475286 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	307
0.1-0.2	897
0.2-0.3	1889
0.3-0.4	2335
0.4-0.5	2109
0.5-0.6	1340
0.6-0.7	261
0.7-0.8	12
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7716	Intermediate Similarity	NPD7459	Phase 2
0.71	Intermediate Similarity	NPD5685	Approved
0.71	Intermediate Similarity	NPD5686	Approved
0.7095	Intermediate Similarity	NPD7704	Clinical (unspecified phase)
0.7094	Intermediate Similarity	NPD2289	Phase 3

Showing 1 to 5 of 200 entries

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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