NPASS Compound

Structure

NPC469838 OpenBabel07101718222D 21 21 0 0 1 0 0 0 0 0999 V2000 7.6391 5.7396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8959 6.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9449 6.0997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7370 5.1216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7859 4.8126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5780 3.8344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6270 3.5254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4190 2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4680 2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0032 0.5909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2601 1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7953 -0.3872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0032 0.5909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 2.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 13 1 0 0 0 0 10 11 1 0 0 0 0 11 18 1 0 0 0 0 12 10 1 1 0 0 0 12 15 1 0 0 0 0 12 17 1 0 0 0 0 13 14 2 0 0 0 0 13 19 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 15 20 2 0 0 0 0 16 17 2 0 0 0 0 16 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	297.19
Volume:	314.984
LogP:	4.313
LogD:	3.11
LogS:	-3.681
# Rotatable Bonds:	11
TPSA:	93.55
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.372
Synthetic Accessibility Score:	2.762
Fsp3:	0.688
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.94
MDCK Permeability:	2.347308509342838e-05
Pgp-inhibitor:	0.021
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.021
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.659
Plasma Protein Binding (PPB):	95.49227142333984%
Volume Distribution (VD):	0.81
Pgp-substrate:	2.3950319290161133%

ADMET: Metabolism

CYP1A2-inhibitor:	0.799
CYP1A2-substrate:	0.691
CYP2C19-inhibitor:	0.4
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.556
CYP2C9-substrate:	0.906
CYP2D6-inhibitor:	0.798
CYP2D6-substrate:	0.255
CYP3A4-inhibitor:	0.302
CYP3A4-substrate:	0.097

ADMET: Excretion

Clearance (CL):	4.419
Half-life (T1/2):	0.813

ADMET: Toxicity

hERG Blockers:	0.018
Human Hepatotoxicity (H-HT):	0.198
Drug-inuced Liver Injury (DILI):	0.909
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.197
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.783
Carcinogencity:	0.155
Eye Corrosion:	0.003
Eye Irritation:	0.183
Respiratory Toxicity:	0.912

Download Data

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

Natural Product: NPC469838

Natural Product ID:	NPC469838
*Common Name:**	OSWGMRUTKTWVOY-JOLOJFPGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OSWGMRUTKTWVOY-JOLOJFPGSA-N
Standard InCHI:	InChI=1S/C16H27NO4/c1-2-3-4-5-6-7-8-9-13(19)14-15(20)12(10-11-18)17-16(14)21/h12,18-19H,2-11H2,1H3,(H,17,21)/b14-13-/t12-/m0/s1
SMILES:	CCCCCCCCC/C(=C1/C(=N[C@H](C1=O)CCO)O)/O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1213657
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000218] Pyrrolidines [CHEMONTID:0001158] Pyrrolidones [CHEMONTID:0003032] Pyrrolidine-3-ones

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10556916]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19406895]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19917748]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20932054]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25043228]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25960261]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32603106]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	Antarctic	n.a.	PMID[8882433]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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	NP ID	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
EC50	2
IC50	1
Kd	1
MIC	1
Others	3

Activity Type	# Activity
Cell Line	1
Individual Protein	2
Organism	1
Others	3
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT15	Cell Line	Jurkat	Homo sapiens	EC50	=	52000.0	nM	PMID[491600]
NPT4195	Individual Protein	Transcriptional activator protein lasR	Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)	Ratio	=	0.96	n.a.	PMID[491600]
NPT4195	Individual Protein	Transcriptional activator protein lasR	Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)	Activity	=	21.0	%	PMID[491600]
NPT2	Others	Unspecified		EC50	=	29000.0	nM	PMID[491600]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	100000.0	nM	PMID[491601]
NPT2	Others	Unspecified		IC50	=	42000.0	nM	PMID[491601]
NPT26070	SINGLE PROTEIN	Receptor-histidine kinase AgrC	Staphylococcus aureus	Kd	=	222000.0	nM	PMID[491601]
NPT2	Others	Unspecified		FC	=	10.0	n.a.	PMID[491601]

☑ 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 NPC469838 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	64
0.1-0.2	726
0.2-0.3	16834
0.3-0.4	18027
0.4-0.5	6128
0.5-0.6	845
0.6-0.7	59
0.7-0.8	10
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC469833
0.8947	High Similarity	NPC469835
0.8684	High Similarity	NPC469836
0.7407	Intermediate Similarity	NPC4706
0.7245	Intermediate Similarity	NPC313234
0.6931	Remote Similarity	NPC474563
0.6827	Remote Similarity	NPC140251
0.6827	Remote Similarity	NPC307903
0.6759	Remote Similarity	NPC476814
0.6759	Remote Similarity	NPC476813
0.6569	Remote Similarity	NPC175531
0.6538	Remote Similarity	NPC472616
0.6449	Remote Similarity	NPC24389
0.642	Remote Similarity	NPC29468
0.641	Remote Similarity	NPC40148
0.6404	Remote Similarity	NPC263266
0.6389	Remote Similarity	NPC476290
0.6321	Remote Similarity	NPC472615
0.6289	Remote Similarity	NPC34754
0.6279	Remote Similarity	NPC103712
0.6279	Remote Similarity	NPC291196
0.6273	Remote Similarity	NPC476269
0.6262	Remote Similarity	NPC475800
0.6261	Remote Similarity	NPC469515
0.6239	Remote Similarity	NPC469494
0.6196	Remote Similarity	NPC477485
0.619	Remote Similarity	NPC469598
0.618	Remote Similarity	NPC288086
0.6176	Remote Similarity	NPC175614
0.617	Remote Similarity	NPC474312
0.6154	Remote Similarity	NPC477484
0.6154	Remote Similarity	NPC477486
0.6147	Remote Similarity	NPC474725
0.6147	Remote Similarity	NPC133729
0.6136	Remote Similarity	NPC320865
0.6136	Remote Similarity	NPC477641
0.6136	Remote Similarity	NPC477643
0.6117	Remote Similarity	NPC167380
0.6098	Remote Similarity	NPC130807
0.6092	Remote Similarity	NPC471022
0.6092	Remote Similarity	NPC477642
0.6092	Remote Similarity	NPC45060
0.6092	Remote Similarity	NPC280065
0.6091	Remote Similarity	NPC113012
0.6091	Remote Similarity	NPC122926
0.6067	Remote Similarity	NPC144419
0.6053	Remote Similarity	NPC476190
0.5979	Remote Similarity	NPC307126
0.5979	Remote Similarity	NPC68303
0.5978	Remote Similarity	NPC46268
0.5962	Remote Similarity	NPC4834
0.5957	Remote Similarity	NPC47653
0.5943	Remote Similarity	NPC474873
0.5941	Remote Similarity	NPC472264
0.5934	Remote Similarity	NPC264417
0.5934	Remote Similarity	NPC217095
0.5909	Remote Similarity	NPC236208
0.5905	Remote Similarity	NPC234542
0.59	Remote Similarity	NPC159369
0.59	Remote Similarity	NPC39290
0.5893	Remote Similarity	NPC170375
0.5889	Remote Similarity	NPC314678
0.5888	Remote Similarity	NPC128501
0.5877	Remote Similarity	NPC471645
0.5873	Remote Similarity	NPC328070
0.5865	Remote Similarity	NPC121857
0.5859	Remote Similarity	NPC472614
0.5851	Remote Similarity	NPC258231
0.5849	Remote Similarity	NPC473224
0.5841	Remote Similarity	NPC469865
0.5841	Remote Similarity	NPC7797
0.5833	Remote Similarity	NPC476877
0.5825	Remote Similarity	NPC116930
0.5824	Remote Similarity	NPC227396
0.5816	Remote Similarity	NPC319913
0.5814	Remote Similarity	NPC477525
0.581	Remote Similarity	NPC265662
0.5806	Remote Similarity	NPC473536
0.5804	Remote Similarity	NPC127578
0.5795	Remote Similarity	NPC249713
0.5789	Remote Similarity	NPC91332
0.5789	Remote Similarity	NPC162741
0.5783	Remote Similarity	NPC329003
0.5783	Remote Similarity	NPC326524
0.5783	Remote Similarity	NPC325550
0.5773	Remote Similarity	NPC185256
0.5769	Remote Similarity	NPC150041
0.5766	Remote Similarity	NPC475150
0.5765	Remote Similarity	NPC145658
0.5761	Remote Similarity	NPC476924
0.5758	Remote Similarity	NPC322672
0.575	Remote Similarity	NPC16709
0.5747	Remote Similarity	NPC187315
0.5732	Remote Similarity	NPC192843
0.5729	Remote Similarity	NPC82799
0.5727	Remote Similarity	NPC472433
0.5727	Remote Similarity	NPC476876
0.5726	Remote Similarity	NPC296361
0.5714	Remote Similarity	NPC298484
0.5714	Remote Similarity	NPC6795
0.5701	Remote Similarity	NPC233932
0.57	Remote Similarity	NPC473525
0.5699	Remote Similarity	NPC256640
0.5699	Remote Similarity	NPC205615
0.5699	Remote Similarity	NPC16279
0.5692	Remote Similarity	NPC473052
0.5692	Remote Similarity	NPC473055
0.5691	Remote Similarity	NPC329919
0.5691	Remote Similarity	NPC477793
0.5676	Remote Similarity	NPC251330
0.567	Remote Similarity	NPC477487
0.567	Remote Similarity	NPC473810
0.5663	Remote Similarity	NPC321030
0.566	Remote Similarity	NPC476344
0.5652	Remote Similarity	NPC5485
0.5649	Remote Similarity	NPC322526
0.5648	Remote Similarity	NPC188785
0.5648	Remote Similarity	NPC77703
0.5648	Remote Similarity	NPC316250
0.5641	Remote Similarity	NPC216335
0.5641	Remote Similarity	NPC316325
0.5636	Remote Similarity	NPC74035
0.5636	Remote Similarity	NPC14537
0.5631	Remote Similarity	NPC314500
0.5625	Remote Similarity	NPC217188
0.5618	Remote Similarity	NPC28348
0.5618	Remote Similarity	NPC477452
0.5618	Remote Similarity	NPC474299
0.5618	Remote Similarity	NPC475808
0.5618	Remote Similarity	NPC474298
0.5618	Remote Similarity	NPC473985
0.5612	Remote Similarity	NPC471595
0.5603	Remote Similarity	NPC50694

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 NPC469838 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	66
0.1-0.2	815
0.2-0.3	4854
0.3-0.4	2973
0.4-0.5	398
0.5-0.6	44
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
0.6136	Remote Similarity	NPD2256	Clinical (unspecified phase)
0.5946	Remote Similarity	NPD6420	Discontinued
0.5929	Remote Similarity	NPD1376	Discontinued
0.5893	Remote Similarity	NPD7601	Clinical (unspecified phase)
0.5856	Remote Similarity	NPD6413	Approved
0.5854	Remote Similarity	NPD6914	Discontinued
0.5747	Remote Similarity	NPD3704	Approved
0.5714	Remote Similarity	NPD4228	Discovery
0.5641	Remote Similarity	NPD7500	Approved
0.5614	Remote Similarity	NPD7116	Clinical (unspecified phase)

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