NPASS Compound

Structure

CID182758 OpenBabel06191715562D 22 21 0 0 0 0 0 0 0 0999 V2000 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 2 1 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 11 1 0 0 0 0 10 12 2 0 0 0 0 11 14 2 0 0 0 0 12 15 1 0 0 0 0 13 16 1 0 0 0 0 13 19 1 0 0 0 0 14 17 1 0 0 0 0 14 18 1 0 0 0 0 15 19 2 3 0 0 0 15 20 1 0 0 0 0 16 21 2 0 0 0 0 16 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	437.02
Volume:	350.681
LogP:	5.967
LogD:	2.982
LogS:	-3.823
# Rotatable Bonds:	14
TPSA:	66.73
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.301
Synthetic Accessibility Score:	3.033
Fsp3:	0.688
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.111
MDCK Permeability:	3.732563345693052e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.048
20% Bioavailability (F20%):	0.939
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.85
Plasma Protein Binding (PPB):	96.79589080810547%
Volume Distribution (VD):	0.433
Pgp-substrate:	3.471371650695801%

ADMET: Metabolism

CYP1A2-inhibitor:	0.185
CYP1A2-substrate:	0.169
CYP2C19-inhibitor:	0.24
CYP2C19-substrate:	0.122
CYP2C9-inhibitor:	0.67
CYP2C9-substrate:	0.629
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.073
CYP3A4-inhibitor:	0.047
CYP3A4-substrate:	0.057

ADMET: Excretion

Clearance (CL):	0.844
Half-life (T1/2):	0.261

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.874
Drug-inuced Liver Injury (DILI):	0.866
AMES Toxicity:	0.75
Rat Oral Acute Toxicity:	0.268
Maximum Recommended Daily Dose:	0.019
Skin Sensitization:	0.967
Carcinogencity:	0.595
Eye Corrosion:	0.893
Eye Irritation:	0.964
Respiratory Toxicity:	0.96

Download Data

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

Natural Product: NPC182758

Natural Product ID:	NPC182758
*Common Name:**	Motualevic Acid A
IUPAC Name:	2-[[(2E)-14,14-dibromotetradeca-2,13-dienoyl]amino]acetic acid
Synonyms:
Standard InCHIKey:	ZLIHRGDEFDFVOK-ZRDIBKRKSA-N
Standard InCHI:	InChI=1S/C16H25Br2NO3/c17-14(18)11-9-7-5-3-1-2-4-6-8-10-12-15(20)19-13-16(21)22/h10-12H,1-9,13H2,(H,19,20)(H,21,22)/b12-10+
SMILES:	C(CCCC/C=C/C(=NCC(=O)O)O)CCCCC=C(Br)Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1171537
PubChem CID:	25242622
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0001189] N-acyl-alpha amino acids and derivatives [CHEMONTID:0002402] N-acyl-alpha amino acids

*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
NPO30959	Siliquariaspongia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[19191563]

☑ 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
MIC	4
Others	5

Activity Type	# Activity
Organism	9

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	8.0	mm	PMID[570072]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	IZ	=	8.0	mm	PMID[570072]
NPT1605	Organism	Enterococcus	Enterococcus	IZ	=	8.0	mm	PMID[570072]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	11.0	ug.mL-1	PMID[570072]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	9.3	ug.mL-1	PMID[570072]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	9.3	ug.mL-1	PMID[570072]
NPT1605	Organism	Enterococcus	Enterococcus	MIC	=	12.0	ug.mL-1	PMID[570072]

☑ 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 NPC182758 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	51
0.1-0.2	6415
0.2-0.3	25695
0.3-0.4	8665
0.4-0.5	1538
0.5-0.6	259
0.6-0.7	60
0.7-0.8	13
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7576	Intermediate Similarity	NPC316674
0.7536	Intermediate Similarity	NPC249713
0.75	Intermediate Similarity	NPC325734
0.7385	Intermediate Similarity	NPC312826
0.7302	Intermediate Similarity	NPC273023
0.7188	Intermediate Similarity	NPC306420
0.7188	Intermediate Similarity	NPC104138
0.7188	Intermediate Similarity	NPC261158
0.7188	Intermediate Similarity	NPC24216
0.7183	Intermediate Similarity	NPC280065
0.7183	Intermediate Similarity	NPC45060
0.7164	Intermediate Similarity	NPC273614
0.7059	Intermediate Similarity	NPC77891
0.7031	Intermediate Similarity	NPC297020
0.7015	Intermediate Similarity	NPC6795
0.7015	Intermediate Similarity	NPC130807
0.7	Intermediate Similarity	NPC187315
0.6984	Remote Similarity	NPC303672
0.6875	Remote Similarity	NPC14234
0.6875	Remote Similarity	NPC132669
0.6875	Remote Similarity	NPC184014
0.6875	Remote Similarity	NPC246519
0.6875	Remote Similarity	NPC269800
0.6875	Remote Similarity	NPC44193
0.6825	Remote Similarity	NPC195986
0.6667	Remote Similarity	NPC54542
0.6667	Remote Similarity	NPC243539
0.6667	Remote Similarity	NPC304223
0.6667	Remote Similarity	NPC145032
0.6667	Remote Similarity	NPC267340
0.6667	Remote Similarity	NPC29468
0.662	Remote Similarity	NPC477525
0.6615	Remote Similarity	NPC13011
0.6615	Remote Similarity	NPC124382
0.6522	Remote Similarity	NPC309877
0.6515	Remote Similarity	NPC471991
0.6515	Remote Similarity	NPC471992
0.6508	Remote Similarity	NPC267692
0.6508	Remote Similarity	NPC307435
0.6462	Remote Similarity	NPC119655
0.6377	Remote Similarity	NPC329003
0.6377	Remote Similarity	NPC326524
0.6377	Remote Similarity	NPC150505
0.6377	Remote Similarity	NPC325550
0.6377	Remote Similarity	NPC74617
0.6364	Remote Similarity	NPC163912
0.6364	Remote Similarity	NPC305288
0.6364	Remote Similarity	NPC167759
0.6364	Remote Similarity	NPC56028
0.6338	Remote Similarity	NPC471023
0.6324	Remote Similarity	NPC245650
0.6269	Remote Similarity	NPC242930
0.6267	Remote Similarity	NPC471022
0.6267	Remote Similarity	NPC103712
0.6267	Remote Similarity	NPC291196
0.6232	Remote Similarity	NPC321030
0.6197	Remote Similarity	NPC324077
0.6176	Remote Similarity	NPC477049
0.6133	Remote Similarity	NPC474812
0.6119	Remote Similarity	NPC123669
0.6066	Remote Similarity	NPC86121
0.6049	Remote Similarity	NPC474833
0.6029	Remote Similarity	NPC474513
0.6029	Remote Similarity	NPC146551
0.6029	Remote Similarity	NPC470963
0.6029	Remote Similarity	NPC45626
0.6027	Remote Similarity	NPC253468
0.6027	Remote Similarity	NPC235311
0.5952	Remote Similarity	NPC474312
0.5949	Remote Similarity	NPC288086
0.5942	Remote Similarity	NPC4881
0.5942	Remote Similarity	NPC311648
0.5942	Remote Similarity	NPC470964
0.5875	Remote Similarity	NPC476923
0.5867	Remote Similarity	NPC129995
0.5867	Remote Similarity	NPC315141
0.5857	Remote Similarity	NPC48968
0.5857	Remote Similarity	NPC594
0.5821	Remote Similarity	NPC129458
0.5797	Remote Similarity	NPC152668
0.5783	Remote Similarity	NPC157173
0.5781	Remote Similarity	NPC308331
0.5758	Remote Similarity	NPC329181
0.5758	Remote Similarity	NPC59051
0.5758	Remote Similarity	NPC319110
0.5735	Remote Similarity	NPC225066
0.5735	Remote Similarity	NPC10081
0.5714	Remote Similarity	NPC304079
0.5714	Remote Similarity	NPC6963
0.5676	Remote Similarity	NPC55068
0.5672	Remote Similarity	NPC261571
0.5638	Remote Similarity	NPC175614
0.5634	Remote Similarity	NPC265551
0.5634	Remote Similarity	NPC44542
0.5634	Remote Similarity	NPC212730
0.5625	Remote Similarity	NPC314678
0.5618	Remote Similarity	NPC472614
0.5616	Remote Similarity	NPC471278

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 NPC182758 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	39
0.1-0.2	1678
0.2-0.3	5918
0.3-0.4	1344
0.4-0.5	149
0.5-0.6	22
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
0.5846	Remote Similarity	NPD4220	Pre-registration
0.5676	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD39	Approved

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