Structure

Physi-Chem Properties

Molecular Weight:  160.12
Volume:  166.566
LogP:  -3.561
LogD:  -2.465
LogS:  0.131
# Rotatable Bonds:  4
TPSA:  66.15
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.491
Synthetic Accessibility Score:  4.452
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.934
MDCK Permeability:  0.0010471842251718044
Pgp-inhibitor:  0.0
Pgp-substrate:  0.022
Human Intestinal Absorption (HIA):  0.709
20% Bioavailability (F20%):  0.973
30% Bioavailability (F30%):  0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.31
Plasma Protein Binding (PPB):  12.521713256835938%
Volume Distribution (VD):  0.689
Pgp-substrate:  97.10395050048828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.086
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.044
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.143
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.452
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.041

ADMET: Excretion

Clearance (CL):  2.078
Half-life (T1/2):  0.836

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.629
Drug-inuced Liver Injury (DILI):  0.01
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.075
Maximum Recommended Daily Dose:  0.776
Skin Sensitization:  0.094
Carcinogencity:  0.521
Eye Corrosion:  0.028
Eye Irritation:  0.088
Respiratory Toxicity:  0.393

Download Data

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

  Natural Product: NPC17244

Natural Product ID:  NPC17244
Common Name*:   (R)-Aminocarnitine
IUPAC Name:   (3R)-3-amino-4-(trimethylazaniumyl)butanoate
Synonyms:   (R)-Aminocarnitine
Standard InCHIKey:  DAWBGYHPBBDHMQ-ZCFIWIBFSA-N
Standard InCHI:  InChI=1S/C7H16N2O2/c1-9(2,3)5-6(8)4-7(10)11/h6H,4-5,8H2,1-3H3/t6-/m1/s1
SMILES:  C[N+](C)(C)C[C@@H](CC(=O)[O-])N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2114397
PubChem CID:   121830
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:0001878] Beta amino acids and derivatives

*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
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[10757727]
NPO4291 Laurencia brongniartii Species Rhodomelaceae Eukaryota n.a. Formosan red alga n.a. PMID[15921441]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4291 Laurencia brongniartii Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT91 Cell Line KB Homo sapiens IC50 = 970.0 nM PMID[521851]
NPT1375 Individual Protein Carnitine palmitoyltransferase 2 Homo sapiens IC50 = 3900.0 nM PMID[521851]
NPT1376 Individual Protein Carnitine palmitoyltransferase 1B Rattus norvegicus IC50 = 27300.0 nM PMID[521851]
NPT1377 Individual Protein Carnitine palmitoyltransferase 2 Rattus norvegicus IC50 = 5100.0 nM PMID[521851]
NPT1378 Individual Protein Carnitine O-palmitoyltransferase 1, muscle isoform Homo sapiens IC50 > 100000.0 nM PMID[521851]
NPT1379 Individual Protein Carnitine O-palmitoyltransferase 1, liver isoform Homo sapiens IC50 = 76400.0 nM PMID[521851]
NPT1377 Individual Protein Carnitine palmitoyltransferase 2 Rattus norvegicus IC50 = 800.0 nM PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 36.0 % PMID[521849]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 11.0 % PMID[521849]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 90.0 % PMID[521850]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 59.0 % PMID[521850]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 16.0 % PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 88.0 % PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 1034.0 % PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 244.0 % PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 684.0 % PMID[521851]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 68.0 % PMID[521851]
NPT2 Others Unspecified "" IC50 = 5400.0 nM PMID[521851]
NPT2 Others Unspecified "" IC50 = 12000.0 nM PMID[521851]
NPT2 Others Unspecified "" IC50 = 3200.0 nM PMID[521851]

☑ 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 NPC17244 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7333 Intermediate Similarity NPC229838
0.7083 Intermediate Similarity NPC66043
0.6863 Remote Similarity NPC329263
0.6724 Remote Similarity NPC278209
0.6667 Remote Similarity NPC18188
0.6667 Remote Similarity NPC177191
0.6429 Remote Similarity NPC202525
0.64 Remote Similarity NPC237525
0.64 Remote Similarity NPC326992
0.64 Remote Similarity NPC326212
0.64 Remote Similarity NPC168375
0.64 Remote Similarity NPC121517
0.6379 Remote Similarity NPC10915
0.6316 Remote Similarity NPC245768
0.6226 Remote Similarity NPC118459
0.6226 Remote Similarity NPC327698
0.6154 Remote Similarity NPC291186
0.6154 Remote Similarity NPC167986
0.614 Remote Similarity NPC155156
0.614 Remote Similarity NPC200550
0.6038 Remote Similarity NPC126925
0.6038 Remote Similarity NPC132307
0.6038 Remote Similarity NPC325097
0.6038 Remote Similarity NPC198301
0.6 Remote Similarity NPC38463
0.6 Remote Similarity NPC136159
0.5965 Remote Similarity NPC273330
0.5965 Remote Similarity NPC137958
0.5932 Remote Similarity NPC316889
0.5932 Remote Similarity NPC321118
0.5926 Remote Similarity NPC208793
0.5926 Remote Similarity NPC285322
0.5893 Remote Similarity NPC93081
0.5893 Remote Similarity NPC153370
0.5893 Remote Similarity NPC140872
0.5882 Remote Similarity NPC322274
0.5873 Remote Similarity NPC143722
0.5833 Remote Similarity NPC327831
0.5833 Remote Similarity NPC2801
0.5818 Remote Similarity NPC198196
0.5818 Remote Similarity NPC297220
0.5806 Remote Similarity NPC176164
0.5806 Remote Similarity NPC189301
0.5789 Remote Similarity NPC245027
0.5789 Remote Similarity NPC84636
0.5789 Remote Similarity NPC174246
0.5789 Remote Similarity NPC316231
0.5789 Remote Similarity NPC226027
0.5789 Remote Similarity NPC62045
0.5789 Remote Similarity NPC43204
0.5789 Remote Similarity NPC328378
0.5789 Remote Similarity NPC112890
0.5789 Remote Similarity NPC324825
0.5789 Remote Similarity NPC162620
0.5781 Remote Similarity NPC322206
0.5769 Remote Similarity NPC53449
0.5763 Remote Similarity NPC325180
0.5763 Remote Similarity NPC35816
0.5763 Remote Similarity NPC197087
0.5763 Remote Similarity NPC190184
0.5738 Remote Similarity NPC325985
0.5735 Remote Similarity NPC81647
0.5714 Remote Similarity NPC316826
0.5714 Remote Similarity NPC321468
0.5714 Remote Similarity NPC317143
0.5714 Remote Similarity NPC254541
0.5714 Remote Similarity NPC327748
0.5714 Remote Similarity NPC321536
0.5694 Remote Similarity NPC327272
0.569 Remote Similarity NPC198398
0.569 Remote Similarity NPC125736
0.569 Remote Similarity NPC27359
0.569 Remote Similarity NPC295832
0.5672 Remote Similarity NPC325534
0.5672 Remote Similarity NPC287693
0.5652 Remote Similarity NPC133183
0.5645 Remote Similarity NPC318260
0.5645 Remote Similarity NPC317147
0.5625 Remote Similarity NPC114517
0.5625 Remote Similarity NPC329564
0.5625 Remote Similarity NPC327170
0.5614 Remote Similarity NPC327542
0.5606 Remote Similarity NPC57420
0.56 Remote Similarity NPC272614
0.56 Remote Similarity NPC21290
0.56 Remote Similarity NPC116709

  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 NPC17244 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD9230 Discontinued
0.6923 Remote Similarity NPD5382 Phase 2
0.6667 Remote Similarity NPD8623 Phase 1
0.6275 Remote Similarity NPD8609 Approved
0.6154 Remote Similarity NPD8804 Approved
0.6154 Remote Similarity NPD8805 Approved
0.6061 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6038 Remote Similarity NPD8798 Approved
0.5968 Remote Similarity NPD9671 Phase 2
0.5968 Remote Similarity NPD9670 Phase 2
0.5965 Remote Similarity NPD8871 Approved
0.5965 Remote Similarity NPD8872 Phase 3
0.5926 Remote Similarity NPD8610 Approved
0.5893 Remote Similarity NPD8614 Approved
0.5893 Remote Similarity NPD8808 Approved
0.5893 Remote Similarity NPD8809 Approved
0.5818 Remote Similarity NPD9020 Approved
0.5806 Remote Similarity NPD9433 Approved
0.5806 Remote Similarity NPD8784 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9044 Approved
0.5789 Remote Similarity NPD9017 Approved
0.5789 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9018 Approved
0.5763 Remote Similarity NPD8785 Approved
0.5763 Remote Similarity NPD9660 Approved
0.5763 Remote Similarity NPD8851 Phase 1
0.5714 Remote Similarity NPD398 Approved
0.5714 Remote Similarity NPD400 Approved
0.5714 Remote Similarity NPD399 Approved
0.569 Remote Similarity NPD9225 Phase 3
0.569 Remote Similarity NPD9226 Approved
0.5672 Remote Similarity NPD8952 Approved
0.5636 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5625 Remote Similarity NPD902 Approved
0.56 Remote Similarity NPD8211 Approved
0.56 Remote Similarity NPD8210 Phase 3

  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