Structure

Physi-Chem Properties

Molecular Weight:  161.11
Volume:  164.359
LogP:  -3.031
LogD:  -2.232
LogS:  0.008
# Rotatable Bonds:  4
TPSA:  60.36
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.494
Synthetic Accessibility Score:  4.162
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:  -5.954
MDCK Permeability:  0.001504228450357914
Pgp-inhibitor:  0.0
Pgp-substrate:  0.018
Human Intestinal Absorption (HIA):  0.737
20% Bioavailability (F20%):  0.982
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.267
Plasma Protein Binding (PPB):  10.11424732208252%
Volume Distribution (VD):  0.755
Pgp-substrate:  93.84790802001953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.32
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.043
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.167
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.208
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.02

ADMET: Excretion

Clearance (CL):  2.174
Half-life (T1/2):  0.893

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.331
Drug-inuced Liver Injury (DILI):  0.003
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.053
Maximum Recommended Daily Dose:  0.875
Skin Sensitization:  0.054
Carcinogencity:  0.111
Eye Corrosion:  0.237
Eye Irritation:  0.788
Respiratory Toxicity:  0.208

Download Data

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

  Natural Product: NPC27359

Natural Product ID:  NPC27359
Common Name*:   D-Carnitine
IUPAC Name:   (3S)-3-hydroxy-4-(trimethylazaniumyl)butanoate
Synonyms:   D-Carnitine
Standard InCHIKey:  PHIQHXFUZVPYII-LURJTMIESA-N
Standard InCHI:  InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/t6-/m0/s1
SMILES:  O[C@H](C[N+](C)(C)C)CC(=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL503189
PubChem CID:   2724480
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0000503] Quaternary ammonium salts
          • [CHEMONTID:0001609] Carnitines

*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
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1596 Taraxacum borealisinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13668 Taraxacum platycarpum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23327 Taraxacum coreanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23327 Taraxacum coreanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13668 Taraxacum platycarpum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26622 Taraxacum officinale Species Asteraceae 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
NPT589 Individual Protein Serum albumin Bos taurus K = 2.15 10'4L/mol PMID[458317]
NPT589 Individual Protein Serum albumin Bos taurus K = 3.18 10'4L/mol PMID[458317]
NPT1871 Individual Protein Solute carrier family 22 member 16 Homo sapiens Ki = 30000.0 nM PMID[458318]
NPT1543 Individual Protein Solute carrier family 22 member 4 Homo sapiens Activity = 53.9 % PMID[458319]

☑ 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 NPC27359 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
1.0 High Similarity NPC198398
1.0 High Similarity NPC295832
0.8077 Intermediate Similarity NPC35816
0.8077 Intermediate Similarity NPC325180
0.8 Intermediate Similarity NPC327542
0.7174 Intermediate Similarity NPC229838
0.717 Intermediate Similarity NPC93888
0.717 Intermediate Similarity NPC270805
0.6957 Remote Similarity NPC168052
0.6957 Remote Similarity NPC250870
0.6957 Remote Similarity NPC191084
0.6562 Remote Similarity NPC325117
0.6562 Remote Similarity NPC326651
0.6562 Remote Similarity NPC322319
0.6406 Remote Similarity NPC472609
0.6406 Remote Similarity NPC160661
0.6338 Remote Similarity NPC315780
0.62 Remote Similarity NPC18188
0.5873 Remote Similarity NPC473599
0.5849 Remote Similarity NPC219143
0.5849 Remote Similarity NPC35661
0.5849 Remote Similarity NPC226265
0.5818 Remote Similarity NPC329263
0.5806 Remote Similarity NPC293551
0.58 Remote Similarity NPC1591
0.58 Remote Similarity NPC5505
0.5781 Remote Similarity NPC177191
0.5763 Remote Similarity NPC155156
0.5763 Remote Similarity NPC202525
0.5763 Remote Similarity NPC200550
0.5745 Remote Similarity NPC325909
0.5741 Remote Similarity NPC107645
0.5735 Remote Similarity NPC135539
0.5735 Remote Similarity NPC78312
0.5735 Remote Similarity NPC196359
0.5735 Remote Similarity NPC221764
0.5714 Remote Similarity NPC93861
0.5714 Remote Similarity NPC190385
0.5714 Remote Similarity NPC112224
0.5714 Remote Similarity NPC43169
0.5714 Remote Similarity NPC327895
0.569 Remote Similarity NPC17244
0.5667 Remote Similarity NPC329495
0.5667 Remote Similarity NPC189178
0.5667 Remote Similarity NPC245768
0.5667 Remote Similarity NPC263065
0.566 Remote Similarity NPC168375
0.566 Remote Similarity NPC326992
0.566 Remote Similarity NPC121517
0.5652 Remote Similarity NPC107224
0.5652 Remote Similarity NPC136014
0.5636 Remote Similarity NPC198301
0.5625 Remote Similarity NPC59650
0.5625 Remote Similarity NPC170172
0.5625 Remote Similarity NPC471421
0.5625 Remote Similarity NPC233364
0.5614 Remote Similarity NPC181588
0.5614 Remote Similarity NPC81384
0.56 Remote Similarity NPC316242

  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 NPC27359 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 NPD9226 Approved
1.0 High Similarity NPD9225 Phase 3
0.8654 High Similarity NPD9659 Approved
0.8077 Intermediate Similarity NPD9660 Approved
0.717 Intermediate Similarity NPD8624 Approved
0.7097 Intermediate Similarity NPD9442 Clinical (unspecified phase)
0.6471 Remote Similarity NPD9457 Approved
0.6471 Remote Similarity NPD9456 Approved
0.6393 Remote Similarity NPD8951 Approved
0.6316 Remote Similarity NPD2693 Approved
0.6316 Remote Similarity NPD2692 Approved
0.62 Remote Similarity NPD8623 Phase 1
0.6111 Remote Similarity NPD9658 Clinical (unspecified phase)
0.6042 Remote Similarity NPD8800 Approved
0.5938 Remote Similarity NPD3192 Approved
0.5938 Remote Similarity NPD3193 Approved
0.5893 Remote Similarity NPD1458 Approved
0.5893 Remote Similarity NPD1459 Approved
0.5849 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5849 Remote Similarity NPD8216 Approved
0.58 Remote Similarity NPD9236 Approved
0.58 Remote Similarity NPD9235 Approved
0.5753 Remote Similarity NPD11 Approved
0.5753 Remote Similarity NPD376 Approved
0.5735 Remote Similarity NPD8868 Approved
0.5714 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5694 Remote Similarity NPD355 Phase 2
0.569 Remote Similarity NPD9230 Discontinued
0.5667 Remote Similarity NPD9204 Approved
0.5667 Remote Similarity NPD9205 Approved
0.5652 Remote Similarity NPD9262 Approved
0.5652 Remote Similarity NPD8821 Approved
0.5652 Remote Similarity NPD8818 Approved
0.5652 Remote Similarity NPD8820 Approved
0.5652 Remote Similarity NPD110 Approved
0.5652 Remote Similarity NPD8817 Phase 3
0.5652 Remote Similarity NPD8819 Approved
0.5636 Remote Similarity NPD9229 Approved
0.5625 Remote Similarity NPD8795 Approved
0.5625 Remote Similarity NPD8796 Approved
0.5625 Remote Similarity NPD8799 Approved
0.5614 Remote Similarity NPD9462 Approved
0.5614 Remote Similarity NPD9463 Phase 3
0.5614 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5606 Remote Similarity NPD4283 Discontinued

  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