Structure

Physi-Chem Properties

Molecular Weight:  131.07
Volume:  123.038
LogP:  -2.888
LogD:  -1.585
LogS:  -1.026
# Rotatable Bonds:  3
TPSA:  90.41
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.327
Synthetic Accessibility Score:  2.594
Fsp3:  0.5
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:  -6.489
MDCK Permeability:  0.0056636338122189045
Pgp-inhibitor:  0.0
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.042
20% Bioavailability (F20%):  0.078
30% Bioavailability (F30%):  0.043

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.363
Plasma Protein Binding (PPB):  7.6842474937438965%
Volume Distribution (VD):  0.718
Pgp-substrate:  87.24092102050781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.062
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.051
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.257
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.014

ADMET: Excretion

Clearance (CL):  3.214
Half-life (T1/2):  0.615

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.049
Drug-inuced Liver Injury (DILI):  0.332
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.189
Carcinogencity:  0.096
Eye Corrosion:  0.004
Eye Irritation:  0.082
Respiratory Toxicity:  0.181

Download Data

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

  Natural Product: NPC195448

Natural Product ID:  NPC195448
Common Name*:   Creatine
IUPAC Name:   2-[carbamimidoyl(methyl)amino]acetic acid
Synonyms:   Creatine
Standard InCHIKey:  CVSVTCORWBXHQV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)
SMILES:  CN(CC(=O)O)C(=N)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL283800
PubChem CID:   586
59098743
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

*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

☑ 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
NPT5109 Individual Protein Creatine kinase M Homo sapiens Reaction rate = 100.0 n.a. PMID[493050]
NPT5109 Individual Protein Creatine kinase M Homo sapiens Activity = 100.0 n.a. PMID[493051]
NPT1006 Individual Protein Proton-coupled amino acid transporter 1 Homo sapiens Ki = 3200000.0 nM PMID[493053]
NPT1006 Individual Protein Proton-coupled amino acid transporter 1 Homo sapiens pKi = -0.51 mM PMID[493053]
NPT2 Others Unspecified Inhibition = 92.0 % PMID[493050]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 92.0 % PMID[493051]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 41.68 % PMID[493055]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Hit score = 0.1325 n.a. PMID[493056]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 27.56 % PMID[493057]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 13.55 % PMID[493058]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.06 % PMID[493059]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.01 % PMID[493060]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[493061]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[493061]

☑ 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 NPC195448 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
0.8636 High Similarity NPC40511
0.6905 Remote Similarity NPC59650
0.6875 Remote Similarity NPC27836
0.6818 Remote Similarity NPC134570
0.6667 Remote Similarity NPC245768
0.6522 Remote Similarity NPC216443
0.6522 Remote Similarity NPC69179
0.6429 Remote Similarity NPC10915
0.64 Remote Similarity NPC198301
0.6333 Remote Similarity NPC322206
0.6182 Remote Similarity NPC202525
0.6154 Remote Similarity NPC133183
0.6129 Remote Similarity NPC226453
0.6129 Remote Similarity NPC103130
0.6032 Remote Similarity NPC278881
0.6 Remote Similarity NPC260324
0.5938 Remote Similarity NPC325534
0.5938 Remote Similarity NPC327985
0.5938 Remote Similarity NPC193559
0.5849 Remote Similarity NPC297220
0.5849 Remote Similarity NPC141953
0.5849 Remote Similarity NPC153556
0.5814 Remote Similarity NPC126681
0.5806 Remote Similarity NPC118429
0.5758 Remote Similarity NPC81647
0.5741 Remote Similarity NPC314598
0.5741 Remote Similarity NPC182969
0.5714 Remote Similarity NPC204607
0.5625 Remote Similarity NPC1591
0.56 Remote Similarity NPC327250

  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 NPC195448 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 NPD8621 Approved
0.8571 High Similarity NPD8545 Approved
0.7885 Intermediate Similarity NPD8864 Clinical (unspecified phase)
0.7381 Intermediate Similarity NPD8800 Approved
0.6905 Remote Similarity NPD8799 Approved
0.6905 Remote Similarity NPD8796 Approved
0.6905 Remote Similarity NPD8795 Approved
0.6875 Remote Similarity NPD8607 Phase 3
0.6458 Remote Similarity NPD331 Approved
0.6458 Remote Similarity NPD335 Approved
0.6327 Remote Similarity NPD1433 Approved
0.6327 Remote Similarity NPD1437 Approved
0.6327 Remote Similarity NPD334 Phase 3
0.6129 Remote Similarity NPD9045 Approved
0.6129 Remote Similarity NPD9046 Phase 3
0.6129 Remote Similarity NPD9047 Approved
0.6129 Remote Similarity NPD9048 Approved
0.6111 Remote Similarity NPD2264 Approved
0.6111 Remote Similarity NPD2265 Approved
0.6094 Remote Similarity NPD9232 Phase 2
0.6094 Remote Similarity NPD9233 Phase 3
0.6094 Remote Similarity NPD9231 Phase 3
0.6078 Remote Similarity NPD2260 Approved
0.6078 Remote Similarity NPD2261 Phase 3
0.6042 Remote Similarity NPD336 Approved
0.6042 Remote Similarity NPD333 Approved
0.6042 Remote Similarity NPD9043 Approved
0.6042 Remote Similarity NPD330 Approved
0.6042 Remote Similarity NPD332 Approved
0.5938 Remote Similarity NPD8952 Approved
0.5918 Remote Similarity NPD1438 Approved
0.5918 Remote Similarity NPD1434 Approved
0.5918 Remote Similarity NPD1435 Approved
0.5918 Remote Similarity NPD1436 Approved
0.5849 Remote Similarity NPD8587 Approved
0.5814 Remote Similarity NPD7371 Approved
0.5806 Remote Similarity NPD9014 Approved
0.5625 Remote Similarity NPD9236 Approved
0.5625 Remote Similarity NPD9235 Approved
0.5625 Remote Similarity NPD9042 Approved
0.5614 Remote Similarity NPD2693 Approved
0.5614 Remote Similarity NPD2692 Approved
0.56 Remote Similarity NPD8968 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