Structure

Physi-Chem Properties

Molecular Weight:  86.04
Volume:  90.048
LogP:  0.759
LogD:  0.783
LogS:  0.373
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.475
Synthetic Accessibility Score:  2.663
Fsp3:  0.25
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:  -4.874
MDCK Permeability:  1.7919934180099517e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.023
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.136

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.933
Plasma Protein Binding (PPB):  33.04345703125%
Volume Distribution (VD):  0.329
Pgp-substrate:  70.88937377929688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.051
CYP2C9-substrate:  0.391
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.169
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.072

ADMET: Excretion

Clearance (CL):  4.847
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.804
Drug-inuced Liver Injury (DILI):  0.096
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.421
Maximum Recommended Daily Dose:  0.045
Skin Sensitization:  0.941
Carcinogencity:  0.051
Eye Corrosion:  0.986
Eye Irritation:  0.996
Respiratory Toxicity:  0.51

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

  Natural Product: NPC60672

Natural Product ID:  NPC60672
Common Name*:   Canavanine
IUPAC Name:   (2S)-2-azaniumyl-4-(diaminomethylideneamino)oxybutanoate
Synonyms:   L-Canavanine; L-Canavanine Sulfate
Standard InCHIKey:  FSBIGDSBMBYOPN-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C5H12N4O3/c6-3(4(10)11)1-2-12-9-5(7)8/h3H,1-2,6H2,(H,10,11)(H4,7,8,9)/t3-/m0/s1
SMILES:  C(CONC(=N)N)[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443732
PubChem CID:   46224610
439202
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:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-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
NPO21208 Solanum chrysotrichum Species Solanaceae Eukaryota Leaves n.a. n.a. PMID[12502320]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[19006373]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. stem n.a. PMID[19006373]
NPO24668 Ophiocoma dentata Species Ophiocomidae Eukaryota n.a. n.a. n.a. PMID[8145229]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21208 Solanum chrysotrichum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18585 Sphaerostephanos arbuscula Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28743 Ticorea longiflora n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26620 Pulicaria arabica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16870 Athanasia linifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6635 Deamia testudo Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24668 Ophiocoma dentata Species Ophiocomidae 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
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens Ki = 220000.0 nM PMID[526868]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus IC50 = 60000.0 nM PMID[526869]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus IC50 = 60000.0 nM PMID[526870]
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 3981.1 nM PMID[526873]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens Potency = 15848.9 nM PMID[526873]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 31622.8 nM PMID[526874]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 6.0 nM PMID[526874]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens AC50 = 15848.93 nM PMID[526873]
NPT71 Cell Line HEK293 Homo sapiens Potency n.a. 651.0 nM PMID[526874]
NPT519 Cell Line SH-SY5Y Homo sapiens Potency n.a. 3548.1 nM PMID[526874]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 9466.2 nM PMID[526874]
NPT478 Individual Protein Ataxin-2 Homo sapiens Potency n.a. 3548.1 nM PMID[526874]
NPT197 Protein-Protein Interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 39810.7 nM PMID[526872]
NPT792 Individual Protein Arachidonate 15-lipoxygenase Homo sapiens Potency = 1995.3 nM PMID[526873]
NPT95 Individual Protein Muscarinic acetylcholine receptor M1 Rattus norvegicus Potency = 31.6 nM PMID[526873]
NPT7 Individual Protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus Potency n.a. 1584.9 nM PMID[526874]
NPT2 Others Unspecified Potency n.a. 6510.4 nM PMID[526874]
NPT2 Others Unspecified Potency n.a. 6510.4 nM PMID[526872]
NPT2 Others Unspecified Potency n.a. 6510.4 nM PMID[526875]
NPT2 Others Unspecified Potency n.a. 6510.4 nM PMID[526876]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 91.69 % PMID[526877]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 101.56 % PMID[526877]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 2.77 % PMID[526878]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.09 % PMID[526879]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[526880]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[526880]

☑ 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 NPC60672 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 NPC322091
0.8776 High Similarity NPC136159
0.7885 Intermediate Similarity NPC153370
0.7308 Intermediate Similarity NPC208793
0.7308 Intermediate Similarity NPC285322
0.7213 Intermediate Similarity NPC322206
0.72 Intermediate Similarity NPC326992
0.72 Intermediate Similarity NPC168375
0.72 Intermediate Similarity NPC121517
0.717 Intermediate Similarity NPC309658
0.7069 Intermediate Similarity NPC327831
0.6981 Remote Similarity NPC329263
0.6923 Remote Similarity NPC291186
0.6923 Remote Similarity NPC167986
0.6863 Remote Similarity NPC237525
0.6863 Remote Similarity NPC326212
0.6863 Remote Similarity NPC66043
0.6792 Remote Similarity NPC132307
0.6792 Remote Similarity NPC126925
0.6792 Remote Similarity NPC325097
0.6786 Remote Similarity NPC270805
0.6786 Remote Similarity NPC93888
0.678 Remote Similarity NPC10915
0.6769 Remote Similarity NPC327985
0.6727 Remote Similarity NPC181588
0.6721 Remote Similarity NPC190385
0.6667 Remote Similarity NPC118459
0.6667 Remote Similarity NPC327698
0.6607 Remote Similarity NPC140872
0.6607 Remote Similarity NPC93081
0.6545 Remote Similarity NPC49952
0.6545 Remote Similarity NPC297220
0.6545 Remote Similarity NPC136476
0.6538 Remote Similarity NPC53449
0.6491 Remote Similarity NPC316231
0.6491 Remote Similarity NPC324825
0.6491 Remote Similarity NPC328378
0.6491 Remote Similarity NPC112890
0.6462 Remote Similarity NPC103130
0.6462 Remote Similarity NPC226453
0.6452 Remote Similarity NPC93861
0.6452 Remote Similarity NPC327895
0.6452 Remote Similarity NPC43169
0.6452 Remote Similarity NPC112224
0.6441 Remote Similarity NPC197087
0.6441 Remote Similarity NPC190184
0.6441 Remote Similarity NPC329495
0.6429 Remote Similarity NPC316168
0.6415 Remote Similarity NPC219143
0.6415 Remote Similarity NPC226265
0.6406 Remote Similarity NPC118429
0.64 Remote Similarity NPC116709
0.64 Remote Similarity NPC21290
0.64 Remote Similarity NPC272614
0.6379 Remote Similarity NPC125736
0.6364 Remote Similarity NPC278881
0.6333 Remote Similarity NPC321118
0.6333 Remote Similarity NPC316889
0.6316 Remote Similarity NPC227850
0.6275 Remote Similarity NPC63621
0.6271 Remote Similarity NPC202525
0.625 Remote Similarity NPC185755
0.625 Remote Similarity NPC213876
0.6212 Remote Similarity NPC106216
0.6212 Remote Similarity NPC88898
0.6207 Remote Similarity NPC170739
0.6207 Remote Similarity NPC43204
0.6207 Remote Similarity NPC84636
0.6207 Remote Similarity NPC174246
0.6207 Remote Similarity NPC152451
0.6207 Remote Similarity NPC62045
0.6207 Remote Similarity NPC193989
0.6207 Remote Similarity NPC226027
0.6207 Remote Similarity NPC245027
0.6207 Remote Similarity NPC162620
0.6182 Remote Similarity NPC198301
0.6176 Remote Similarity NPC118524
0.6167 Remote Similarity NPC245768
0.6154 Remote Similarity NPC18188
0.6154 Remote Similarity NPC273037
0.6129 Remote Similarity NPC325985
0.6129 Remote Similarity NPC38463
0.6102 Remote Similarity NPC137958
0.6102 Remote Similarity NPC273330
0.6102 Remote Similarity NPC315977
0.6094 Remote Similarity NPC320598
0.6094 Remote Similarity NPC321536
0.6034 Remote Similarity NPC327542
0.6029 Remote Similarity NPC325534
0.6 Remote Similarity NPC133183
0.6 Remote Similarity NPC68974
0.5968 Remote Similarity NPC2801
0.5942 Remote Similarity NPC78312
0.5942 Remote Similarity NPC221764
0.5942 Remote Similarity NPC135539
0.5942 Remote Similarity NPC196359
0.5938 Remote Similarity NPC176164
0.5938 Remote Similarity NPC189301
0.5932 Remote Similarity NPC286989
0.5902 Remote Similarity NPC317815
0.5862 Remote Similarity NPC204364
0.5857 Remote Similarity NPC107224
0.5846 Remote Similarity NPC317143
0.5846 Remote Similarity NPC316826
0.5846 Remote Similarity NPC327748
0.5846 Remote Similarity NPC254541
0.5846 Remote Similarity NPC321468
0.5833 Remote Similarity NPC114990
0.5833 Remote Similarity NPC328457
0.5833 Remote Similarity NPC319175
0.5818 Remote Similarity NPC326808
0.5818 Remote Similarity NPC110533
0.5818 Remote Similarity NPC254482
0.5818 Remote Similarity NPC317691
0.5806 Remote Similarity NPC183845
0.5806 Remote Similarity NPC279661
0.58 Remote Similarity NPC114517
0.5781 Remote Similarity NPC278209
0.5781 Remote Similarity NPC317147
0.5781 Remote Similarity NPC318260
0.5769 Remote Similarity NPC9294
0.5758 Remote Similarity NPC327170
0.5758 Remote Similarity NPC143722
0.5758 Remote Similarity NPC329564
0.5758 Remote Similarity NPC321419
0.5738 Remote Similarity NPC155156
0.5738 Remote Similarity NPC200550
0.5714 Remote Similarity NPC107645
0.5714 Remote Similarity NPC276294
0.5714 Remote Similarity NPC102815
0.5714 Remote Similarity NPC322573
0.569 Remote Similarity NPC198196
0.566 Remote Similarity NPC69179
0.5634 Remote Similarity NPC81647
0.5634 Remote Similarity NPC319046
0.5625 Remote Similarity NPC313263
0.5614 Remote Similarity NPC323974
0.5606 Remote Similarity NPC473599

  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 NPC60672 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
0.7885 Intermediate Similarity NPD8614 Approved
0.7308 Intermediate Similarity NPD8610 Approved
0.6923 Remote Similarity NPD8805 Approved
0.6923 Remote Similarity NPD8804 Approved
0.6792 Remote Similarity NPD8798 Approved
0.6786 Remote Similarity NPD8624 Approved
0.6731 Remote Similarity NPD8609 Approved
0.6727 Remote Similarity NPD8810 Clinical (unspecified phase)
0.6721 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6607 Remote Similarity NPD8808 Approved
0.6607 Remote Similarity NPD8809 Approved
0.6491 Remote Similarity NPD9044 Approved
0.6462 Remote Similarity NPD9048 Approved
0.6462 Remote Similarity NPD9045 Approved
0.6462 Remote Similarity NPD9047 Approved
0.6462 Remote Similarity NPD9046 Phase 3
0.6441 Remote Similarity NPD8785 Approved
0.6429 Remote Similarity NPD8209 Phase 2
0.6429 Remote Similarity NPD8208 Clinical (unspecified phase)
0.6415 Remote Similarity NPD8216 Approved
0.6415 Remote Similarity NPD8217 Clinical (unspecified phase)
0.6406 Remote Similarity NPD9014 Approved
0.64 Remote Similarity NPD8210 Phase 3
0.64 Remote Similarity NPD8211 Approved
0.625 Remote Similarity NPD8801 Approved
0.625 Remote Similarity NPD8982 Approved
0.6207 Remote Similarity NPD8802 Approved
0.6207 Remote Similarity NPD9018 Approved
0.6207 Remote Similarity NPD8803 Clinical (unspecified phase)
0.6207 Remote Similarity NPD9021 Approved
0.6207 Remote Similarity NPD9017 Approved
0.6207 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6176 Remote Similarity NPD9232 Phase 2
0.6176 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6176 Remote Similarity NPD9231 Phase 3
0.6176 Remote Similarity NPD9233 Phase 3
0.6154 Remote Similarity NPD8623 Phase 1
0.6111 Remote Similarity NPD366 Approved
0.6102 Remote Similarity NPD8872 Phase 3
0.6102 Remote Similarity NPD8871 Approved
0.6102 Remote Similarity NPD9025 Approved
0.6066 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6029 Remote Similarity NPD8952 Approved
0.5942 Remote Similarity NPD8868 Approved
0.5942 Remote Similarity NPD8842 Clinical (unspecified phase)
0.5938 Remote Similarity NPD9433 Approved
0.5902 Remote Similarity NPD8849 Clinical (unspecified phase)
0.5902 Remote Similarity NPD8851 Phase 1
0.5857 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5857 Remote Similarity NPD9452 Clinical (unspecified phase)
0.5818 Remote Similarity NPD8214 Approved
0.5818 Remote Similarity NPD8215 Approved
0.5763 Remote Similarity NPD8873 Approved
0.569 Remote Similarity NPD9020 Approved
0.5634 Remote Similarity NPD337 Discontinued
0.5625 Remote Similarity NPD8980 Approved
0.5625 Remote Similarity NPD8979 Approved
0.5625 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4829 Discontinued
0.5614 Remote Similarity NPD9019 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