Structure

Physi-Chem Properties

Molecular Weight:  163.07
Volume:  156.782
LogP:  -2.685
LogD:  -2.611
LogS:  -0.077
# Rotatable Bonds:  4
TPSA:  66.15
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.504
Synthetic Accessibility Score:  4.726
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.401
MDCK Permeability:  0.00014392781304195523
Pgp-inhibitor:  0.0
Pgp-substrate:  0.926
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.204
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.175
Plasma Protein Binding (PPB):  18.62612533569336%
Volume Distribution (VD):  0.914
Pgp-substrate:  86.11825561523438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.065
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.43
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.129
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.168
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  2.0
Half-life (T1/2):  0.914

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.919
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.153
Carcinogencity:  0.666
Eye Corrosion:  0.008
Eye Irritation:  0.039
Respiratory Toxicity:  0.045

Download Data

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

  Natural Product: NPC198196

Natural Product ID:  NPC198196
Common Name*:   S-Methylmethionine Sufonium
IUPAC Name:   (2S)-2-amino-4-dimethylsulfoniobutanoate
Synonyms:  
Standard InCHIKey:  YDBYJHTYSHBBAU-YFKPBYRVSA-N
Standard InCHI:  InChI=1S/C6H13NO2S/c1-10(2)4-3-5(7)6(8)9/h5H,3-4,7H2,1-2H3/t5-/m0/s1
SMILES:  C[S+](C)CC[C@@H](C(=O)[O-])N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2074824
PubChem CID:   10197842
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:0004143] Methionine 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
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[18270436]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23793896]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. seed n.a. PMID[24967651]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22132 Hordeum vulgare Species Poaceae 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
NPT705 Individual Protein Solute carrier family 22 member 5 Homo sapiens Activity = 8.7 % PMID[505598]

☑ 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 NPC198196 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
0.9333 High Similarity NPC170739
0.9333 High Similarity NPC152451
0.9333 High Similarity NPC193989
0.8889 High Similarity NPC204364
0.875 High Similarity NPC317815
0.84 Intermediate Similarity NPC102815
0.8261 Intermediate Similarity NPC49952
0.8261 Intermediate Similarity NPC136476
0.8043 Intermediate Similarity NPC191136
0.7959 Intermediate Similarity NPC114990
0.7636 Intermediate Similarity NPC321419
0.76 Intermediate Similarity NPC125736
0.7556 Intermediate Similarity NPC121517
0.7556 Intermediate Similarity NPC168375
0.7556 Intermediate Similarity NPC326992
0.75 Intermediate Similarity NPC185755
0.75 Intermediate Similarity NPC145235
0.75 Intermediate Similarity NPC213876
0.7391 Intermediate Similarity NPC110533
0.7391 Intermediate Similarity NPC254482
0.7391 Intermediate Similarity NPC317691
0.7391 Intermediate Similarity NPC326808
0.7234 Intermediate Similarity NPC291186
0.7234 Intermediate Similarity NPC167986
0.7091 Intermediate Similarity NPC283786
0.7091 Intermediate Similarity NPC82239
0.7083 Intermediate Similarity NPC132307
0.7083 Intermediate Similarity NPC325097
0.7083 Intermediate Similarity NPC126925
0.6939 Remote Similarity NPC118459
0.6939 Remote Similarity NPC327698
0.6809 Remote Similarity NPC66043
0.6809 Remote Similarity NPC53449
0.68 Remote Similarity NPC228932
0.6667 Remote Similarity NPC21290
0.6667 Remote Similarity NPC118187
0.6667 Remote Similarity NPC116709
0.6667 Remote Similarity NPC272614
0.6604 Remote Similarity NPC319175
0.66 Remote Similarity NPC329263
0.6538 Remote Similarity NPC318523
0.6471 Remote Similarity NPC248970
0.6471 Remote Similarity NPC306238
0.6415 Remote Similarity NPC270805
0.6415 Remote Similarity NPC162620
0.6415 Remote Similarity NPC62045
0.6415 Remote Similarity NPC226027
0.6415 Remote Similarity NPC245027
0.6415 Remote Similarity NPC174246
0.6415 Remote Similarity NPC84636
0.6415 Remote Similarity NPC93888
0.6415 Remote Similarity NPC43204
0.64 Remote Similarity NPC198301
0.6346 Remote Similarity NPC136159
0.6296 Remote Similarity NPC315977
0.6275 Remote Similarity NPC285322
0.6275 Remote Similarity NPC208793
0.6226 Remote Similarity NPC153370
0.6226 Remote Similarity NPC93081
0.6226 Remote Similarity NPC140872
0.617 Remote Similarity NPC63621
0.6154 Remote Similarity NPC309658
0.6154 Remote Similarity NPC297220
0.6129 Remote Similarity NPC289691
0.6122 Remote Similarity NPC326212
0.6122 Remote Similarity NPC237525
0.6111 Remote Similarity NPC112890
0.6111 Remote Similarity NPC316231
0.6111 Remote Similarity NPC324825
0.6111 Remote Similarity NPC328378
0.6042 Remote Similarity NPC18188
0.6032 Remote Similarity NPC325597
0.6032 Remote Similarity NPC174304
0.6 Remote Similarity NPC137958
0.6 Remote Similarity NPC14778
0.6 Remote Similarity NPC273330
0.5965 Remote Similarity NPC321118
0.5965 Remote Similarity NPC316889
0.5957 Remote Similarity NPC9294
0.5918 Remote Similarity NPC329545
0.5862 Remote Similarity NPC2801
0.5818 Remote Similarity NPC17244
0.5789 Remote Similarity NPC190184
0.5789 Remote Similarity NPC197087
0.5763 Remote Similarity NPC38463
0.5758 Remote Similarity NPC319046
0.5741 Remote Similarity NPC181588
0.569 Remote Similarity NPC60672
0.569 Remote Similarity NPC183845
0.569 Remote Similarity NPC279661
0.569 Remote Similarity NPC322091
0.5686 Remote Similarity NPC226265
0.5686 Remote Similarity NPC219143
0.5672 Remote Similarity NPC126779
0.5667 Remote Similarity NPC278209
0.5652 Remote Similarity NPC315897
0.5614 Remote Similarity NPC200550
0.5614 Remote Similarity NPC155156

  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 NPC198196 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 NPD9020 Approved
0.9333 High Similarity NPD8803 Clinical (unspecified phase)
0.9333 High Similarity NPD8802 Approved
0.9333 High Similarity NPD9021 Approved
0.8367 Intermediate Similarity NPD8849 Clinical (unspecified phase)
0.8298 Intermediate Similarity NPD8873 Approved
0.7959 Intermediate Similarity NPD9025 Approved
0.75 Intermediate Similarity NPD8982 Approved
0.75 Intermediate Similarity NPD8801 Approved
0.7391 Intermediate Similarity NPD8214 Approved
0.7391 Intermediate Similarity NPD8215 Approved
0.7234 Intermediate Similarity NPD8805 Approved
0.7234 Intermediate Similarity NPD8804 Approved
0.7083 Intermediate Similarity NPD8798 Approved
0.6774 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8848 Approved
0.6667 Remote Similarity NPD8609 Approved
0.6667 Remote Similarity NPD8210 Phase 3
0.6667 Remote Similarity NPD8211 Approved
0.6538 Remote Similarity NPD8577 Discontinued
0.6471 Remote Similarity NPD8870 Approved
0.6462 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6415 Remote Similarity NPD9018 Approved
0.6415 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6415 Remote Similarity NPD8624 Approved
0.6415 Remote Similarity NPD9017 Approved
0.6364 Remote Similarity NPD9386 Approved
0.6275 Remote Similarity NPD8610 Approved
0.6226 Remote Similarity NPD9213 Approved
0.6226 Remote Similarity NPD8809 Approved
0.6226 Remote Similarity NPD8808 Approved
0.6226 Remote Similarity NPD9214 Phase 3
0.6226 Remote Similarity NPD8614 Approved
0.6167 Remote Similarity NPD902 Approved
0.6111 Remote Similarity NPD9044 Approved
0.6094 Remote Similarity NPD886 Clinical (unspecified phase)
0.6042 Remote Similarity NPD8623 Phase 1
0.6032 Remote Similarity NPD348 Approved
0.6 Remote Similarity NPD329 Discontinued
0.6 Remote Similarity NPD8872 Phase 3
0.6 Remote Similarity NPD8871 Approved
0.5818 Remote Similarity NPD9230 Discontinued
0.5789 Remote Similarity NPD8851 Phase 1
0.5789 Remote Similarity NPD8785 Approved
0.5789 Remote Similarity NPD9420 Clinical (unspecified phase)
0.5769 Remote Similarity NPD8869 Approved
0.5758 Remote Similarity NPD4241 Registered
0.5758 Remote Similarity NPD337 Discontinued
0.5741 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7368 Approved
0.5714 Remote Similarity NPD7367 Approved
0.5714 Remote Similarity NPD51 Approved
0.5686 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5686 Remote Similarity NPD8216 Approved
0.5672 Remote Similarity NPD4242 Approved
0.5652 Remote Similarity NPD1825 Clinical (unspecified phase)

  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