Structure

Physi-Chem Properties

Molecular Weight:  280.09
Volume:  261.626
LogP:  -0.198
LogD:  -0.123
LogS:  -1.519
# Rotatable Bonds:  10
TPSA:  92.42
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.566
Synthetic Accessibility Score:  2.963
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.041
MDCK Permeability:  4.139047632634174e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.943
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.268
Plasma Protein Binding (PPB):  16.328784942626953%
Volume Distribution (VD):  0.405
Pgp-substrate:  77.26542663574219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.057
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.376
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.165
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.052

ADMET: Excretion

Clearance (CL):  3.859
Half-life (T1/2):  0.909

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.119
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.016
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.06
Carcinogencity:  0.602
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.073

Download Data

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

  Natural Product: NPC321419

Natural Product ID:  NPC321419
Common Name*:   Met-Met
IUPAC Name:   (2S)-2-[[(2S)-2-azaniumyl-4-methylsulfanylbutanoyl]amino]-4-methylsulfanylbutanoate
Synonyms:   Met-Met
Standard InCHIKey:  ZYTPOUNUXRBYGW-YUMQZZPRSA-N
Standard InCHI:  InChI=1S/C10H20N2O3S2/c1-16-5-3-7(11)9(13)12-8(10(14)15)4-6-17-2/h7-8H,3-6,11H2,1-2H3,(H,12,13)(H,14,15)/t7-,8-/m0/s1
SMILES:  CSCCC(C(=O)NC(CCSC)C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1222165
PubChem CID:   6993081
6993082
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:0000348] Peptides
            • [CHEMONTID:0004830] Dipeptides

*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
NPO30193 Mycoplasma genitalium Species Mycoplasmataceae Bacteria n.a. n.a. n.a. PMID[22817898]

☑ 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
NPT1037 Individual Protein Solute carrier family 15 member 2 Homo sapiens Ki = 3000.0 nM PMID[515276]
NPT1037 Individual Protein Solute carrier family 15 member 2 Homo sapiens Ki = 3019.95 nM PMID[515276]
NPT21154 SINGLE PROTEIN General amino-acid permease GAP1 Saccharomyces cerevisiae Inhibition < 15.0 % PMID[515275]

☑ 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 NPC321419 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
0.8182 Intermediate Similarity NPC193989
0.8182 Intermediate Similarity NPC152451
0.8182 Intermediate Similarity NPC170739
0.8036 Intermediate Similarity NPC319175
0.8036 Intermediate Similarity NPC125736
0.7931 Intermediate Similarity NPC321118
0.7931 Intermediate Similarity NPC316889
0.7818 Intermediate Similarity NPC204364
0.7812 Intermediate Similarity NPC325597
0.7812 Intermediate Similarity NPC174304
0.7759 Intermediate Similarity NPC317815
0.7719 Intermediate Similarity NPC114990
0.7656 Intermediate Similarity NPC289691
0.7636 Intermediate Similarity NPC198196
0.7636 Intermediate Similarity NPC297220
0.7612 Intermediate Similarity NPC126779
0.75 Intermediate Similarity NPC102815
0.7463 Intermediate Similarity NPC319046
0.7321 Intermediate Similarity NPC213876
0.7321 Intermediate Similarity NPC136476
0.7321 Intermediate Similarity NPC185755
0.7321 Intermediate Similarity NPC306238
0.7321 Intermediate Similarity NPC248970
0.7321 Intermediate Similarity NPC49952
0.7302 Intermediate Similarity NPC327748
0.7302 Intermediate Similarity NPC254541
0.7302 Intermediate Similarity NPC316826
0.7302 Intermediate Similarity NPC317143
0.7302 Intermediate Similarity NPC321468
0.7286 Intermediate Similarity NPC315897
0.7241 Intermediate Similarity NPC328378
0.7213 Intermediate Similarity NPC327831
0.7188 Intermediate Similarity NPC327170
0.7188 Intermediate Similarity NPC329564
0.7143 Intermediate Similarity NPC176164
0.7143 Intermediate Similarity NPC189301
0.7097 Intermediate Similarity NPC38463
0.7069 Intermediate Similarity NPC153370
0.7031 Intermediate Similarity NPC321536
0.7031 Intermediate Similarity NPC320598
0.6984 Remote Similarity NPC317147
0.6984 Remote Similarity NPC318260
0.6923 Remote Similarity NPC143722
0.6825 Remote Similarity NPC325985
0.6774 Remote Similarity NPC145235
0.6727 Remote Similarity NPC168375
0.6727 Remote Similarity NPC121517
0.6727 Remote Similarity NPC326992
0.6719 Remote Similarity NPC283786
0.6667 Remote Similarity NPC322573
0.6613 Remote Similarity NPC197087
0.6613 Remote Similarity NPC190184
0.6613 Remote Similarity NPC329495
0.6607 Remote Similarity NPC326808
0.6607 Remote Similarity NPC110533
0.6607 Remote Similarity NPC254482
0.6607 Remote Similarity NPC317691
0.6491 Remote Similarity NPC167986
0.6491 Remote Similarity NPC291186
0.6462 Remote Similarity NPC82239
0.6441 Remote Similarity NPC228932
0.6379 Remote Similarity NPC126925
0.6379 Remote Similarity NPC325097
0.6379 Remote Similarity NPC132307
0.6271 Remote Similarity NPC327698
0.6271 Remote Similarity NPC118459
0.6271 Remote Similarity NPC191136
0.6271 Remote Similarity NPC329263
0.623 Remote Similarity NPC227850
0.6212 Remote Similarity NPC278209
0.6197 Remote Similarity NPC470108
0.619 Remote Similarity NPC322946
0.6182 Remote Similarity NPC69179
0.6143 Remote Similarity NPC315744
0.614 Remote Similarity NPC53449
0.614 Remote Similarity NPC66043
0.6111 Remote Similarity NPC470109
0.6102 Remote Similarity NPC198301
0.6067 Remote Similarity NPC117829
0.6066 Remote Similarity NPC118187
0.6066 Remote Similarity NPC136159
0.6053 Remote Similarity NPC476248
0.6027 Remote Similarity NPC470110
0.6 Remote Similarity NPC327252
0.6 Remote Similarity NPC272614
0.6 Remote Similarity NPC116709
0.6 Remote Similarity NPC21290
0.6 Remote Similarity NPC328457
0.5968 Remote Similarity NPC318523
0.5968 Remote Similarity NPC140872
0.5968 Remote Similarity NPC93081
0.5965 Remote Similarity NPC327250
0.5946 Remote Similarity NPC472579
0.5873 Remote Similarity NPC324825
0.5873 Remote Similarity NPC162620
0.5873 Remote Similarity NPC174246
0.5873 Remote Similarity NPC226027
0.5873 Remote Similarity NPC112890
0.5873 Remote Similarity NPC245027
0.5873 Remote Similarity NPC84636
0.5873 Remote Similarity NPC93888
0.5873 Remote Similarity NPC43204
0.5873 Remote Similarity NPC62045
0.5873 Remote Similarity NPC270805
0.5873 Remote Similarity NPC316231
0.587 Remote Similarity NPC132931
0.5862 Remote Similarity NPC237525
0.5862 Remote Similarity NPC326212
0.5857 Remote Similarity NPC477644
0.5846 Remote Similarity NPC263065
0.5846 Remote Similarity NPC189178
0.5811 Remote Similarity NPC81647
0.5797 Remote Similarity NPC473599
0.5781 Remote Similarity NPC327239
0.5781 Remote Similarity NPC315977
0.5781 Remote Similarity NPC329181
0.5781 Remote Similarity NPC319110
0.5758 Remote Similarity NPC322091
0.5758 Remote Similarity NPC60672
0.5747 Remote Similarity NPC193386
0.5738 Remote Similarity NPC285322
0.5738 Remote Similarity NPC208793
0.5714 Remote Similarity NPC177191
0.5714 Remote Similarity NPC199072
0.5692 Remote Similarity NPC19576
0.5692 Remote Similarity NPC29950
0.5684 Remote Similarity NPC325339
0.5684 Remote Similarity NPC72401
0.5645 Remote Similarity NPC309658
0.5614 Remote Similarity NPC63621

  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 NPC321419 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
0.8182 Intermediate Similarity NPD9021 Approved
0.8182 Intermediate Similarity NPD8803 Clinical (unspecified phase)
0.8182 Intermediate Similarity NPD8802 Approved
0.8182 Intermediate Similarity NPD2262 Clinical (unspecified phase)
0.8036 Intermediate Similarity NPD329 Discontinued
0.8 Intermediate Similarity NPD9452 Clinical (unspecified phase)
0.7846 Intermediate Similarity NPD886 Clinical (unspecified phase)
0.7812 Intermediate Similarity NPD348 Approved
0.7727 Intermediate Similarity NPD4241 Registered
0.7636 Intermediate Similarity NPD9020 Approved
0.7612 Intermediate Similarity NPD4242 Approved
0.7463 Intermediate Similarity NPD337 Discontinued
0.7458 Intermediate Similarity NPD8849 Clinical (unspecified phase)
0.7458 Intermediate Similarity NPD9386 Approved
0.7368 Intermediate Similarity NPD8873 Approved
0.7368 Intermediate Similarity NPD9214 Phase 3
0.7368 Intermediate Similarity NPD9213 Approved
0.7321 Intermediate Similarity NPD8982 Approved
0.7321 Intermediate Similarity NPD8870 Approved
0.7286 Intermediate Similarity NPD1825 Clinical (unspecified phase)
0.7167 Intermediate Similarity NPD9420 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD9433 Approved
0.7119 Intermediate Similarity NPD9025 Approved
0.7069 Intermediate Similarity NPD8614 Approved
0.7013 Intermediate Similarity NPD7643 Phase 1
0.6964 Remote Similarity NPD8869 Approved
0.6857 Remote Similarity NPD1815 Discontinued
0.6842 Remote Similarity NPD397 Phase 2
0.678 Remote Similarity NPD8577 Discontinued
0.6724 Remote Similarity NPD8801 Approved
0.6613 Remote Similarity NPD8785 Approved
0.6607 Remote Similarity NPD8214 Approved
0.6607 Remote Similarity NPD8215 Approved
0.6571 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6491 Remote Similarity NPD8804 Approved
0.6491 Remote Similarity NPD8805 Approved
0.6379 Remote Similarity NPD8798 Approved
0.6377 Remote Similarity NPD364 Discontinued
0.6364 Remote Similarity NPD8848 Approved
0.6296 Remote Similarity NPD3733 Clinical (unspecified phase)
0.625 Remote Similarity NPD9419 Clinical (unspecified phase)
0.619 Remote Similarity NPD9441 Phase 2
0.6176 Remote Similarity NPD902 Approved
0.6133 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6111 Remote Similarity NPD842 Phase 3
0.6092 Remote Similarity NPD1749 Approved
0.6087 Remote Similarity NPD574 Approved
0.6027 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6023 Remote Similarity NPD2251 Approved
0.6023 Remote Similarity NPD2252 Approved
0.6 Remote Similarity NPD575 Clinical (unspecified phase)
0.6 Remote Similarity NPD8210 Phase 3
0.6 Remote Similarity NPD8211 Approved
0.6 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5968 Remote Similarity NPD8809 Approved
0.5968 Remote Similarity NPD8808 Approved
0.5921 Remote Similarity NPD1147 Phase 2
0.5873 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5873 Remote Similarity NPD9017 Approved
0.5873 Remote Similarity NPD9018 Approved
0.5873 Remote Similarity NPD8624 Approved
0.5873 Remote Similarity NPD9044 Approved
0.5846 Remote Similarity NPD9205 Approved
0.5846 Remote Similarity NPD9204 Approved
0.5844 Remote Similarity NPD366 Approved
0.5738 Remote Similarity NPD8610 Approved
0.5714 Remote Similarity NPD326 Approved
0.5714 Remote Similarity NPD9577 Approved
0.5692 Remote Similarity NPD8846 Approved
0.5692 Remote Similarity NPD61 Approved
0.5692 Remote Similarity NPD8847 Approved
0.5676 Remote Similarity NPD2263 Discontinued
0.5652 Remote Similarity NPD1784 Approved
0.561 Remote Similarity NPD9578 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