Structure

Physi-Chem Properties

Molecular Weight:  168.96
Volume:  28730992.48
LogP:  -3.141
LogD:  -1.225
LogS:  -0.872
# Rotatable Bonds:  2
TPSA:  63.32
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.504
Synthetic Accessibility Score:  4.304
Fsp3:  0.667
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:  -6.011
MDCK Permeability:  0.009165583178400993
Pgp-inhibitor:  0.001
Pgp-substrate:  0.117
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.674
Plasma Protein Binding (PPB):  7.747786521911621%
Volume Distribution (VD):  0.377
Pgp-substrate:  91.4777603149414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.041
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.401
CYP2D6-inhibitor:  0.032
CYP2D6-substrate:  0.236
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.02

ADMET: Excretion

Clearance (CL):  9.247
Half-life (T1/2):  0.635

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.045
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.152
Rat Oral Acute Toxicity:  0.062
Maximum Recommended Daily Dose:  0.01
Skin Sensitization:  0.295
Carcinogencity:  0.196
Eye Corrosion:  0.048
Eye Irritation:  0.161
Respiratory Toxicity:  0.374

Download Data

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

  Natural Product: NPC63621

Natural Product ID:  NPC63621
Common Name*:   Selenocysteine
IUPAC Name:   (2R)-2-amino-3-selanylpropanoic acid
Synonyms:  
Standard InCHIKey:  ZKZBPNGNEQAJSX-REOHCLBHSA-N
Standard InCHI:  InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
SMILES:  N[C@H](C(=O)O)C[SeH]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL109962
PubChem CID:   25076
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

☑ 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
NPT3171 Cell Line V79 Cricetulus griseus IC50 = 34000.0 nM PMID[517716]
NPT2 Others Unspecified "" Fold induction = 4.2 n.a. PMID[517716]

☑ 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 NPC63621 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
0.9189 High Similarity NPC53449
0.9143 High Similarity NPC116709
0.9143 High Similarity NPC21290
0.9143 High Similarity NPC272614
0.8718 High Similarity NPC291186
0.8718 High Similarity NPC167986
0.8205 Intermediate Similarity NPC237525
0.8205 Intermediate Similarity NPC168375
0.8205 Intermediate Similarity NPC326212
0.8205 Intermediate Similarity NPC121517
0.8205 Intermediate Similarity NPC326992
0.8 Intermediate Similarity NPC219143
0.8 Intermediate Similarity NPC226265
0.8 Intermediate Similarity NPC326808
0.8 Intermediate Similarity NPC254482
0.8 Intermediate Similarity NPC317691
0.8 Intermediate Similarity NPC110533
0.7778 Intermediate Similarity NPC114517
0.7647 Intermediate Similarity NPC126681
0.7619 Intermediate Similarity NPC325097
0.7619 Intermediate Similarity NPC132307
0.7619 Intermediate Similarity NPC126925
0.7619 Intermediate Similarity NPC198301
0.7442 Intermediate Similarity NPC329263
0.7442 Intermediate Similarity NPC208793
0.7442 Intermediate Similarity NPC118459
0.7442 Intermediate Similarity NPC285322
0.7442 Intermediate Similarity NPC327698
0.7317 Intermediate Similarity NPC66043
0.7273 Intermediate Similarity NPC309658
0.7273 Intermediate Similarity NPC228932
0.7273 Intermediate Similarity NPC297220
0.7273 Intermediate Similarity NPC49952
0.7273 Intermediate Similarity NPC136476
0.7273 Intermediate Similarity NPC213876
0.7273 Intermediate Similarity NPC185755
0.7179 Intermediate Similarity NPC9294
0.7111 Intermediate Similarity NPC316168
0.7111 Intermediate Similarity NPC136159
0.7111 Intermediate Similarity NPC181588
0.7111 Intermediate Similarity NPC118187
0.7111 Intermediate Similarity NPC204364
0.6957 Remote Similarity NPC153370
0.6957 Remote Similarity NPC93081
0.6957 Remote Similarity NPC140872
0.6957 Remote Similarity NPC318523
0.6829 Remote Similarity NPC18188
0.6809 Remote Similarity NPC270805
0.6809 Remote Similarity NPC245027
0.6809 Remote Similarity NPC226027
0.6809 Remote Similarity NPC62045
0.6809 Remote Similarity NPC43204
0.6809 Remote Similarity NPC193989
0.6809 Remote Similarity NPC324825
0.6809 Remote Similarity NPC84636
0.6809 Remote Similarity NPC174246
0.6809 Remote Similarity NPC112890
0.6809 Remote Similarity NPC152451
0.6809 Remote Similarity NPC162620
0.6809 Remote Similarity NPC286989
0.6809 Remote Similarity NPC170739
0.6809 Remote Similarity NPC93888
0.6809 Remote Similarity NPC316231
0.6667 Remote Similarity NPC137958
0.6667 Remote Similarity NPC114990
0.6667 Remote Similarity NPC315977
0.6667 Remote Similarity NPC125736
0.6667 Remote Similarity NPC273330
0.6531 Remote Similarity NPC200550
0.6531 Remote Similarity NPC155156
0.65 Remote Similarity NPC134570
0.6458 Remote Similarity NPC328378
0.64 Remote Similarity NPC190184
0.64 Remote Similarity NPC317815
0.64 Remote Similarity NPC329495
0.64 Remote Similarity NPC197087
0.6327 Remote Similarity NPC319175
0.6304 Remote Similarity NPC191136
0.6275 Remote Similarity NPC279661
0.6275 Remote Similarity NPC60672
0.6275 Remote Similarity NPC321118
0.6275 Remote Similarity NPC322091
0.6275 Remote Similarity NPC316889
0.6275 Remote Similarity NPC183845
0.6275 Remote Similarity NPC145235
0.6222 Remote Similarity NPC107645
0.6222 Remote Similarity NPC276294
0.619 Remote Similarity NPC69179
0.619 Remote Similarity NPC216443
0.617 Remote Similarity NPC198196
0.6154 Remote Similarity NPC145217
0.6154 Remote Similarity NPC10915
0.6154 Remote Similarity NPC327831
0.6154 Remote Similarity NPC102815
0.6154 Remote Similarity NPC84444
0.6154 Remote Similarity NPC2801
0.6087 Remote Similarity NPC323974
0.6038 Remote Similarity NPC325985
0.6038 Remote Similarity NPC38463
0.5926 Remote Similarity NPC283786
0.5926 Remote Similarity NPC82239
0.5926 Remote Similarity NPC278209
0.5918 Remote Similarity NPC327542
0.5833 Remote Similarity NPC248970
0.5833 Remote Similarity NPC306238
0.5818 Remote Similarity NPC112224
0.5818 Remote Similarity NPC11433
0.5818 Remote Similarity NPC93861
0.5818 Remote Similarity NPC302003
0.5818 Remote Similarity NPC176164
0.5818 Remote Similarity NPC327895
0.5818 Remote Similarity NPC43169
0.5818 Remote Similarity NPC245346
0.5818 Remote Similarity NPC189301
0.5818 Remote Similarity NPC190385
0.5714 Remote Similarity NPC276928
0.5714 Remote Similarity NPC316826
0.5714 Remote Similarity NPC321468
0.5714 Remote Similarity NPC64250
0.5714 Remote Similarity NPC317143
0.5714 Remote Similarity NPC327748
0.5714 Remote Similarity NPC101249
0.5714 Remote Similarity NPC254541
0.5714 Remote Similarity NPC320598
0.5714 Remote Similarity NPC321536
0.5714 Remote Similarity NPC268927
0.5636 Remote Similarity NPC318260
0.5636 Remote Similarity NPC317147
0.5614 Remote Similarity NPC327170
0.5614 Remote Similarity NPC143722
0.5614 Remote Similarity NPC68974
0.5614 Remote Similarity NPC329564
0.5614 Remote Similarity NPC321419
0.5614 Remote Similarity NPC177191
0.561 Remote Similarity NPC260324
0.56 Remote Similarity NPC227850

  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 NPC63621 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
0.9143 High Similarity NPD8211 Approved
0.9143 High Similarity NPD8210 Phase 3
0.8718 High Similarity NPD8804 Approved
0.8718 High Similarity NPD8805 Approved
0.8 Intermediate Similarity NPD8217 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD8216 Approved
0.8 Intermediate Similarity NPD8215 Approved
0.8 Intermediate Similarity NPD8214 Approved
0.7647 Intermediate Similarity NPD7371 Approved
0.7619 Intermediate Similarity NPD8798 Approved
0.7442 Intermediate Similarity NPD8610 Approved
0.7273 Intermediate Similarity NPD8982 Approved
0.7111 Intermediate Similarity NPD8208 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD8810 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD8209 Phase 2
0.7059 Intermediate Similarity NPD7368 Approved
0.7059 Intermediate Similarity NPD51 Approved
0.7059 Intermediate Similarity NPD7367 Approved
0.6957 Remote Similarity NPD8809 Approved
0.6957 Remote Similarity NPD8614 Approved
0.6957 Remote Similarity NPD8808 Approved
0.6957 Remote Similarity NPD8873 Approved
0.6889 Remote Similarity NPD8801 Approved
0.6829 Remote Similarity NPD8623 Phase 1
0.6809 Remote Similarity NPD8803 Clinical (unspecified phase)
0.6809 Remote Similarity NPD9017 Approved
0.6809 Remote Similarity NPD9044 Approved
0.6809 Remote Similarity NPD9021 Approved
0.6809 Remote Similarity NPD8802 Approved
0.6809 Remote Similarity NPD8624 Approved
0.6809 Remote Similarity NPD9018 Approved
0.6809 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6744 Remote Similarity NPD8609 Approved
0.6667 Remote Similarity NPD8872 Phase 3
0.6667 Remote Similarity NPD8871 Approved
0.6667 Remote Similarity NPD9025 Approved
0.64 Remote Similarity NPD8849 Clinical (unspecified phase)
0.64 Remote Similarity NPD8851 Phase 1
0.64 Remote Similarity NPD8785 Approved
0.617 Remote Similarity NPD9020 Approved
0.6087 Remote Similarity NPD9019 Approved
0.5833 Remote Similarity NPD8870 Approved
0.5818 Remote Similarity NPD8848 Approved
0.5818 Remote Similarity NPD8865 Approved
0.5818 Remote Similarity NPD9433 Approved
0.5818 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5741 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5741 Remote Similarity NPD8979 Approved
0.5741 Remote Similarity NPD8980 Approved
0.5714 Remote Similarity NPD8867 Approved
0.5714 Remote Similarity NPD8866 Approved
0.5714 Remote Similarity NPD8850 Approved
0.56 Remote Similarity NPD9213 Approved
0.56 Remote Similarity NPD8577 Discontinued
0.56 Remote Similarity NPD9214 Phase 3

  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