Structure

Physi-Chem Properties

Molecular Weight:  117.04
Volume:  109.835
LogP:  -3.191
LogD:  -1.144
LogS:  -0.774
# Rotatable Bonds:  3
TPSA:  80.39
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.464
Synthetic Accessibility Score:  3.21
Fsp3:  0.5
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:  -5.892
MDCK Permeability:  0.005922551732510328
Pgp-inhibitor:  0.001
Pgp-substrate:  0.134
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.183
Plasma Protein Binding (PPB):  22.418947219848633%
Volume Distribution (VD):  0.463
Pgp-substrate:  82.66767120361328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.04
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.219
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.165
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  8.493
Half-life (T1/2):  0.61

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.011
AMES Toxicity:  0.292
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.821
Carcinogencity:  0.026
Eye Corrosion:  0.152
Eye Irritation:  0.179
Respiratory Toxicity:  0.525

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

  Natural Product: NPC309658

Natural Product ID:  NPC309658
Common Name*:   Aspartate Semi-Aldehyde
IUPAC Name:   (2S)-2-amino-4-oxobutanoic acid
Synonyms:   Aspartate Semi-Aldehyde
Standard InCHIKey:  HOSWPDPVFBCLSY-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C4H7NO3/c5-3(1-2-6)4(7)8/h2-3H,1,5H2,(H,7,8)/t3-/m0/s1
SMILES:  O=CC[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL404100
PubChem CID:   439235
5287708
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
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0003-9861(62)90112-1]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[11035032]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[12902239]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[13835567]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[14389294]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[1449509]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[14607989]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[15375647]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[15744050]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[16850348]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[17439666]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[22031445]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[2405251]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[24305546]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[24678285]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[24733517]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[24831709]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[24981409]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[2687322]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[3289762]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[4266242]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[4616942]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[5764336]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[6306574]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[767332]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[7929110]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[8017107]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[8798704]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[8852895]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[8971708]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[9748245]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae 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
NPT4435 Individual Protein Dihydrodipicolinate synthase Escherichia coli K-12 Kiuc = 26.0 uM PMID[533997]
NPT4435 Individual Protein Dihydrodipicolinate synthase Escherichia coli K-12 Kic = 31.0 uM PMID[533997]
NPT2 Others Unspecified Ki = 14000000.0 nM PMID[533996]

☑ 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 NPC309658 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
0.8444 Intermediate Similarity NPC208793
0.8444 Intermediate Similarity NPC285322
0.8085 Intermediate Similarity NPC136159
0.7955 Intermediate Similarity NPC326992
0.7955 Intermediate Similarity NPC168375
0.7955 Intermediate Similarity NPC121517
0.7609 Intermediate Similarity NPC167986
0.7609 Intermediate Similarity NPC291186
0.7556 Intermediate Similarity NPC66043
0.7447 Intermediate Similarity NPC132307
0.7447 Intermediate Similarity NPC126925
0.7447 Intermediate Similarity NPC325097
0.7442 Intermediate Similarity NPC116709
0.7442 Intermediate Similarity NPC272614
0.7442 Intermediate Similarity NPC21290
0.74 Intermediate Similarity NPC270805
0.74 Intermediate Similarity NPC93888
0.7391 Intermediate Similarity NPC219143
0.7391 Intermediate Similarity NPC226265
0.7292 Intermediate Similarity NPC329263
0.7292 Intermediate Similarity NPC118459
0.7292 Intermediate Similarity NPC327698
0.7273 Intermediate Similarity NPC43169
0.7273 Intermediate Similarity NPC112224
0.7273 Intermediate Similarity NPC327895
0.7273 Intermediate Similarity NPC63621
0.7273 Intermediate Similarity NPC93861
0.72 Intermediate Similarity NPC153370
0.7174 Intermediate Similarity NPC326212
0.7174 Intermediate Similarity NPC237525
0.7174 Intermediate Similarity NPC53449
0.717 Intermediate Similarity NPC60672
0.717 Intermediate Similarity NPC322091
0.7143 Intermediate Similarity NPC136476
0.7143 Intermediate Similarity NPC49952
0.7037 Intermediate Similarity NPC327831
0.7 Intermediate Similarity NPC181588
0.6863 Remote Similarity NPC140872
0.6863 Remote Similarity NPC93081
0.6744 Remote Similarity NPC114517
0.6739 Remote Similarity NPC18188
0.6735 Remote Similarity NPC198301
0.6731 Remote Similarity NPC193989
0.6731 Remote Similarity NPC174246
0.6731 Remote Similarity NPC226027
0.6731 Remote Similarity NPC316231
0.6731 Remote Similarity NPC84636
0.6731 Remote Similarity NPC62045
0.6731 Remote Similarity NPC112890
0.6731 Remote Similarity NPC170739
0.6731 Remote Similarity NPC43204
0.6731 Remote Similarity NPC324825
0.6731 Remote Similarity NPC245027
0.6731 Remote Similarity NPC162620
0.6731 Remote Similarity NPC152451
0.6667 Remote Similarity NPC190385
0.6667 Remote Similarity NPC326808
0.6667 Remote Similarity NPC110533
0.6667 Remote Similarity NPC254482
0.6667 Remote Similarity NPC317691
0.6604 Remote Similarity NPC315977
0.6604 Remote Similarity NPC137958
0.6604 Remote Similarity NPC125736
0.6604 Remote Similarity NPC273330
0.6538 Remote Similarity NPC227850
0.6538 Remote Similarity NPC327542
0.6481 Remote Similarity NPC155156
0.6481 Remote Similarity NPC200550
0.6471 Remote Similarity NPC185755
0.6471 Remote Similarity NPC213876
0.6471 Remote Similarity NPC297220
0.6429 Remote Similarity NPC2801
0.6415 Remote Similarity NPC328378
0.6415 Remote Similarity NPC286989
0.6364 Remote Similarity NPC190184
0.6364 Remote Similarity NPC197087
0.6364 Remote Similarity NPC317815
0.6364 Remote Similarity NPC329495
0.6346 Remote Similarity NPC316168
0.6346 Remote Similarity NPC101249
0.6346 Remote Similarity NPC204364
0.6333 Remote Similarity NPC322206
0.6304 Remote Similarity NPC9294
0.625 Remote Similarity NPC321118
0.625 Remote Similarity NPC183845
0.625 Remote Similarity NPC279661
0.625 Remote Similarity NPC316889
0.62 Remote Similarity NPC276294
0.62 Remote Similarity NPC107645
0.619 Remote Similarity NPC126681
0.6167 Remote Similarity NPC68974
0.6154 Remote Similarity NPC198196
0.6154 Remote Similarity NPC228932
0.614 Remote Similarity NPC102815
0.6129 Remote Similarity NPC88898
0.6129 Remote Similarity NPC106216
0.6078 Remote Similarity NPC323974
0.6038 Remote Similarity NPC118187
0.6034 Remote Similarity NPC325985
0.6034 Remote Similarity NPC38463
0.6 Remote Similarity NPC114990
0.5962 Remote Similarity NPC191136
0.5932 Remote Similarity NPC278209
0.5926 Remote Similarity NPC318523
0.5862 Remote Similarity NPC10915
0.5846 Remote Similarity NPC135539
0.5846 Remote Similarity NPC196359
0.5846 Remote Similarity NPC221764
0.5846 Remote Similarity NPC78312
0.5833 Remote Similarity NPC189301
0.5833 Remote Similarity NPC302003
0.5833 Remote Similarity NPC176164
0.5833 Remote Similarity NPC245346
0.5833 Remote Similarity NPC11433
0.5778 Remote Similarity NPC145217
0.5778 Remote Similarity NPC84444
0.5763 Remote Similarity NPC313263
0.5758 Remote Similarity NPC107224
0.5738 Remote Similarity NPC321536
0.5738 Remote Similarity NPC64250
0.5738 Remote Similarity NPC316826
0.5738 Remote Similarity NPC327748
0.5738 Remote Similarity NPC321468
0.5738 Remote Similarity NPC320598
0.5738 Remote Similarity NPC254541
0.5738 Remote Similarity NPC317143
0.5738 Remote Similarity NPC268927
0.5738 Remote Similarity NPC276928
0.5714 Remote Similarity NPC319175
0.569 Remote Similarity NPC145235
0.5667 Remote Similarity NPC317147
0.5667 Remote Similarity NPC318260
0.5645 Remote Similarity NPC329564
0.5645 Remote Similarity NPC143722
0.5645 Remote Similarity NPC321419
0.5645 Remote Similarity NPC177191
0.5645 Remote Similarity NPC327170
0.5606 Remote Similarity NPC118524

  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 NPC309658 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
0.8444 Intermediate Similarity NPD8610 Approved
0.7778 Intermediate Similarity NPD8609 Approved
0.7609 Intermediate Similarity NPD8804 Approved
0.7609 Intermediate Similarity NPD8805 Approved
0.7447 Intermediate Similarity NPD8798 Approved
0.7442 Intermediate Similarity NPD8211 Approved
0.7442 Intermediate Similarity NPD8210 Phase 3
0.74 Intermediate Similarity NPD8624 Approved
0.7391 Intermediate Similarity NPD8217 Clinical (unspecified phase)
0.7391 Intermediate Similarity NPD8216 Approved
0.72 Intermediate Similarity NPD8614 Approved
0.7 Intermediate Similarity NPD8810 Clinical (unspecified phase)
0.6863 Remote Similarity NPD8808 Approved
0.6863 Remote Similarity NPD8809 Approved
0.68 Remote Similarity NPD8801 Approved
0.6739 Remote Similarity NPD8623 Phase 1
0.6731 Remote Similarity NPD9018 Approved
0.6731 Remote Similarity NPD9017 Approved
0.6731 Remote Similarity NPD8803 Clinical (unspecified phase)
0.6731 Remote Similarity NPD9044 Approved
0.6731 Remote Similarity NPD9021 Approved
0.6731 Remote Similarity NPD8802 Approved
0.6731 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8214 Approved
0.6667 Remote Similarity NPD8215 Approved
0.6604 Remote Similarity NPD8872 Phase 3
0.6604 Remote Similarity NPD8871 Approved
0.6604 Remote Similarity NPD9025 Approved
0.6471 Remote Similarity NPD8982 Approved
0.6364 Remote Similarity NPD8851 Phase 1
0.6364 Remote Similarity NPD8785 Approved
0.6364 Remote Similarity NPD8849 Clinical (unspecified phase)
0.6346 Remote Similarity NPD8209 Phase 2
0.6346 Remote Similarity NPD8208 Clinical (unspecified phase)
0.6346 Remote Similarity NPD8866 Approved
0.6346 Remote Similarity NPD8867 Approved
0.6226 Remote Similarity NPD8873 Approved
0.619 Remote Similarity NPD7371 Approved
0.6154 Remote Similarity NPD9020 Approved
0.6078 Remote Similarity NPD9019 Approved
0.5965 Remote Similarity NPD9419 Clinical (unspecified phase)
0.5873 Remote Similarity NPD1151 Approved
0.5846 Remote Similarity NPD8868 Approved
0.5833 Remote Similarity NPD8865 Approved
0.5833 Remote Similarity NPD9433 Approved
0.5763 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5763 Remote Similarity NPD8979 Approved
0.5763 Remote Similarity NPD8980 Approved
0.5741 Remote Similarity NPD8850 Approved
0.5741 Remote Similarity NPD8973 Approved
0.5741 Remote Similarity NPD8972 Approved
0.5714 Remote Similarity NPD51 Approved
0.5714 Remote Similarity NPD7368 Approved
0.5714 Remote Similarity NPD7367 Approved
0.5682 Remote Similarity NPD8619 Approved
0.5682 Remote Similarity NPD8617 Approved
0.5606 Remote Similarity NPD1429 Clinical (unspecified phase)
0.5606 Remote Similarity NPD8842 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