Structure

Physi-Chem Properties

Molecular Weight:  149.03
Volume:  127.415
LogP:  -2.599
LogD:  -1.792
LogS:  -0.321
# Rotatable Bonds:  3
TPSA:  120.85
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.255
Synthetic Accessibility Score:  3.476
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.197
MDCK Permeability:  0.00941032636910677
Pgp-inhibitor:  0.001
Pgp-substrate:  0.096
Human Intestinal Absorption (HIA):  0.363
20% Bioavailability (F20%):  0.03
30% Bioavailability (F30%):  0.611

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.707
Plasma Protein Binding (PPB):  13.69000244140625%
Volume Distribution (VD):  0.281
Pgp-substrate:  79.63150787353516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.028
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.048
CYP2C9-inhibitor:  0.038
CYP2C9-substrate:  0.105
CYP2D6-inhibitor:  0.045
CYP2D6-substrate:  0.15
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  2.059
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.217
Drug-inuced Liver Injury (DILI):  0.256
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.314
Carcinogencity:  0.008
Eye Corrosion:  0.003
Eye Irritation:  0.078
Respiratory Toxicity:  0.281

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

  Natural Product: NPC112224

Natural Product ID:  NPC112224
Common Name*:   (2S,3S)-2-Amino-3-Hydroxybutanedioic Acid
IUPAC Name:   (2S,3S)-2-amino-3-hydroxybutanedioic acid
Synonyms:  
Standard InCHIKey:  YYLQUHNPNCGKJQ-LWMBPPNESA-N
Standard InCHI:  InChI=1S/C4H7NO5/c5-1(3(7)8)2(6)4(9)10/h1-2,6H,5H2,(H,7,8)(H,9,10)/t1-,2-/m0/s1
SMILES:  [C@H]([C@@H](C(=O)O)O)(C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1231330
PubChem CID:   443239
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:0004317] Aspartic acid 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
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota Fruits n.a. n.a. PMID[10757716]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota roots n.a. n.a. PMID[20346658]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[23439553]
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota n.a. Tibet, China n.a. PMID[24645629]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. tuber n.a. Database[Article]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1574 Penstemon cyathophorus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6078 Arthrinium phaeospermum Species Apiosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10357 Krameria sonorae Species Krameriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2156 Parkia bicolor Species Fabaceae 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
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 12589.3 nM PMID[506601]
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 39810.7 nM PMID[506601]
NPT53 Individual Protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 3548.1 nM PMID[506602]
NPT53 Individual Protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 89125.1 nM PMID[506601]
NPT58 Individual Protein Bloom syndrome protein Homo sapiens Potency = 28.2 nM PMID[506603]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens Potency = 31.6 nM PMID[506601]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 35481.3 nM PMID[506604]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 26679.5 nM PMID[506604]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 4107.8 nM PMID[506604]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens AC50 = 31.62 nM PMID[506601]
NPT208 Individual Protein Cytochrome P450 1A2 Homo sapiens AC50 = 39810.72 nM PMID[506601]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 50118.7 nM PMID[506601]
NPT1519 Individual Protein Excitatory amino acid transporter 2 Homo sapiens IC50 = 9600.0 nM PMID[506606]
NPT1520 Individual Protein Excitatory amino acid transporter 1 Homo sapiens IC50 = 3900.0 nM PMID[506606]
NPT1518 Individual Protein Excitatory amino acid transporter 3 Homo sapiens IC50 = 9600.0 nM PMID[506606]
NPT1520 Individual Protein Excitatory amino acid transporter 1 Homo sapiens IC50 = 3890.45 nM PMID[506606]
NPT1519 Individual Protein Excitatory amino acid transporter 2 Homo sapiens IC50 = 9549.93 nM PMID[506606]
NPT1518 Individual Protein Excitatory amino acid transporter 3 Homo sapiens IC50 = 9549.93 nM PMID[506606]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 3548.1 nM PMID[506602]
NPT755 Individual Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 Homo sapiens Potency n.a. 19011.5 nM PMID[506604]
NPT2 Others Unspecified Potency n.a. 3981.1 nM PMID[506601]
NPT2 Others Unspecified Potency n.a. 3981.1 nM PMID[506603]
NPT2 Others Unspecified Potency n.a. 3981.1 nM PMID[506605]
NPT2 Others Unspecified Potency n.a. 3981.1 nM PMID[506602]
NPT2 Others Unspecified Potency n.a. 12589.3 nM PMID[506601]
NPT2 Others Unspecified Potency n.a. 14125.4 nM PMID[506601]
NPT22676 SINGLE PROTEIN Excitatory amino acid transporter 4 Rattus norvegicus IC50 = 2800.0 nM PMID[506606]
NPT22676 SINGLE PROTEIN Excitatory amino acid transporter 4 Rattus norvegicus IC50 = 2818.38 nM PMID[506606]

☑ 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 NPC112224 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 NPC93861
1.0 High Similarity NPC327895
1.0 High Similarity NPC43169
0.7818 Intermediate Similarity NPC93888
0.7818 Intermediate Similarity NPC270805
0.7736 Intermediate Similarity NPC285322
0.7736 Intermediate Similarity NPC208793
0.7619 Intermediate Similarity NPC106216
0.7619 Intermediate Similarity NPC88898
0.7273 Intermediate Similarity NPC309658
0.717 Intermediate Similarity NPC19044
0.717 Intermediate Similarity NPC24751
0.717 Intermediate Similarity NPC121018
0.717 Intermediate Similarity NPC226265
0.717 Intermediate Similarity NPC219143
0.717 Intermediate Similarity NPC100742
0.717 Intermediate Similarity NPC97444
0.717 Intermediate Similarity NPC192402
0.7143 Intermediate Similarity NPC136159
0.7018 Intermediate Similarity NPC327542
0.6852 Remote Similarity NPC35661
0.6825 Remote Similarity NPC190385
0.6613 Remote Similarity NPC327831
0.6557 Remote Similarity NPC329495
0.6552 Remote Similarity NPC181588
0.6452 Remote Similarity NPC322091
0.6452 Remote Similarity NPC60672
0.6441 Remote Similarity NPC153370
0.6429 Remote Similarity NPC107645
0.6364 Remote Similarity NPC168375
0.6364 Remote Similarity NPC66043
0.6364 Remote Similarity NPC326992
0.6364 Remote Similarity NPC121517
0.6333 Remote Similarity NPC286989
0.6167 Remote Similarity NPC227850
0.614 Remote Similarity NPC291186
0.614 Remote Similarity NPC167986
0.6076 Remote Similarity NPC314466
0.6071 Remote Similarity NPC326212
0.6071 Remote Similarity NPC237525
0.6066 Remote Similarity NPC328954
0.6056 Remote Similarity NPC135539
0.6056 Remote Similarity NPC221764
0.6056 Remote Similarity NPC118524
0.6056 Remote Similarity NPC196359
0.6056 Remote Similarity NPC78312
0.6034 Remote Similarity NPC126925
0.6034 Remote Similarity NPC132307
0.6034 Remote Similarity NPC325097
0.6029 Remote Similarity NPC322206
0.5972 Remote Similarity NPC107224
0.597 Remote Similarity NPC473599
0.5938 Remote Similarity NPC19676
0.5938 Remote Similarity NPC323401
0.5932 Remote Similarity NPC329263
0.5932 Remote Similarity NPC327698
0.5932 Remote Similarity NPC118459
0.5926 Remote Similarity NPC116709
0.5926 Remote Similarity NPC272614
0.5926 Remote Similarity NPC159089
0.5926 Remote Similarity NPC21290
0.5882 Remote Similarity NPC68974
0.5862 Remote Similarity NPC259982
0.5862 Remote Similarity NPC228782
0.5862 Remote Similarity NPC313565
0.5846 Remote Similarity NPC6883
0.5833 Remote Similarity NPC136476
0.5833 Remote Similarity NPC49952
0.5818 Remote Similarity NPC63621
0.5789 Remote Similarity NPC53449
0.5781 Remote Similarity NPC277878
0.5738 Remote Similarity NPC316168
0.5714 Remote Similarity NPC27359
0.5714 Remote Similarity NPC295832
0.5714 Remote Similarity NPC198398
0.5714 Remote Similarity NPC125736
0.5714 Remote Similarity NPC315977
0.5714 Remote Similarity NPC137958
0.5714 Remote Similarity NPC273330
0.5692 Remote Similarity NPC196612
0.5679 Remote Similarity NPC219340
0.5667 Remote Similarity NPC242655
0.5667 Remote Similarity NPC38891
0.5667 Remote Similarity NPC270088
0.566 Remote Similarity NPC114517
0.5658 Remote Similarity NPC185084
0.5645 Remote Similarity NPC140872
0.5645 Remote Similarity NPC93081
0.5636 Remote Similarity NPC5505
0.5636 Remote Similarity NPC1037
0.5606 Remote Similarity NPC2801

  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 NPC112224 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
0.7818 Intermediate Similarity NPD8624 Approved
0.7736 Intermediate Similarity NPD8610 Approved
0.717 Intermediate Similarity NPD8599 Approved
0.717 Intermediate Similarity NPD8609 Approved
0.717 Intermediate Similarity NPD8602 Approved
0.717 Intermediate Similarity NPD8598 Approved
0.717 Intermediate Similarity NPD8216 Approved
0.717 Intermediate Similarity NPD8603 Approved
0.717 Intermediate Similarity NPD8605 Approved
0.717 Intermediate Similarity NPD8217 Clinical (unspecified phase)
0.717 Intermediate Similarity NPD8604 Approved
0.717 Intermediate Similarity NPD8601 Approved
0.717 Intermediate Similarity NPD8600 Approved
0.6825 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6567 Remote Similarity NPD1151 Approved
0.6552 Remote Similarity NPD8810 Clinical (unspecified phase)
0.6441 Remote Similarity NPD8614 Approved
0.614 Remote Similarity NPD8804 Approved
0.614 Remote Similarity NPD8805 Approved
0.6056 Remote Similarity NPD8868 Approved
0.6034 Remote Similarity NPD8798 Approved
0.5926 Remote Similarity NPD8211 Approved
0.5926 Remote Similarity NPD8210 Phase 3
0.5833 Remote Similarity NPD8842 Clinical (unspecified phase)
0.5797 Remote Similarity NPD3193 Approved
0.5797 Remote Similarity NPD3192 Approved
0.5781 Remote Similarity NPD66 Approved
0.5781 Remote Similarity NPD8960 Approved
0.5781 Remote Similarity NPD72 Approved
0.5781 Remote Similarity NPD9007 Approved
0.5781 Remote Similarity NPD9008 Approved
0.5781 Remote Similarity NPD9011 Approved
0.5781 Remote Similarity NPD9009 Approved
0.5781 Remote Similarity NPD64 Approved
0.5781 Remote Similarity NPD65 Approved
0.5781 Remote Similarity NPD9010 Approved
0.5738 Remote Similarity NPD8209 Phase 2
0.5738 Remote Similarity NPD8208 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9225 Phase 3
0.5714 Remote Similarity NPD8872 Phase 3
0.5714 Remote Similarity NPD9226 Approved
0.5714 Remote Similarity NPD9025 Approved
0.5714 Remote Similarity NPD8871 Approved
0.5645 Remote Similarity NPD8808 Approved
0.5645 Remote Similarity NPD8809 Approved
0.5641 Remote Similarity NPD1453 Phase 1
0.5641 Remote Similarity NPD376 Approved
0.5641 Remote Similarity NPD11 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