Structure

Physi-Chem Properties

Molecular Weight:  135.05
Volume:  121.262
LogP:  -2.602
LogD:  -1.937
LogS:  -0.224
# Rotatable Bonds:  3
TPSA:  103.78
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.35
Synthetic Accessibility Score:  3.066
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.07
MDCK Permeability:  0.0198017
Pgp-inhibitor:  0
Pgp-substrate:  0.037
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.201
Plasma Protein Binding (PPB):  10.61%
Volume Distribution (VD):  0.571
Pgp-substrate:  89.72%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.045
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.026
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.131
CYP3A4-inhibitor:  0.024
CYP3A4-substrate:  0.052

ADMET: Excretion

Clearance (CL):  1.966
Half-life (T1/2):  0.803

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.369
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.052
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.01
Skin Sensitization:  0.055
Carcinogencity:  0.049
Eye Corrosion:  0.009
Eye Irritation:  0.475
Respiratory Toxicity:  0.088

Download Data

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

  Natural Product: NPC107645

Natural Product ID:  NPC107645
Common Name*:   2-Ammonio-3-Hydroxy-2-(Hydroxymethyl)Propanoate
IUPAC Name:   2-amino-3-hydroxy-2-(hydroxymethyl)propanoic acid
Synonyms:  
Standard InCHIKey:  ZRPDXDBGEYHEBJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H9NO4/c5-4(1-6,2-7)3(8)9/h6-7H,1-2,5H2,(H,8,9)
SMILES:  OCC(C(=O)O)(CO)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3099359
PubChem CID:   439893
25201639
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
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(00)97029-8]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota seeds n.a. n.a. PMID[18603435]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota Seeds n.a. n.a. PMID[20469887]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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
NPT4227 Individual Protein Serine racemase Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) Ki = 661000000.0 nM PMID[503756]
NPT4227 Individual Protein Serine racemase Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) Ki = 167000000.0 nM PMID[503756]

☑ 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 NPC107645 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
0.8 Intermediate Similarity NPC9294
0.7907 Intermediate Similarity NPC226265
0.7907 Intermediate Similarity NPC219143
0.75 Intermediate Similarity NPC270805
0.75 Intermediate Similarity NPC93888
0.7447 Intermediate Similarity NPC181588
0.7436 Intermediate Similarity NPC313303
0.74 Intermediate Similarity NPC329495
0.7143 Intermediate Similarity NPC286989
0.6939 Remote Similarity NPC327542
0.6522 Remote Similarity NPC326992
0.6522 Remote Similarity NPC53449
0.6522 Remote Similarity NPC168375
0.6522 Remote Similarity NPC121517
0.6458 Remote Similarity NPC132307
0.6458 Remote Similarity NPC325097
0.6458 Remote Similarity NPC126925
0.6429 Remote Similarity NPC327895
0.6429 Remote Similarity NPC43169
0.6429 Remote Similarity NPC93861
0.6429 Remote Similarity NPC112224
0.64 Remote Similarity NPC136159
0.6364 Remote Similarity NPC116709
0.6364 Remote Similarity NPC21290
0.6364 Remote Similarity NPC272614
0.625 Remote Similarity NPC167986
0.625 Remote Similarity NPC291186
0.6222 Remote Similarity NPC63621
0.62 Remote Similarity NPC185755
0.62 Remote Similarity NPC309658
0.62 Remote Similarity NPC213876
0.619 Remote Similarity NPC328569
0.617 Remote Similarity NPC326212
0.617 Remote Similarity NPC237525
0.6136 Remote Similarity NPC168052
0.6136 Remote Similarity NPC250870
0.6136 Remote Similarity NPC191084
0.6122 Remote Similarity NPC198301
0.6 Remote Similarity NPC329263
0.6 Remote Similarity NPC327698
0.6 Remote Similarity NPC118459
0.6 Remote Similarity NPC208793
0.6 Remote Similarity NPC285322
0.5952 Remote Similarity NPC241404
0.5926 Remote Similarity NPC155512
0.5882 Remote Similarity NPC49952
0.5882 Remote Similarity NPC297220
0.5882 Remote Similarity NPC136476
0.5862 Remote Similarity NPC190385
0.5849 Remote Similarity NPC43204
0.5849 Remote Similarity NPC62045
0.5849 Remote Similarity NPC245027
0.5849 Remote Similarity NPC162620
0.5849 Remote Similarity NPC174246
0.5849 Remote Similarity NPC84636
0.5849 Remote Similarity NPC226027
0.5833 Remote Similarity NPC66043
0.5769 Remote Similarity NPC204364
0.575 Remote Similarity NPC3343
0.5745 Remote Similarity NPC18188
0.5741 Remote Similarity NPC114990
0.5741 Remote Similarity NPC295832
0.5741 Remote Similarity NPC273330
0.5741 Remote Similarity NPC137958
0.5741 Remote Similarity NPC27359
0.5741 Remote Similarity NPC125736
0.5741 Remote Similarity NPC315977
0.5741 Remote Similarity NPC198398
0.5714 Remote Similarity NPC317691
0.5714 Remote Similarity NPC110533
0.5714 Remote Similarity NPC35661
0.5714 Remote Similarity NPC322091
0.5714 Remote Similarity NPC254482
0.5714 Remote Similarity NPC60672
0.5714 Remote Similarity NPC326808
0.5682 Remote Similarity NPC114517
0.566 Remote Similarity NPC153370
0.566 Remote Similarity NPC93081
0.566 Remote Similarity NPC140872
0.5652 Remote Similarity NPC159089
0.5625 Remote Similarity NPC118524
0.5614 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 NPC107645 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
0.7907 Intermediate Similarity NPD8216 Approved
0.7907 Intermediate Similarity NPD8217 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD8624 Approved
0.7447 Intermediate Similarity NPD8810 Clinical (unspecified phase)
0.7436 Intermediate Similarity NPD8558 Approved
0.7436 Intermediate Similarity NPD8557 Approved
0.6458 Remote Similarity NPD8798 Approved
0.64 Remote Similarity NPD8850 Approved
0.6364 Remote Similarity NPD8210 Phase 3
0.6364 Remote Similarity NPD8211 Approved
0.6346 Remote Similarity NPD9025 Approved
0.625 Remote Similarity NPD8805 Approved
0.625 Remote Similarity NPD8804 Approved
0.62 Remote Similarity NPD8982 Approved
0.6154 Remote Similarity NPD8947 Approved
0.6154 Remote Similarity NPD8946 Approved
0.6136 Remote Similarity NPD9136 Clinical (unspecified phase)
0.6 Remote Similarity NPD8610 Approved
0.5962 Remote Similarity NPD8873 Approved
0.5902 Remote Similarity NPD1151 Approved
0.5882 Remote Similarity NPD8801 Approved
0.5862 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5849 Remote Similarity NPD9018 Approved
0.5849 Remote Similarity NPD9017 Approved
0.5745 Remote Similarity NPD8623 Phase 1
0.5741 Remote Similarity NPD8871 Approved
0.5741 Remote Similarity NPD8872 Phase 3
0.5741 Remote Similarity NPD9212 Clinical (unspecified phase)
0.5741 Remote Similarity NPD9226 Approved
0.5741 Remote Similarity NPD9225 Phase 3
0.5714 Remote Similarity NPD8215 Approved
0.5714 Remote Similarity NPD8214 Approved
0.5714 Remote Similarity NPD9442 Clinical (unspecified phase)
0.566 Remote Similarity NPD8809 Approved
0.566 Remote Similarity NPD8808 Approved
0.566 Remote Similarity NPD8614 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