Structure

Physi-Chem Properties

Molecular Weight:  213.1
Volume:  211.208
LogP:  -1.098
LogD:  2.308
LogS:  -2.11
# Rotatable Bonds:  3
TPSA:  86.63
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.593
Synthetic Accessibility Score:  4.009
Fsp3:  0.6
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:  -6.173
MDCK Permeability:  0.00014943121641408652
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.348
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.321
Plasma Protein Binding (PPB):  22.709922790527344%
Volume Distribution (VD):  0.407
Pgp-substrate:  63.940025329589844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.89
CYP2D6-inhibitor:  0.071
CYP2D6-substrate:  0.138
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.019

ADMET: Excretion

Clearance (CL):  5.999
Half-life (T1/2):  0.685

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.224
Drug-inuced Liver Injury (DILI):  0.31
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.33
Maximum Recommended Daily Dose:  0.076
Skin Sensitization:  0.342
Carcinogencity:  0.4
Eye Corrosion:  0.045
Eye Irritation:  0.054
Respiratory Toxicity:  0.447

Download Data

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

  Natural Product: NPC90476

Natural Product ID:  NPC90476
Common Name*:   (2S,3S,4R)-3-(Carboxymethyl)-4-Prop-1-En-2-Ylpyrrolidine-2-Carboxylic Acid
IUPAC Name:   (2S,3S,4R)-3-(carboxymethyl)-4-prop-1-en-2-ylpyrrolidine-2-carboxylic acid
Synonyms:  
Standard InCHIKey:  VLSMHEGGTFMBBZ-ZKWXMUAHSA-N
Standard InCHI:  InChI=1S/C10H15NO4/c1-5(2)7-4-11-9(10(14)15)6(7)3-8(12)13/h6-7,9,11H,1,3-4H2,2H3,(H,12,13)(H,14,15)/t6-,7-,9-/m0/s1
SMILES:  C=C(C)[C@@H]1CN[C@@H]([C@H]1CC(=O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1598042
PubChem CID:   6603893
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:0001801] Kainoids

*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
NPO8159 Digenea simplex Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[31117523]
NPO8159 Digenea simplex Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8159 Digenea simplex Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8159 Digenea simplex Species Rhodomelaceae 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
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 39810.7 nM PMID[496143]

☑ 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 NPC90476 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 NPC69374
0.8977 High Similarity NPC40663
0.7531 Intermediate Similarity NPC15864
0.6867 Remote Similarity NPC188231
0.6867 Remote Similarity NPC222327
0.6709 Remote Similarity NPC11433
0.6709 Remote Similarity NPC245346
0.6709 Remote Similarity NPC302003
0.6705 Remote Similarity NPC327272
0.6627 Remote Similarity NPC50047
0.6571 Remote Similarity NPC265094
0.6545 Remote Similarity NPC76660
0.6545 Remote Similarity NPC276995
0.6542 Remote Similarity NPC271562
0.6531 Remote Similarity NPC304455
0.6481 Remote Similarity NPC15413
0.6476 Remote Similarity NPC471258
0.6322 Remote Similarity NPC322274
0.6311 Remote Similarity NPC3604
0.6296 Remote Similarity NPC471259
0.6279 Remote Similarity NPC60424
0.6279 Remote Similarity NPC314221
0.625 Remote Similarity NPC469466
0.622 Remote Similarity NPC276928
0.622 Remote Similarity NPC64250
0.622 Remote Similarity NPC268927
0.6174 Remote Similarity NPC209734
0.6154 Remote Similarity NPC471257
0.6129 Remote Similarity NPC314680
0.6092 Remote Similarity NPC196359
0.6092 Remote Similarity NPC135539
0.6092 Remote Similarity NPC78312
0.6092 Remote Similarity NPC221764
0.6075 Remote Similarity NPC188785
0.6044 Remote Similarity NPC320221
0.6 Remote Similarity NPC236644
0.598 Remote Similarity NPC47230
0.598 Remote Similarity NPC17143
0.5977 Remote Similarity NPC325534
0.5977 Remote Similarity NPC287693
0.5976 Remote Similarity NPC278209
0.5963 Remote Similarity NPC471260
0.5962 Remote Similarity NPC313265
0.5941 Remote Similarity NPC322966
0.5932 Remote Similarity NPC471261
0.5877 Remote Similarity NPC147238
0.5875 Remote Similarity NPC8488
0.5875 Remote Similarity NPC274499
0.5875 Remote Similarity NPC333075
0.5847 Remote Similarity NPC235625
0.5823 Remote Similarity NPC137958
0.5823 Remote Similarity NPC273330
0.5802 Remote Similarity NPC183845
0.5802 Remote Similarity NPC279661
0.5783 Remote Similarity NPC473936
0.5772 Remote Similarity NPC474371
0.575 Remote Similarity NPC139867
0.5743 Remote Similarity NPC202056
0.5739 Remote Similarity NPC30911
0.5739 Remote Similarity NPC316984
0.5732 Remote Similarity NPC2801
0.5714 Remote Similarity NPC67043
0.5696 Remote Similarity NPC174246
0.5696 Remote Similarity NPC245027
0.5696 Remote Similarity NPC162620
0.5696 Remote Similarity NPC226027
0.5696 Remote Similarity NPC84636
0.5696 Remote Similarity NPC62045
0.5696 Remote Similarity NPC43204
0.5686 Remote Similarity NPC304454
0.5686 Remote Similarity NPC324506
0.5682 Remote Similarity NPC160661
0.5673 Remote Similarity NPC236322
0.5673 Remote Similarity NPC476019
0.5667 Remote Similarity NPC107224
0.5656 Remote Similarity NPC471262
0.5641 Remote Similarity NPC193471
0.5641 Remote Similarity NPC130124
0.562 Remote Similarity NPC88190
0.5614 Remote Similarity NPC171734
0.5612 Remote Similarity NPC219340

  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 NPC90476 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
0.7159 Intermediate Similarity NPD617 Approved
0.6747 Remote Similarity NPD9201 Clinical (unspecified phase)
0.6709 Remote Similarity NPD8865 Approved
0.6667 Remote Similarity NPD9421 Phase 1
0.6633 Remote Similarity NPD2682 Approved
0.6559 Remote Similarity NPD1125 Discovery
0.6404 Remote Similarity NPD9217 Clinical (unspecified phase)
0.625 Remote Similarity NPD3713 Approved
0.625 Remote Similarity NPD3714 Approved
0.625 Remote Similarity NPD3715 Approved
0.6222 Remote Similarity NPD9109 Discontinued
0.6092 Remote Similarity NPD8868 Approved
0.6087 Remote Similarity NPD747 Discontinued
0.6049 Remote Similarity NPD9454 Approved
0.6042 Remote Similarity NPD857 Phase 3
0.5977 Remote Similarity NPD8952 Approved
0.5962 Remote Similarity NPD573 Clinical (unspecified phase)
0.596 Remote Similarity NPD7759 Phase 2
0.596 Remote Similarity NPD7760 Phase 2
0.5943 Remote Similarity NPD842 Phase 3
0.5902 Remote Similarity NPD3073 Approved
0.5902 Remote Similarity NPD3071 Approved
0.5902 Remote Similarity NPD3072 Approved
0.5889 Remote Similarity NPD9649 Approved
0.5889 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5842 Remote Similarity NPD621 Discontinued
0.5823 Remote Similarity NPD8872 Phase 3
0.5823 Remote Similarity NPD8871 Approved
0.582 Remote Similarity NPD4761 Approved
0.582 Remote Similarity NPD4762 Approved
0.5778 Remote Similarity NPD620 Approved
0.5773 Remote Similarity NPD9385 Clinical (unspecified phase)
0.575 Remote Similarity NPD1689 Approved
0.5748 Remote Similarity NPD5263 Approved
0.5748 Remote Similarity NPD4676 Approved
0.5739 Remote Similarity NPD2204 Approved
0.5732 Remote Similarity NPD8971 Approved
0.5714 Remote Similarity NPD9307 Phase 1
0.5696 Remote Similarity NPD9018 Approved
0.5696 Remote Similarity NPD9017 Approved
0.5696 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5679 Remote Similarity NPD8851 Phase 1
0.5669 Remote Similarity NPD4177 Approved
0.5669 Remote Similarity NPD4175 Approved
0.5667 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5648 Remote Similarity NPD8038 Phase 2
0.5639 Remote Similarity NPD6077 Discontinued
0.5632 Remote Similarity NPD9676 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