Structure

Physi-Chem Properties

Molecular Weight:  330.02
Volume:  264.888
LogP:  -1.566
LogD:  -0.141
LogS:  0.532
# Rotatable Bonds:  3
TPSA:  81.95
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.592
Synthetic Accessibility Score:  5.127
Fsp3:  0.5
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:  -5.728
MDCK Permeability:  0.00012655669706873596
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.98
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.488
Plasma Protein Binding (PPB):  23.252460479736328%
Volume Distribution (VD):  0.65
Pgp-substrate:  75.00396728515625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.104
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.778
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.262
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.034

ADMET: Excretion

Clearance (CL):  1.524
Half-life (T1/2):  0.94

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.973
Drug-inuced Liver Injury (DILI):  0.954
AMES Toxicity:  0.075
Rat Oral Acute Toxicity:  0.113
Maximum Recommended Daily Dose:  0.945
Skin Sensitization:  0.879
Carcinogencity:  0.928
Eye Corrosion:  0.009
Eye Irritation:  0.047
Respiratory Toxicity:  0.739

Download Data

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

  Natural Product: NPC158394

Natural Product ID:  NPC158394
Common Name*:   Damituricin
IUPAC Name:   (2R,4R)-4-(4-bromo-1H-pyrrole-2-carbonyl)oxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Synonyms:   damituricin
Standard InCHIKey:  STWZXBZABSCBFO-PSASIEDQSA-N
Standard InCHI:  InChI=1S/C12H15BrN2O4/c1-15(2)6-8(4-10(15)11(16)17)19-12(18)9-3-7(13)5-14-9/h3,5,8,10H,4,6H2,1-2H3,(H-,14,16,17,18)/t8-,10-/m1/s1
SMILES:  BrC1=CC(=C(O[C@@H]2C[C@@H]([N+](C2)(C)C)C(=O)O)[O-])N=C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL239547
PubChem CID:   23653240
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:0004322] Proline 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
NPO15231 Axinella damicornis Species Axinellidae Eukaryota n.a. Mediterranean n.a. PMID[17582775]
NPO15231 Axinella damicornis Species Axinellidae 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
NPT681 Cell Line PC-12 Rattus norvegicus Activity = 43.8 % PMID[547008]

☑ 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 NPC158394 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
0.6304 Remote Similarity NPC160661
0.5812 Remote Similarity NPC475149
0.5812 Remote Similarity NPC471097
0.5776 Remote Similarity NPC475791
0.5776 Remote Similarity NPC13175
0.5752 Remote Similarity NPC313265
0.569 Remote Similarity NPC475758
0.567 Remote Similarity NPC135539
0.567 Remote Similarity NPC221764
0.567 Remote Similarity NPC196359
0.567 Remote Similarity NPC78312
0.5625 Remote Similarity NPC474576

  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 NPC158394 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
0.567 Remote Similarity NPD8868 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