Structure

Physi-Chem Properties

Molecular Weight:  215.09
Volume:  204.53
LogP:  -1.839
LogD:  -0.538
LogS:  -1.102
# Rotatable Bonds:  7
TPSA:  136.83
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.362
Synthetic Accessibility Score:  3.669
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:  -6.248
MDCK Permeability:  0.0009962634649127722
Pgp-inhibitor:  0.0
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.424
20% Bioavailability (F20%):  0.969
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.802
Plasma Protein Binding (PPB):  15.629040718078613%
Volume Distribution (VD):  0.34
Pgp-substrate:  74.48941040039062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.03
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.136
CYP2D6-inhibitor:  0.023
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  3.276
Half-life (T1/2):  0.649

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.195
Drug-inuced Liver Injury (DILI):  0.098
AMES Toxicity:  0.525
Rat Oral Acute Toxicity:  0.081
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.242
Carcinogencity:  0.315
Eye Corrosion:  0.012
Eye Irritation:  0.188
Respiratory Toxicity:  0.129

Download Data

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

  Natural Product: NPC122471

Natural Product ID:  NPC122471
Common Name*:   Lysianadioic Acid
IUPAC Name:   (2Z)-2-[3-(diaminomethylideneamino)propylidene]butanedioic acid
Synonyms:   2-(3-Carbamimidamidopropylidene)Butanedioic Acid
Standard InCHIKey:  FQUBLGQMXQHASY-DJWKRKHSSA-N
Standard InCHI:  InChI=1S/C8H13N3O4/c9-8(10)11-3-1-2-5(7(14)15)4-6(12)13/h2H,1,3-4H2,(H,12,13)(H,14,15)(H4,9,10,11)/b5-2-
SMILES:  NC(=N)NCC/C=C(C(=O)O)/CC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL253846
PubChem CID:   25110755
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty 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
NPO27576 Lysiana subfalcata Species Loranthaceae Eukaryota n.a. n.a. n.a. PMID[18222087]
NPO27576 Lysiana subfalcata Species Loranthaceae 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
NPT6507 Individual Protein Carboxypeptidase B Homo sapiens IC50 = 360.0 nM PMID[449366]

☑ 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 NPC122471 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
0.7013 Intermediate Similarity NPC98329
0.7013 Intermediate Similarity NPC7392
0.6842 Remote Similarity NPC133758
0.6842 Remote Similarity NPC4668
0.6522 Remote Similarity NPC122212
0.6522 Remote Similarity NPC137419
0.6413 Remote Similarity NPC320057
0.6289 Remote Similarity NPC471257
0.6286 Remote Similarity NPC147238
0.625 Remote Similarity NPC245768
0.6184 Remote Similarity NPC471619
0.617 Remote Similarity NPC304455
0.6026 Remote Similarity NPC305973
0.6026 Remote Similarity NPC322206
0.6022 Remote Similarity NPC202056
0.6 Remote Similarity NPC87137
0.5962 Remote Similarity NPC471259
0.5952 Remote Similarity NPC133700
0.5926 Remote Similarity NPC112312
0.5893 Remote Similarity NPC471261
0.589 Remote Similarity NPC202525
0.58 Remote Similarity NPC3604
0.5789 Remote Similarity NPC314293
0.575 Remote Similarity NPC273614
0.5732 Remote Similarity NPC193559
0.5676 Remote Similarity NPC153280
0.5673 Remote Similarity NPC471258
0.5652 Remote Similarity NPC169098

  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 NPC122471 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
0.7013 Intermediate Similarity NPD9137 Approved
0.5632 Remote Similarity NPD366 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