Structure

Physi-Chem Properties

Molecular Weight:  384.03
Volume:  321.263
LogP:  1.32
LogD:  1.887
LogS:  -2.991
# Rotatable Bonds:  0
TPSA:  72.82
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.673
Synthetic Accessibility Score:  7.312
Fsp3:  0.389
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:  -5.551
MDCK Permeability:  2.601504274934996e-05
Pgp-inhibitor:  0.08
Pgp-substrate:  0.399
Human Intestinal Absorption (HIA):  0.937
20% Bioavailability (F20%):  0.921
30% Bioavailability (F30%):  0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.379
Plasma Protein Binding (PPB):  92.74313354492188%
Volume Distribution (VD):  1.311
Pgp-substrate:  4.587990760803223%

ADMET: Metabolism

CYP1A2-inhibitor:  0.124
CYP1A2-substrate:  0.539
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.56
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.784
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.56
CYP3A4-inhibitor:  0.06
CYP3A4-substrate:  0.132

ADMET: Excretion

Clearance (CL):  1.274
Half-life (T1/2):  0.573

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.903
Drug-inuced Liver Injury (DILI):  0.538
AMES Toxicity:  0.572
Rat Oral Acute Toxicity:  0.953
Maximum Recommended Daily Dose:  0.913
Skin Sensitization:  0.674
Carcinogencity:  0.974
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.941

Download Data

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

  Natural Product: NPC475610

Natural Product ID:  NPC475610
Common Name*:   Discorhabdin V
IUPAC Name:   n.a.
Synonyms:   Discorhabdin V
Standard InCHIKey:  SSPPRUOFJZYGKW-UHFFFAOYSA-O
Standard InCHI:  InChI=1S/C18H16BrN3O2/c19-9-5-18-2-3-20-14-12(18)15-11-8(7-21-13(11)17(14)24)1-4-22(15)10(6-18)16(9)23/h5,7,10,16,23H,1-4,6H2,(H,20,21,24)/p+1
SMILES:  BrC1=CC23CC[N-]C4=C3C3=C5C(=[NH+]C=C5CC[N+]3C(C1O)C2)C4=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509255
PubChem CID:   20055930
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001626] Phenanthrolines

*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
NPO32524 latrunculid sponges Species n.a. n.a. n.a. South African n.a. PMID[15332840]

☑ 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 1266.0 nM PMID[458900]

☑ 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 NPC475610 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
0.7246 Intermediate Similarity NPC476158
0.6471 Remote Similarity NPC476141
0.6364 Remote Similarity NPC175585
0.6224 Remote Similarity NPC473249
0.609 Remote Similarity NPC119569
0.6042 Remote Similarity NPC313173
0.6026 Remote Similarity NPC473804
0.6 Remote Similarity NPC317654
0.6 Remote Similarity NPC96010
0.5946 Remote Similarity NPC477220
0.594 Remote Similarity NPC469958
0.5938 Remote Similarity NPC119225
0.5938 Remote Similarity NPC25033
0.5938 Remote Similarity NPC470382
0.5938 Remote Similarity NPC471635
0.5938 Remote Similarity NPC476261
0.5903 Remote Similarity NPC66855
0.5896 Remote Similarity NPC230677
0.5882 Remote Similarity NPC472192
0.5882 Remote Similarity NPC469563
0.5865 Remote Similarity NPC474563
0.585 Remote Similarity NPC1702
0.585 Remote Similarity NPC158672
0.5839 Remote Similarity NPC172626
0.5839 Remote Similarity NPC476290
0.5839 Remote Similarity NPC470892
0.5833 Remote Similarity NPC77703
0.5806 Remote Similarity NPC473261
0.5806 Remote Similarity NPC202056
0.5806 Remote Similarity NPC473262
0.5806 Remote Similarity NPC300912
0.5806 Remote Similarity NPC202166
0.5789 Remote Similarity NPC226509
0.5789 Remote Similarity NPC152718
0.5755 Remote Similarity NPC476269
0.5742 Remote Similarity NPC81079
0.5729 Remote Similarity NPC469562
0.5729 Remote Similarity NPC220594
0.5714 Remote Similarity NPC181086
0.5714 Remote Similarity NPC100810
0.5714 Remote Similarity NPC144714
0.5714 Remote Similarity NPC313234
0.5698 Remote Similarity NPC476250
0.5693 Remote Similarity NPC140251
0.5693 Remote Similarity NPC307903
0.5687 Remote Similarity NPC130714
0.5676 Remote Similarity NPC262880
0.5676 Remote Similarity NPC247902
0.5672 Remote Similarity NPC247060
0.5672 Remote Similarity NPC58200
0.5672 Remote Similarity NPC50815
0.5664 Remote Similarity NPC470300
0.5652 Remote Similarity NPC133729
0.5646 Remote Similarity NPC36254
0.5642 Remote Similarity NPC474258
0.5638 Remote Similarity NPC260270
0.5635 Remote Similarity NPC473628
0.5634 Remote Similarity NPC288629
0.5613 Remote Similarity NPC304257
0.5606 Remote Similarity NPC241426

  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 NPC475610 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
0.6403 Remote Similarity NPD7623 Phase 3
0.6403 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6331 Remote Similarity NPD7739 Clinical (unspecified phase)
0.6224 Remote Similarity NPD7746 Phase 1
0.6224 Remote Similarity NPD7747 Phase 1
0.5878 Remote Similarity NPD6914 Discontinued
0.5724 Remote Similarity NPD2838 Clinical (unspecified phase)
0.5683 Remote Similarity NPD7116 Clinical (unspecified phase)

  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