Structure

Physi-Chem Properties

Molecular Weight:  424.08
Volume:  369.753
LogP:  -0.281
LogD:  0.154
LogS:  -3.193
# Rotatable Bonds:  0
TPSA:  115.22
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  7
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.508
Synthetic Accessibility Score:  6.784
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.975
MDCK Permeability:  1.0112865311384667e-05
Pgp-inhibitor:  0.306
Pgp-substrate:  0.044
Human Intestinal Absorption (HIA):  0.769
20% Bioavailability (F20%):  0.052
30% Bioavailability (F30%):  0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  44.48274612426758%
Volume Distribution (VD):  0.352
Pgp-substrate:  46.02029800415039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.113
CYP2C19-inhibitor:  0.076
CYP2C19-substrate:  0.855
CYP2C9-inhibitor:  0.822
CYP2C9-substrate:  0.136
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.052
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.973

ADMET: Excretion

Clearance (CL):  9.956
Half-life (T1/2):  0.882

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.433
Drug-inuced Liver Injury (DILI):  0.993
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.946
Maximum Recommended Daily Dose:  0.931
Skin Sensitization:  0.375
Carcinogencity:  0.964
Eye Corrosion:  0.003
Eye Irritation:  0.006
Respiratory Toxicity:  0.004

Download Data

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

  Natural Product: NPC309731

Natural Product ID:  NPC309731
Common Name*:   Rostratin B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ICKHXBRXCAORGF-ZJNFRVSGSA-N
Standard InCHI:  InChI=1S/C18H20N2O6S2/c21-9-1-3-11(23)13-7(9)5-17-15(25)20-14-8(10(22)2-4-12(14)24)6-18(20,28-27-17)16(26)19(13)17/h7-8,11-14,23-24H,1-6H2/t7-,8-,11+,12+,13-,14-,17-,18-/m1/s1
SMILES:  C1C[C@@H]([C@H]2[C@H](C[C@@]34C(=O)N5[C@@H]6[C@H](C[C@]5(C(=O)N23)SS4)C(=O)CC[C@@H]6O)C1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL516314
PubChem CID:   11487079
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002389] Diazinanes
        • [CHEMONTID:0000189] Piperazines
          • [CHEMONTID:0001731] Dioxopiperazines
            • [CHEMONTID:0003684] 2,5-dioxopiperazines
              • [CHEMONTID:0001732] Thiodioxopiperazines
                • [CHEMONTID:0001790] Epipolythiodioxopiperazines

*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
NPO30056 Exserohilum rostratum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[15332857]
NPO30056 Exserohilum rostratum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[18774863]
NPO30056 Exserohilum rostratum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[25537529]

☑ 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 = 4400.0 nM PMID[506300]

☑ 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 NPC309731 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
0.9369 High Similarity NPC266910
0.9182 High Similarity NPC28542
0.8889 High Similarity NPC220396
0.8814 High Similarity NPC25327
0.875 High Similarity NPC271115
0.8632 High Similarity NPC211848
0.8347 Intermediate Similarity NPC8325
0.8062 Intermediate Similarity NPC469800
0.7744 Intermediate Similarity NPC276822
0.7742 Intermediate Similarity NPC262880
0.7742 Intermediate Similarity NPC247902
0.7687 Intermediate Similarity NPC243412
0.7154 Intermediate Similarity NPC41162
0.6667 Remote Similarity NPC168017
0.6619 Remote Similarity NPC88943
0.6549 Remote Similarity NPC178632
0.6434 Remote Similarity NPC956
0.6218 Remote Similarity NPC134504
0.6218 Remote Similarity NPC47076
0.621 Remote Similarity NPC241394
0.6202 Remote Similarity NPC272166
0.6174 Remote Similarity NPC322966
0.6161 Remote Similarity NPC124359
0.6129 Remote Similarity NPC128303
0.6116 Remote Similarity NPC220111
0.6056 Remote Similarity NPC82129
0.6038 Remote Similarity NPC29326
0.6029 Remote Similarity NPC97580
0.6028 Remote Similarity NPC475987
0.6028 Remote Similarity NPC313348
0.5965 Remote Similarity NPC277918
0.5932 Remote Similarity NPC312637
0.584 Remote Similarity NPC470592
0.5839 Remote Similarity NPC473477
0.5822 Remote Similarity NPC473955
0.5821 Remote Similarity NPC17581
0.5821 Remote Similarity NPC476155
0.5806 Remote Similarity NPC475342
0.5798 Remote Similarity NPC476019
0.5789 Remote Similarity NPC66007
0.5772 Remote Similarity NPC292819
0.5763 Remote Similarity NPC237535
0.5755 Remote Similarity NPC309525
0.5714 Remote Similarity NPC233274
0.5714 Remote Similarity NPC194750
0.5714 Remote Similarity NPC287638
0.5669 Remote Similarity NPC265094
0.5625 Remote Similarity NPC475239
0.562 Remote Similarity NPC13351
0.5614 Remote Similarity NPC470783
0.561 Remote Similarity NPC174117
0.56 Remote Similarity NPC220234

  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 NPC309731 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
0.6637 Remote Similarity NPD2682 Approved
0.6581 Remote Similarity NPD3714 Approved
0.6581 Remote Similarity NPD3715 Approved
0.6581 Remote Similarity NPD3713 Approved
0.6434 Remote Similarity NPD5193 Discontinued
0.621 Remote Similarity NPD6920 Discontinued
0.6202 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5984 Remote Similarity NPD3104 Approved
0.5984 Remote Similarity NPD3103 Approved
0.5984 Remote Similarity NPD3102 Approved
0.5984 Remote Similarity NPD3101 Approved
0.5913 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5785 Remote Similarity NPD2637 Approved
0.5785 Remote Similarity NPD2636 Clinical (unspecified phase)
0.5701 Remote Similarity NPD2220 Clinical (unspecified phase)
0.568 Remote Similarity NPD5359 Clinical (unspecified phase)
0.5667 Remote Similarity NPD4780 Clinical (unspecified phase)
0.5614 Remote Similarity NPD7763 Phase 2
0.5614 Remote Similarity NPD7762 Phase 2
0.561 Remote Similarity NPD7841 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