Structure

Physi-Chem Properties

Molecular Weight:  714.43
Volume:  752.913
LogP:  5.642
LogD:  4.204
LogS:  -4.767
# Rotatable Bonds:  13
TPSA:  144.14
# H-Bond Aceptor:  10
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.121
Synthetic Accessibility Score:  6.177
Fsp3:  0.683
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.891
MDCK Permeability:  3.619178096414544e-05
Pgp-inhibitor:  0.984
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.759

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.047
Plasma Protein Binding (PPB):  97.9482192993164%
Volume Distribution (VD):  0.602
Pgp-substrate:  4.972864627838135%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.945
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.739
CYP2C9-inhibitor:  0.206
CYP2C9-substrate:  0.078
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.451
CYP3A4-substrate:  0.608

ADMET: Excretion

Clearance (CL):  11.017
Half-life (T1/2):  0.018

ADMET: Toxicity

hERG Blockers:  0.407
Human Hepatotoxicity (H-HT):  0.714
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.271
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.981
Skin Sensitization:  0.848
Carcinogencity:  0.387
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC300616

Natural Product ID:  NPC300616
Common Name*:   RSEQTLWKMNSLEF-PELKAZGASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RSEQTLWKMNSLEF-PELKAZGASA-N
Standard InCHI:  InChI=1S/C12H13Br2N5O/c1-18-7-5(6(13)9(18)14)8-12(17-11(15)16-8)3-2-4-19(12)10(7)20/h8H,2-4H2,1H3,(H3,15,16,17)/t8-,12+/m1/s1
SMILES:  Cn1c2c(c(c1Br)Br)[C@@H]1[C@@]3(CCCN3C2=O)NC(=N)N1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10927557
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0000475] Carboxylic acid amides
            • [CHEMONTID:0004817] 2-heteroaryl carboxamides

*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
NPO17228 Streptosporangium sibiricum Species Streptosporangiaceae Bacteria n.a. n.a. n.a. PMID[21612226]
NPO17228 Streptosporangium sibiricum Species Streptosporangiaceae Bacteria n.a. n.a. n.a. PMID[25960001]
NPO10821 Magnolia praecocissima Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13082 Veratrum californicum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10821 Magnolia praecocissima Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13082 Veratrum californicum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13082 Veratrum californicum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13082 Veratrum californicum Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO261 Sulfurospirillum multivorans Species Campylobacteraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10821 Magnolia praecocissima Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16568 Vernonia cotoneaster Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17379 Lepidium syvaschicum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17927 Streptomyces thioluteus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17228 Streptosporangium sibiricum Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5061 Rhaphiolepis indica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11624 Didymella lethalis Species Didymellaceae 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

☑ 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 NPC300616 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

  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 NPC300616 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

  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