Structure

Physi-Chem Properties

Molecular Weight:  438.43
Volume:  499.836
LogP:  3.638
LogD:  3.08
LogS:  -2.481
# Rotatable Bonds:  12
TPSA:  65.19
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.327
Synthetic Accessibility Score:  3.591
Fsp3:  0.962
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.779
MDCK Permeability:  3.0626160878455266e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.82
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.083
Plasma Protein Binding (PPB):  67.00423431396484%
Volume Distribution (VD):  0.692
Pgp-substrate:  49.3211669921875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.527
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.01
CYP2D6-inhibitor:  0.85
CYP2D6-substrate:  0.7
CYP3A4-inhibitor:  0.14
CYP3A4-substrate:  0.347

ADMET: Excretion

Clearance (CL):  5.05
Half-life (T1/2):  0.105

ADMET: Toxicity

hERG Blockers:  0.287
Human Hepatotoxicity (H-HT):  0.175
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.451
Maximum Recommended Daily Dose:  0.306
Skin Sensitization:  0.971
Carcinogencity:  0.013
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.934

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

  Natural Product: NPC476537

Natural Product ID:  NPC476537
Common Name*:   8-Tridecyl-1,5,9,13-tetrazacycloheptadecan-6-one
IUPAC Name:   8-tridecyl-1,5,9,13-tetrazacycloheptadecan-6-one
Synonyms:   Budmunchiamine L4
Standard InCHIKey:  BIJLNPCGAYTFAD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C26H54N4O/c1-2-3-4-5-6-7-8-9-10-11-12-17-25-24-26(31)30-23-16-21-28-19-14-13-18-27-20-15-22-29-25/h25,27-29H,2-24H2,1H3,(H,30,31)
SMILES:  CCCCCCCCCCCCCC1CC(=O)NCCCNCCCCNCCCN1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315523
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000064] Macrolactams

*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
NPO4034 Albizia adinocephala Species Fabaceae Eukaryota Stem bark and leaves n.a. n.a. PMID[19299148]
NPO4034 Albizia adinocephala Species Fabaceae 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
NPT306 Cell Line PC-3 Homo sapiens IC50 = 600 nM PMID[19534534]
NPT5520 Cell Line DuPro Homo sapiens IC50 = 600 nM PMID[19534534]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 14000 nM PMID[19299148]

☑ 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 NPC476537 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
1.0 High Similarity NPC216415
0.7037 Intermediate Similarity NPC241279
0.7037 Intermediate Similarity NPC319114
0.6923 Remote Similarity NPC314510
0.6852 Remote Similarity NPC321202
0.6721 Remote Similarity NPC474322
0.6667 Remote Similarity NPC31557
0.6667 Remote Similarity NPC28394
0.6613 Remote Similarity NPC270041
0.6471 Remote Similarity NPC315744
0.6452 Remote Similarity NPC123814
0.6441 Remote Similarity NPC289484
0.6441 Remote Similarity NPC319709
0.6364 Remote Similarity NPC254541
0.6364 Remote Similarity NPC320598
0.6333 Remote Similarity NPC96966
0.6333 Remote Similarity NPC121062
0.6333 Remote Similarity NPC29222
0.6324 Remote Similarity NPC145627
0.6308 Remote Similarity NPC8979
0.6301 Remote Similarity NPC476695
0.6301 Remote Similarity NPC476694
0.6301 Remote Similarity NPC476696
0.6296 Remote Similarity NPC277333
0.6232 Remote Similarity NPC313420
0.6232 Remote Similarity NPC57420
0.623 Remote Similarity NPC80350
0.6212 Remote Similarity NPC176164
0.6212 Remote Similarity NPC189301
0.6182 Remote Similarity NPC326791
0.6143 Remote Similarity NPC262615
0.6129 Remote Similarity NPC329181
0.6129 Remote Similarity NPC319110
0.6111 Remote Similarity NPC470110
0.6111 Remote Similarity NPC74599
0.6081 Remote Similarity NPC306973
0.6061 Remote Similarity NPC471605
0.6061 Remote Similarity NPC471443
0.6027 Remote Similarity NPC268922
0.6 Remote Similarity NPC474468
0.5972 Remote Similarity NPC470109
0.5949 Remote Similarity NPC475363
0.5949 Remote Similarity NPC473971
0.5949 Remote Similarity NPC473972
0.5946 Remote Similarity NPC475694
0.5946 Remote Similarity NPC473710
0.5915 Remote Similarity NPC41429
0.5893 Remote Similarity NPC473035
0.589 Remote Similarity NPC471418
0.589 Remote Similarity NPC195165
0.589 Remote Similarity NPC250953
0.5857 Remote Similarity NPC17455
0.5833 Remote Similarity NPC470108
0.5823 Remote Similarity NPC191774
0.5821 Remote Similarity NPC278209
0.5806 Remote Similarity NPC193872
0.5797 Remote Similarity NPC319131
0.5789 Remote Similarity NPC167301
0.5789 Remote Similarity NPC55274
0.5769 Remote Similarity NPC477002
0.5758 Remote Similarity NPC471423
0.5758 Remote Similarity NPC471442
0.5694 Remote Similarity NPC474928
0.5658 Remote Similarity NPC477200
0.5658 Remote Similarity NPC328457
0.5652 Remote Similarity NPC321536
0.5652 Remote Similarity NPC317143
0.5652 Remote Similarity NPC321468
0.5652 Remote Similarity NPC316826
0.5652 Remote Similarity NPC327748
0.5625 Remote Similarity NPC37681
0.5625 Remote Similarity NPC110136
0.5616 Remote Similarity NPC303798
0.5616 Remote Similarity NPC286851
0.5614 Remote Similarity NPC111686
0.5606 Remote Similarity NPC277072
0.5606 Remote Similarity NPC178263
0.56 Remote Similarity NPC472579

  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 NPC476537 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
0.7101 Intermediate Similarity NPD2704 Phase 3
0.7101 Intermediate Similarity NPD2702 Phase 1
0.7031 Intermediate Similarity NPD1155 Discontinued
0.6667 Remote Similarity NPD3214 Discontinued
0.6667 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6528 Remote Similarity NPD5386 Phase 2
0.6481 Remote Similarity NPD2707 Clinical (unspecified phase)
0.6452 Remote Similarity NPD3215 Phase 1
0.6441 Remote Similarity NPD3211 Approved
0.6429 Remote Similarity NPD9227 Discontinued
0.625 Remote Similarity NPD3213 Discontinued
0.6163 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6143 Remote Similarity NPD6437 Approved
0.6143 Remote Similarity NPD6438 Approved
0.6111 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6081 Remote Similarity NPD5382 Phase 2
0.6049 Remote Similarity NPD4829 Discontinued
0.6 Remote Similarity NPD1154 Phase 3
0.6 Remote Similarity NPD1152 Phase 2
0.5902 Remote Similarity NPD379 Clinical (unspecified phase)
0.5833 Remote Similarity NPD2703 Discontinued
0.5823 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5806 Remote Similarity NPD362 Phase 1
0.5783 Remote Similarity NPD3733 Clinical (unspecified phase)
0.5753 Remote Similarity NPD5380 Approved
0.569 Remote Similarity NPD2273 Clinical (unspecified phase)
0.5645 Remote Similarity NPD399 Approved
0.5645 Remote Similarity NPD400 Approved
0.5645 Remote Similarity NPD398 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