Structure

Physi-Chem Properties

Molecular Weight:  678.17
Volume:  621.678
LogP:  4.375
LogD:  3.309
LogS:  -3.697
# Rotatable Bonds:  6
TPSA:  159.97
# H-Bond Aceptor:  11
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.242
Synthetic Accessibility Score:  6.581
Fsp3:  0.679
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:  -4.977
MDCK Permeability:  2.2823247491032816e-05
Pgp-inhibitor:  0.196
Pgp-substrate:  0.987
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.912

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.887
Plasma Protein Binding (PPB):  96.1777114868164%
Volume Distribution (VD):  0.636
Pgp-substrate:  3.8321831226348877%

ADMET: Metabolism

CYP1A2-inhibitor:  0.077
CYP1A2-substrate:  0.103
CYP2C19-inhibitor:  0.854
CYP2C19-substrate:  0.186
CYP2C9-inhibitor:  0.854
CYP2C9-substrate:  0.862
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.16
CYP3A4-inhibitor:  0.945
CYP3A4-substrate:  0.855

ADMET: Excretion

Clearance (CL):  2.749
Half-life (T1/2):  0.041

ADMET: Toxicity

hERG Blockers:  0.218
Human Hepatotoxicity (H-HT):  0.818
Drug-inuced Liver Injury (DILI):  0.77
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.905
Skin Sensitization:  0.03
Carcinogencity:  0.019
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.719

Download Data

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

  Natural Product: NPC475554

Natural Product ID:  NPC475554
Common Name*:   Lyngbyabellin B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XZRCVAJXDSWDNB-LWCVALJOSA-N
Standard InCHI:  InChI=1S/C28H40Cl2N4O7S2/c1-14(2)19-22-33-16(13-42-22)24(37)40-17(9-8-10-28(7,29)30)26(3,4)25(38)41-20(27(5,6)39)23-32-15(12-43-23)21(36)31-11-18(35)34-19/h13-15,17,19-20,39H,8-12H2,1-7H3,(H,31,36)(H,34,35)/t15-,17-,19-,20+/m0/s1
SMILES:  OC1=N[C@@H](C(C)C)c2scc(n2)C(=O)O[C@@H](CCCC(Cl)(Cl)C)C(C(=O)O[C@H](C2=N[C@H](C(=NC1)O)CS2)C(O)(C)C)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL508049
PubChem CID:   44558912
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10514329]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10654420]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10691708]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. palauan n.a. PMID[10691729]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10843570]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10924172]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10978206]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076571]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076573]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076574]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11277744]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11389621]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11430000]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11473443]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11922791]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[12762816]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[12828459]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[14575437]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[1517734]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[16643028]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17125217]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17441769]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18444683]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Singapore n.a. PMID[19093843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19489598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. eastern Caribbean n.a. PMID[19739598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19839606]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20030365]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. panamanian n.a. PMID[20158242]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Floridian n.a. PMID[20166701]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20936843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21138309]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[2128518]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21341718]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21539315]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21806011]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21999614]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[22035372]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29792428]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[3924698]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[7623050]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[8699186]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9584405]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599278]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599279]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9784156]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria 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
NPT91 Cell Line KB Homo sapiens IC50 = 0.1 ug.mL-1 PMID[572925]
NPT114 Cell Line LoVo Homo sapiens IC50 = 0.83 ug.mL-1 PMID[572925]
NPT1917 Cell Line CA46 Homo sapiens IC50 = 100.0 nM PMID[572927]
NPT1917 Cell Line CA46 Homo sapiens Activity = 28.0 % PMID[572927]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 1100.0 nM PMID[572928]
NPT165 Cell Line HeLa Homo sapiens IC50 = 710.0 nM PMID[572928]
NPT140 Organism Artemia Artemia LD50 = 3.0 ppm PMID[572926]
NPT20 Organism Candida albicans Candida albicans IZ = 10.5 mm PMID[572926]
NPT27 Others Unspecified IC50 = 1000.0 nM PMID[572927]
NPT2 Others Unspecified EC50 > 50000.0 nM PMID[572927]

☑ 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 NPC475554 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
0.925 High Similarity NPC132662
0.9057 High Similarity NPC164006
0.8974 High Similarity NPC216720
0.8917 High Similarity NPC210424
0.8827 High Similarity NPC134480
0.8773 High Similarity NPC473704
0.7471 Intermediate Similarity NPC56058
0.7471 Intermediate Similarity NPC522
0.7301 Intermediate Similarity NPC469801
0.6879 Remote Similarity NPC267605
0.6813 Remote Similarity NPC89592
0.6805 Remote Similarity NPC475390
0.6795 Remote Similarity NPC135558
0.6772 Remote Similarity NPC51692
0.6646 Remote Similarity NPC74917
0.6606 Remote Similarity NPC120917
0.65 Remote Similarity NPC312887
0.648 Remote Similarity NPC127775
0.6457 Remote Similarity NPC119481
0.6456 Remote Similarity NPC214375
0.6444 Remote Similarity NPC237219
0.6444 Remote Similarity NPC231110
0.64 Remote Similarity NPC473398
0.6389 Remote Similarity NPC474538
0.6384 Remote Similarity NPC475737
0.6384 Remote Similarity NPC474094
0.6384 Remote Similarity NPC185665
0.6384 Remote Similarity NPC474067
0.6379 Remote Similarity NPC319751
0.6348 Remote Similarity NPC474090
0.6348 Remote Similarity NPC154873
0.6348 Remote Similarity NPC109498
0.6348 Remote Similarity NPC163147
0.6348 Remote Similarity NPC50274
0.6348 Remote Similarity NPC252616
0.6348 Remote Similarity NPC61667
0.6348 Remote Similarity NPC45576
0.6348 Remote Similarity NPC32583
0.6333 Remote Similarity NPC21126
0.6324 Remote Similarity NPC97078
0.6324 Remote Similarity NPC470146
0.6324 Remote Similarity NPC101980
0.6322 Remote Similarity NPC190329
0.6313 Remote Similarity NPC268063
0.6313 Remote Similarity NPC224609
0.6286 Remote Similarity NPC474069
0.6278 Remote Similarity NPC202591
0.6278 Remote Similarity NPC212214
0.6271 Remote Similarity NPC82436
0.6271 Remote Similarity NPC474103
0.6271 Remote Similarity NPC474068
0.6271 Remote Similarity NPC474064
0.6236 Remote Similarity NPC21449
0.6236 Remote Similarity NPC474079
0.6236 Remote Similarity NPC475683
0.6236 Remote Similarity NPC474080
0.6236 Remote Similarity NPC474102
0.6236 Remote Similarity NPC157194
0.6209 Remote Similarity NPC52587
0.6167 Remote Similarity NPC206724
0.6167 Remote Similarity NPC474515
0.6164 Remote Similarity NPC469858
0.608 Remote Similarity NPC165538
0.6069 Remote Similarity NPC103268
0.6061 Remote Similarity NPC122427
0.6033 Remote Similarity NPC315252
0.598 Remote Similarity NPC329961
0.5954 Remote Similarity NPC474070
0.5904 Remote Similarity NPC222391
0.5895 Remote Similarity NPC34319
0.5895 Remote Similarity NPC256912
0.5895 Remote Similarity NPC24990
0.5808 Remote Similarity NPC137705
0.5798 Remote Similarity NPC201014
0.5798 Remote Similarity NPC110129
0.5795 Remote Similarity NPC161242
0.5736 Remote Similarity NPC25316
0.5736 Remote Similarity NPC263485
0.5736 Remote Similarity NPC229160
0.5728 Remote Similarity NPC145178
0.5728 Remote Similarity NPC475350
0.5728 Remote Similarity NPC14877
0.5714 Remote Similarity NPC476080
0.5714 Remote Similarity NPC145047
0.5714 Remote Similarity NPC86490
0.5714 Remote Similarity NPC475534
0.5685 Remote Similarity NPC475330
0.5657 Remote Similarity NPC174652
0.5648 Remote Similarity NPC251036
0.5638 Remote Similarity NPC217981

  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 NPC475554 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
0.6503 Remote Similarity NPD6916 Clinical (unspecified phase)
0.6384 Remote Similarity NPD6907 Phase 2
0.6369 Remote Similarity NPD6915 Approved
0.6333 Remote Similarity NPD6910 Phase 3
0.6243 Remote Similarity NPD6911 Discontinued
0.5939 Remote Similarity NPD9579 Approved
0.5765 Remote Similarity NPD2957 Phase 2

  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