Structure

Physi-Chem Properties

Molecular Weight:  316.2
Volume:  326.032
LogP:  0.642
LogD:  0.856
LogS:  -0.708
# Rotatable Bonds:  14
TPSA:  95.94
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.26
Synthetic Accessibility Score:  2.366
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.755
MDCK Permeability:  7.886606181273237e-05
Pgp-inhibitor:  0.11
Pgp-substrate:  0.422
Human Intestinal Absorption (HIA):  0.043
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.2

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.982
Plasma Protein Binding (PPB):  11.12749195098877%
Volume Distribution (VD):  0.867
Pgp-substrate:  80.09552001953125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.167
CYP2C19-inhibitor:  0.114
CYP2C19-substrate:  0.071
CYP2C9-inhibitor:  0.135
CYP2C9-substrate:  0.946
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.046
CYP3A4-substrate:  0.12

ADMET: Excretion

Clearance (CL):  9.242
Half-life (T1/2):  0.512

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.34
Drug-inuced Liver Injury (DILI):  0.061
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.057
Skin Sensitization:  0.274
Carcinogencity:  0.017
Eye Corrosion:  0.004
Eye Irritation:  0.051
Respiratory Toxicity:  0.009

Download Data

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

  Natural Product: NPC128559

Natural Product ID:  NPC128559
Common Name*:   Tenacibactin A
IUPAC Name:   methyl 4-[5-[hydroxy(3-methylbutanoyl)amino]pentylamino]-4-oxobutanoate
Synonyms:  
Standard InCHIKey:  HXFAPJCUUWBIQZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H28N2O5/c1-12(2)11-14(19)17(21)10-6-4-5-9-16-13(18)7-8-15(20)22-3/h12,21H,4-11H2,1-3H3,(H,16,18)
SMILES:  CC(C)CC(=O)N(CCCCCN=C(CCC(=O)OC)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL225044
PubChem CID:   16216278
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters
          • [CHEMONTID:0003417] Fatty acid methyl esters

*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
NPO32917 tenacibaculum sp. a4k-17 Species Flavobacteriaceae Bacteria n.a. n.a. n.a. PMID[17319723]

☑ 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
NPT2 Others Unspecified ED50 > 1.0 mM PMID[548075]

☑ 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 NPC128559 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
0.9661 High Similarity NPC105297
0.8906 High Similarity NPC306696
0.7812 Intermediate Similarity NPC263207
0.7794 Intermediate Similarity NPC250953
0.7656 Intermediate Similarity NPC292299
0.7656 Intermediate Similarity NPC34838
0.7353 Intermediate Similarity NPC262615
0.6825 Remote Similarity NPC471131
0.6341 Remote Similarity NPC84128
0.6341 Remote Similarity NPC246005
0.6341 Remote Similarity NPC53858
0.6316 Remote Similarity NPC196007
0.6316 Remote Similarity NPC76297
0.6316 Remote Similarity NPC214532
0.6154 Remote Similarity NPC209156
0.6154 Remote Similarity NPC161774
0.6154 Remote Similarity NPC266888
0.6154 Remote Similarity NPC256312
0.6143 Remote Similarity NPC316826
0.6143 Remote Similarity NPC327748
0.6143 Remote Similarity NPC317143
0.6143 Remote Similarity NPC321468
0.6136 Remote Similarity NPC474593
0.6136 Remote Similarity NPC475801
0.6119 Remote Similarity NPC321118
0.6119 Remote Similarity NPC316889
0.6087 Remote Similarity NPC318260
0.6087 Remote Similarity NPC317147
0.6081 Remote Similarity NPC470108
0.6067 Remote Similarity NPC474576
0.6061 Remote Similarity NPC322946
0.6056 Remote Similarity NPC327170
0.6056 Remote Similarity NPC471129
0.6056 Remote Similarity NPC329564
0.6027 Remote Similarity NPC57420
0.6024 Remote Similarity NPC470783
0.6 Remote Similarity NPC62263
0.6 Remote Similarity NPC470109
0.6 Remote Similarity NPC173763
0.6 Remote Similarity NPC471098
0.5976 Remote Similarity NPC312315
0.5976 Remote Similarity NPC31756
0.5974 Remote Similarity NPC478256
0.5968 Remote Similarity NPC43264
0.5957 Remote Similarity NPC475440
0.5926 Remote Similarity NPC59867
0.5926 Remote Similarity NPC472594
0.5921 Remote Similarity NPC470110
0.5904 Remote Similarity NPC476156
0.5904 Remote Similarity NPC476117
0.5904 Remote Similarity NPC476137
0.5904 Remote Similarity NPC476243
0.589 Remote Similarity NPC327252
0.5889 Remote Similarity NPC477538
0.5875 Remote Similarity NPC472595
0.5833 Remote Similarity NPC475542
0.5833 Remote Similarity NPC476302
0.5775 Remote Similarity NPC328447
0.5769 Remote Similarity NPC476291
0.5769 Remote Similarity NPC476285
0.5765 Remote Similarity NPC6902
0.5765 Remote Similarity NPC184473
0.5758 Remote Similarity NPC328378
0.5714 Remote Similarity NPC10716
0.5694 Remote Similarity NPC254541
0.5679 Remote Similarity NPC327272
0.5658 Remote Similarity NPC128005
0.5658 Remote Similarity NPC84182
0.5647 Remote Similarity NPC23984
0.5641 Remote Similarity NPC314273
0.5641 Remote Similarity NPC29598
0.5641 Remote Similarity NPC212866
0.5641 Remote Similarity NPC193280
0.5632 Remote Similarity NPC472351
0.5625 Remote Similarity NPC141325
0.5625 Remote Similarity NPC315897
0.5625 Remote Similarity NPC220234
0.5625 Remote Similarity NPC475758
0.5606 Remote Similarity NPC227850

  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 NPC128559 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
0.7353 Intermediate Similarity NPD6437 Approved
0.7353 Intermediate Similarity NPD6438 Approved
0.6625 Remote Similarity NPD612 Discontinued
0.6486 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6438 Remote Similarity NPD2263 Discontinued
0.6267 Remote Similarity NPD620 Approved
0.6235 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6129 Remote Similarity NPD9658 Clinical (unspecified phase)
0.6061 Remote Similarity NPD9441 Phase 2
0.6047 Remote Similarity NPD7759 Phase 2
0.6047 Remote Similarity NPD7760 Phase 2
0.6 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5972 Remote Similarity NPD574 Approved
0.5952 Remote Similarity NPD1125 Discovery
0.5926 Remote Similarity NPD2689 Clinical (unspecified phase)
0.589 Remote Similarity NPD575 Clinical (unspecified phase)
0.5857 Remote Similarity NPD9425 Approved
0.5833 Remote Similarity NPD7763 Phase 2
0.5833 Remote Similarity NPD7762 Phase 2
0.5802 Remote Similarity NPD1453 Phase 1
0.5795 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5783 Remote Similarity NPD4815 Discontinued
0.5775 Remote Similarity NPD9661 Approved
0.5765 Remote Similarity NPD2683 Discontinued
0.5714 Remote Similarity NPD322 Phase 1
0.5714 Remote Similarity NPD4261 Phase 1
0.5714 Remote Similarity NPD1456 Approved
0.5698 Remote Similarity NPD4829 Discontinued
0.5684 Remote Similarity NPD8038 Phase 2
0.5676 Remote Similarity NPD9625 Approved
0.5652 Remote Similarity NPD9419 Clinical (unspecified phase)
0.5647 Remote Similarity NPD3628 Phase 3
0.5641 Remote Similarity NPD7840 Approved
0.5625 Remote Similarity NPD1825 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