Structure

Physi-Chem Properties

Molecular Weight:  314.22
Volume:  334.537
LogP:  2.214
LogD:  1.54
LogS:  -2.574
# Rotatable Bonds:  14
TPSA:  109.49
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.453
Synthetic Accessibility Score:  2.451
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.285
MDCK Permeability:  8.046751463552937e-05
Pgp-inhibitor:  0.039
Pgp-substrate:  0.013
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.884
Plasma Protein Binding (PPB):  84.4552993774414%
Volume Distribution (VD):  0.314
Pgp-substrate:  18.541536331176758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.059
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.21
CYP2C9-substrate:  0.962
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.098
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.038

ADMET: Excretion

Clearance (CL):  4.643
Half-life (T1/2):  0.558

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.083
Drug-inuced Liver Injury (DILI):  0.059
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.313
Carcinogencity:  0.048
Eye Corrosion:  0.004
Eye Irritation:  0.036
Respiratory Toxicity:  0.024

Download Data

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

  Natural Product: NPC470109

Natural Product ID:  NPC470109
Common Name*:   Lipoamide B
IUPAC Name:   (2S)-4-amino-2-(10-methylundecanoylamino)-4-oxobutanoic acid
Synonyms:   Lipoamide B
Standard InCHIKey:  HAIPUHCLABEHHT-ZDUSSCGKSA-N
Standard InCHI:  InChI=1S/C16H30N2O4/c1-12(2)9-7-5-3-4-6-8-10-15(20)18-13(16(21)22)11-14(17)19/h12-13H,3-11H2,1-2H3,(H2,17,19)(H,18,20)(H,21,22)/t13-/m0/s1
SMILES:  CC(C)CCCCCCCCC(=O)NC(CC(=O)N)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1773494
PubChem CID:   54581177
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004312] Asparagine and derivatives

*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
NPO32941 bacillus Genus Bacillidae Eukaryota n.a. n.a. n.a. PMID[21401023]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100.0 ug.mL-1 PMID[511520]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 100.0 ug.mL-1 PMID[511520]

☑ 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 NPC470109 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
0.9839 High Similarity NPC470110
0.9836 High Similarity NPC470108
0.7692 Intermediate Similarity NPC321468
0.7692 Intermediate Similarity NPC327748
0.7656 Intermediate Similarity NPC317147
0.7576 Intermediate Similarity NPC329564
0.7576 Intermediate Similarity NPC327170
0.7534 Intermediate Similarity NPC43219
0.746 Intermediate Similarity NPC316889
0.746 Intermediate Similarity NPC321118
0.7432 Intermediate Similarity NPC86064
0.7424 Intermediate Similarity NPC317143
0.7424 Intermediate Similarity NPC316826
0.7385 Intermediate Similarity NPC318260
0.7375 Intermediate Similarity NPC227051
0.7349 Intermediate Similarity NPC477729
0.7342 Intermediate Similarity NPC477730
0.7308 Intermediate Similarity NPC314466
0.7258 Intermediate Similarity NPC329181
0.7258 Intermediate Similarity NPC319110
0.725 Intermediate Similarity NPC95478
0.725 Intermediate Similarity NPC145748
0.725 Intermediate Similarity NPC155670
0.7206 Intermediate Similarity NPC477644
0.7164 Intermediate Similarity NPC254541
0.7143 Intermediate Similarity NPC322946
0.7123 Intermediate Similarity NPC478256
0.7097 Intermediate Similarity NPC328378
0.7077 Intermediate Similarity NPC327831
0.7015 Intermediate Similarity NPC176164
0.7015 Intermediate Similarity NPC189301
0.6988 Remote Similarity NPC477728
0.6933 Remote Similarity NPC320865
0.6933 Remote Similarity NPC477643
0.6933 Remote Similarity NPC315897
0.6933 Remote Similarity NPC477641
0.6923 Remote Similarity NPC316242
0.6912 Remote Similarity NPC320598
0.6892 Remote Similarity NPC477642
0.6857 Remote Similarity NPC327252
0.6835 Remote Similarity NPC315131
0.6835 Remote Similarity NPC315535
0.6835 Remote Similarity NPC478017
0.6818 Remote Similarity NPC322573
0.6757 Remote Similarity NPC472579
0.6757 Remote Similarity NPC473985
0.6757 Remote Similarity NPC474298
0.6757 Remote Similarity NPC474299
0.6757 Remote Similarity NPC475808
0.6757 Remote Similarity NPC28348
0.6753 Remote Similarity NPC472595
0.6667 Remote Similarity NPC227850
0.6667 Remote Similarity NPC321536
0.6667 Remote Similarity NPC476285
0.6667 Remote Similarity NPC153370
0.6623 Remote Similarity NPC476248
0.6622 Remote Similarity NPC195165
0.6582 Remote Similarity NPC472594
0.6571 Remote Similarity NPC143722
0.6562 Remote Similarity NPC80350
0.6528 Remote Similarity NPC145658
0.65 Remote Similarity NPC37681
0.6494 Remote Similarity NPC474403
0.6471 Remote Similarity NPC325985
0.6471 Remote Similarity NPC38463
0.6447 Remote Similarity NPC476291
0.642 Remote Similarity NPC473984
0.641 Remote Similarity NPC138435
0.6364 Remote Similarity NPC477200
0.6349 Remote Similarity NPC297220
0.6308 Remote Similarity NPC245027
0.6308 Remote Similarity NPC62045
0.6308 Remote Similarity NPC162620
0.6301 Remote Similarity NPC315744
0.6282 Remote Similarity NPC141325
0.625 Remote Similarity NPC476324
0.625 Remote Similarity NPC476130
0.6222 Remote Similarity NPC208537
0.6222 Remote Similarity NPC270005
0.6216 Remote Similarity NPC174304
0.6216 Remote Similarity NPC325597
0.619 Remote Similarity NPC84128
0.619 Remote Similarity NPC53858
0.6176 Remote Similarity NPC72722
0.6164 Remote Similarity NPC105297
0.6154 Remote Similarity NPC180402
0.6154 Remote Similarity NPC87359
0.6143 Remote Similarity NPC278209
0.6111 Remote Similarity NPC321419
0.6111 Remote Similarity NPC471129
0.6104 Remote Similarity NPC193280
0.6104 Remote Similarity NPC314273
0.6104 Remote Similarity NPC126779
0.6081 Remote Similarity NPC57420
0.6081 Remote Similarity NPC289691
0.6081 Remote Similarity NPC316674
0.6067 Remote Similarity NPC193386
0.6061 Remote Similarity NPC43204
0.6061 Remote Similarity NPC174246
0.6061 Remote Similarity NPC226027
0.6061 Remote Similarity NPC84636
0.6056 Remote Similarity NPC190385
0.6047 Remote Similarity NPC472351
0.6047 Remote Similarity NPC320936
0.6032 Remote Similarity NPC126925
0.6032 Remote Similarity NPC132307
0.6032 Remote Similarity NPC325097
0.6029 Remote Similarity NPC190184
0.6029 Remote Similarity NPC189178
0.6029 Remote Similarity NPC263065
0.6029 Remote Similarity NPC197087
0.6 Remote Similarity NPC319709
0.6 Remote Similarity NPC128559
0.6 Remote Similarity NPC21844
0.6 Remote Similarity NPC289484
0.5974 Remote Similarity NPC306696
0.5974 Remote Similarity NPC319046
0.5972 Remote Similarity NPC473599
0.5972 Remote Similarity NPC216415
0.5972 Remote Similarity NPC476537
0.597 Remote Similarity NPC327239
0.5968 Remote Similarity NPC241279
0.5946 Remote Similarity NPC145627
0.5938 Remote Similarity NPC55023
0.593 Remote Similarity NPC47135
0.5909 Remote Similarity NPC324793
0.5909 Remote Similarity NPC477878
0.5904 Remote Similarity NPC191774
0.5902 Remote Similarity NPC327250
0.5882 Remote Similarity NPC23984
0.5875 Remote Similarity NPC55274
0.5862 Remote Similarity NPC323180
0.5846 Remote Similarity NPC314679
0.5842 Remote Similarity NPC15413
0.5833 Remote Similarity NPC220234
0.5833 Remote Similarity NPC472578
0.5833 Remote Similarity NPC469492
0.5821 Remote Similarity NPC316231
0.5821 Remote Similarity NPC112890
0.5821 Remote Similarity NPC324825
0.5811 Remote Similarity NPC302188
0.5797 Remote Similarity NPC137327
0.5797 Remote Similarity NPC329495
0.5795 Remote Similarity NPC175419
0.5775 Remote Similarity NPC313263
0.5765 Remote Similarity NPC469517
0.5758 Remote Similarity NPC136159
0.5747 Remote Similarity NPC474312
0.5735 Remote Similarity NPC50457
0.5714 Remote Similarity NPC270041
0.5714 Remote Similarity NPC474402
0.5699 Remote Similarity NPC315237
0.5692 Remote Similarity NPC208793
0.5692 Remote Similarity NPC118459
0.5692 Remote Similarity NPC327698
0.5692 Remote Similarity NPC285322
0.5667 Remote Similarity NPC119633
0.5667 Remote Similarity NPC270957
0.5667 Remote Similarity NPC171698
0.5667 Remote Similarity NPC321340
0.5667 Remote Similarity NPC323958
0.5652 Remote Similarity NPC471131
0.5652 Remote Similarity NPC19576
0.5652 Remote Similarity NPC29950
0.5645 Remote Similarity NPC31557
0.5645 Remote Similarity NPC28394
0.5618 Remote Similarity NPC476523
0.5616 Remote Similarity NPC328447
0.5616 Remote Similarity NPC319279
0.5604 Remote Similarity NPC304454
0.56 Remote Similarity NPC314510

  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 NPC470109 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
0.7681 Intermediate Similarity NPD2263 Discontinued
0.7222 Intermediate Similarity NPD3724 Clinical (unspecified phase)
0.7162 Intermediate Similarity NPD6944 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD9441 Phase 2
0.6957 Remote Similarity NPD574 Approved
0.6944 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6933 Remote Similarity NPD2256 Clinical (unspecified phase)
0.6933 Remote Similarity NPD1825 Clinical (unspecified phase)
0.6914 Remote Similarity NPD4829 Discontinued
0.6857 Remote Similarity NPD575 Clinical (unspecified phase)
0.6835 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6835 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6782 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6774 Remote Similarity NPD379 Clinical (unspecified phase)
0.6765 Remote Similarity NPD9433 Approved
0.6711 Remote Similarity NPD1147 Phase 2
0.6667 Remote Similarity NPD8614 Approved
0.662 Remote Similarity NPD9676 Phase 3
0.6567 Remote Similarity NPD1830 Clinical (unspecified phase)
0.6506 Remote Similarity NPD7643 Phase 1
0.6429 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6375 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6364 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6308 Remote Similarity NPD9018 Approved
0.6279 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6267 Remote Similarity NPD886 Clinical (unspecified phase)
0.6264 Remote Similarity NPD573 Clinical (unspecified phase)
0.6224 Remote Similarity NPD8175 Discontinued
0.6216 Remote Similarity NPD348 Approved
0.6207 Remote Similarity NPD3176 Clinical (unspecified phase)
0.6184 Remote Similarity NPD4241 Registered
0.6176 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6104 Remote Similarity NPD4242 Approved
0.6094 Remote Similarity NPD1152 Phase 2
0.6087 Remote Similarity NPD8394 Approved
0.6076 Remote Similarity NPD3187 Discontinued
0.6061 Remote Similarity NPD9017 Approved
0.6056 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6053 Remote Similarity NPD9421 Phase 1
0.6049 Remote Similarity NPD1453 Phase 1
0.6032 Remote Similarity NPD8798 Approved
0.6029 Remote Similarity NPD9205 Approved
0.6029 Remote Similarity NPD9204 Approved
0.6029 Remote Similarity NPD8785 Approved
0.6 Remote Similarity NPD3211 Approved
0.6 Remote Similarity NPD366 Approved
0.6 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6 Remote Similarity NPD2683 Discontinued
0.5974 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5974 Remote Similarity NPD337 Discontinued
0.597 Remote Similarity NPD329 Discontinued
0.593 Remote Similarity NPD7345 Approved
0.5926 Remote Similarity NPD632 Discontinued
0.5909 Remote Similarity NPD7759 Phase 2
0.5909 Remote Similarity NPD7760 Phase 2
0.5904 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5882 Remote Similarity NPD612 Discontinued
0.5854 Remote Similarity NPD2257 Approved
0.5846 Remote Similarity NPD634 Phase 3
0.5833 Remote Similarity NPD617 Approved
0.5821 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5821 Remote Similarity NPD9044 Approved
0.5811 Remote Similarity NPD9656 Approved
0.5789 Remote Similarity NPD1831 Phase 3
0.5775 Remote Similarity NPD9454 Approved
0.5765 Remote Similarity NPD5354 Approved
0.5714 Remote Similarity NPD3160 Suspended
0.5714 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5696 Remote Similarity NPD620 Approved
0.5692 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5692 Remote Similarity NPD8610 Approved
0.567 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5652 Remote Similarity NPD8846 Approved
0.5652 Remote Similarity NPD8847 Approved
0.5652 Remote Similarity NPD61 Approved
0.5641 Remote Similarity NPD375 Phase 2
0.5638 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5632 Remote Similarity NPD1125 Discovery
0.5616 Remote Similarity NPD9439 Approved
0.5616 Remote Similarity NPD9438 Approved
0.5616 Remote Similarity NPD9661 Approved
0.5606 Remote Similarity NPD8801 Approved
0.56 Remote Similarity NPD6122 Discontinued

  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