Structure

Physi-Chem Properties

Molecular Weight:  395.34
Volume:  453.118
LogP:  7.636
LogD:  4.578
LogS:  -5.492
# Rotatable Bonds:  20
TPSA:  55.4
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.167
Synthetic Accessibility Score:  3.241
Fsp3:  0.833
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:  -4.798
MDCK Permeability:  1.4839104551356286e-05
Pgp-inhibitor:  0.051
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.128
Plasma Protein Binding (PPB):  97.69405364990234%
Volume Distribution (VD):  1.105
Pgp-substrate:  2.6930959224700928%

ADMET: Metabolism

CYP1A2-inhibitor:  0.251
CYP1A2-substrate:  0.201
CYP2C19-inhibitor:  0.547
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.427
CYP2C9-substrate:  0.767
CYP2D6-inhibitor:  0.543
CYP2D6-substrate:  0.091
CYP3A4-inhibitor:  0.857
CYP3A4-substrate:  0.118

ADMET: Excretion

Clearance (CL):  3.165
Half-life (T1/2):  0.188

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.077
Drug-inuced Liver Injury (DILI):  0.058
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.873
Carcinogencity:  0.097
Eye Corrosion:  0.145
Eye Irritation:  0.364
Respiratory Toxicity:  0.531

Download Data

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

  Natural Product: NPC280065

Natural Product ID:  NPC280065
Common Name*:   Semiplenamide E
IUPAC Name:   [(2S)-2-[[(E)-2-methyloctadec-2-enoyl]amino]propyl] acetate
Synonyms:   Semiplenamide E
Standard InCHIKey:  HMEVPMUFHLUBFU-KGAYOUTBSA-N
Standard InCHI:  InChI=1S/C24H45NO3/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-21(2)24(27)25-22(3)20-28-23(4)26/h19,22H,5-18,20H2,1-4H3,(H,25,27)/b21-19+/t22-/m0/s1
SMILES:  CCCCCCCCCCCCCCC/C=C(C)/C(=N[C@@H](C)COC(=O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465163
PubChem CID:   11463588
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[14575438]
NPO15105 Lyngbya semiplena 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
NPT176 Organism Artemia salina Artemia salina LD50 = 19.0 uM PMID[537048]

☑ 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 NPC280065 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 NPC45060
0.9538 High Similarity NPC249713
0.8615 High Similarity NPC29468
0.8182 Intermediate Similarity NPC130807
0.7714 Intermediate Similarity NPC477525
0.7183 Intermediate Similarity NPC316674
0.7183 Intermediate Similarity NPC182758
0.7162 Intermediate Similarity NPC474812
0.7101 Intermediate Similarity NPC325734
0.7073 Intermediate Similarity NPC474312
0.7067 Intermediate Similarity NPC103712
0.7067 Intermediate Similarity NPC291196
0.7 Intermediate Similarity NPC474833
0.7 Intermediate Similarity NPC312826
0.6892 Remote Similarity NPC129995
0.6892 Remote Similarity NPC315141
0.6812 Remote Similarity NPC306420
0.6812 Remote Similarity NPC104138
0.6812 Remote Similarity NPC24216
0.6812 Remote Similarity NPC261158
0.6806 Remote Similarity NPC273614
0.6761 Remote Similarity NPC326524
0.6761 Remote Similarity NPC325550
0.6761 Remote Similarity NPC329003
0.6709 Remote Similarity NPC288086
0.6667 Remote Similarity NPC242930
0.6667 Remote Similarity NPC273023
0.6667 Remote Similarity NPC297020
0.663 Remote Similarity NPC175614
0.662 Remote Similarity NPC321030
0.6582 Remote Similarity NPC314678
0.6559 Remote Similarity NPC4834
0.6486 Remote Similarity NPC471023
0.6486 Remote Similarity NPC77891
0.6486 Remote Similarity NPC55068
0.6479 Remote Similarity NPC249850
0.6479 Remote Similarity NPC293437
0.6447 Remote Similarity NPC187315
0.6438 Remote Similarity NPC309877
0.6438 Remote Similarity NPC6795
0.6413 Remote Similarity NPC17290
0.6413 Remote Similarity NPC3568
0.6413 Remote Similarity NPC192066
0.6413 Remote Similarity NPC256570
0.6413 Remote Similarity NPC23454
0.6413 Remote Similarity NPC70323
0.6413 Remote Similarity NPC262312
0.6413 Remote Similarity NPC35269
0.641 Remote Similarity NPC471022
0.6389 Remote Similarity NPC223679
0.6389 Remote Similarity NPC254095
0.6377 Remote Similarity NPC303672
0.6374 Remote Similarity NPC472264
0.6338 Remote Similarity NPC96663
0.6333 Remote Similarity NPC39290
0.6333 Remote Similarity NPC159369
0.6329 Remote Similarity NPC97614
0.6327 Remote Similarity NPC74035
0.6301 Remote Similarity NPC150505
0.6301 Remote Similarity NPC74617
0.6286 Remote Similarity NPC44193
0.6286 Remote Similarity NPC132669
0.6286 Remote Similarity NPC246519
0.6286 Remote Similarity NPC14234
0.6286 Remote Similarity NPC184014
0.6286 Remote Similarity NPC269800
0.6279 Remote Similarity NPC224072
0.6279 Remote Similarity NPC39966
0.6277 Remote Similarity NPC197294
0.6277 Remote Similarity NPC8098
0.6277 Remote Similarity NPC183449
0.6277 Remote Similarity NPC45313
0.6264 Remote Similarity NPC74672
0.6264 Remote Similarity NPC209047
0.6264 Remote Similarity NPC139782
0.6264 Remote Similarity NPC242503
0.6264 Remote Similarity NPC43074
0.625 Remote Similarity NPC294938
0.625 Remote Similarity NPC135863
0.625 Remote Similarity NPC129150
0.6232 Remote Similarity NPC195986
0.6216 Remote Similarity NPC471278
0.6212 Remote Similarity NPC308331
0.6212 Remote Similarity NPC197467
0.6197 Remote Similarity NPC471992
0.6196 Remote Similarity NPC473604
0.6196 Remote Similarity NPC282705
0.6196 Remote Similarity NPC473950
0.6196 Remote Similarity NPC111567
0.6196 Remote Similarity NPC473581
0.6196 Remote Similarity NPC475125
0.6196 Remote Similarity NPC263545
0.6196 Remote Similarity NPC309898
0.6196 Remote Similarity NPC15851
0.6196 Remote Similarity NPC186840
0.6196 Remote Similarity NPC182632
0.6184 Remote Similarity NPC253468
0.6184 Remote Similarity NPC235311
0.6164 Remote Similarity NPC21946
0.6163 Remote Similarity NPC82799
0.6162 Remote Similarity NPC205176
0.6125 Remote Similarity NPC4299
0.6118 Remote Similarity NPC157173
0.6117 Remote Similarity NPC29501
0.61 Remote Similarity NPC201128
0.6098 Remote Similarity NPC469835
0.6092 Remote Similarity NPC469833
0.6092 Remote Similarity NPC469838
0.6087 Remote Similarity NPC473672
0.6087 Remote Similarity NPC304223
0.6087 Remote Similarity NPC474495
0.6087 Remote Similarity NPC267340
0.6087 Remote Similarity NPC54542
0.6087 Remote Similarity NPC243539
0.6087 Remote Similarity NPC145032
0.6081 Remote Similarity NPC82465
0.6064 Remote Similarity NPC54961
0.6064 Remote Similarity NPC158445
0.6064 Remote Similarity NPC282088
0.6064 Remote Similarity NPC156782
0.6064 Remote Similarity NPC157353
0.6061 Remote Similarity NPC26600
0.6061 Remote Similarity NPC47946
0.6056 Remote Similarity NPC13011
0.6056 Remote Similarity NPC124382
0.6053 Remote Similarity NPC29697
0.6049 Remote Similarity NPC472254
0.6027 Remote Similarity NPC212730
0.6027 Remote Similarity NPC265551
0.6027 Remote Similarity NPC44542
0.6024 Remote Similarity NPC217095
0.6024 Remote Similarity NPC264417
0.602 Remote Similarity NPC188785
0.6 Remote Similarity NPC116934
0.6 Remote Similarity NPC189764
0.6 Remote Similarity NPC470439
0.6 Remote Similarity NPC101622
0.6 Remote Similarity NPC233273
0.6 Remote Similarity NPC50902
0.6 Remote Similarity NPC205546
0.5976 Remote Similarity NPC477085
0.5972 Remote Similarity NPC146551
0.5972 Remote Similarity NPC470963
0.5972 Remote Similarity NPC474513
0.5972 Remote Similarity NPC471991
0.5943 Remote Similarity NPC471645
0.5942 Remote Similarity NPC267692
0.5942 Remote Similarity NPC307435
0.5941 Remote Similarity NPC472433
0.5926 Remote Similarity NPC473361
0.5926 Remote Similarity NPC324638
0.5926 Remote Similarity NPC329904
0.5921 Remote Similarity NPC271282
0.5921 Remote Similarity NPC66460
0.5921 Remote Similarity NPC325929
0.5921 Remote Similarity NPC55376
0.5915 Remote Similarity NPC119655
0.5909 Remote Similarity NPC304079
0.5909 Remote Similarity NPC6963
0.5909 Remote Similarity NPC477487
0.5905 Remote Similarity NPC469968
0.5905 Remote Similarity NPC80834
0.5904 Remote Similarity NPC470994
0.5897 Remote Similarity NPC282760
0.589 Remote Similarity NPC470964
0.589 Remote Similarity NPC311648
0.5875 Remote Similarity NPC474298
0.5875 Remote Similarity NPC475808
0.5875 Remote Similarity NPC473985
0.5875 Remote Similarity NPC474299
0.5875 Remote Similarity NPC28348
0.587 Remote Similarity NPC320057
0.587 Remote Similarity NPC34754
0.5867 Remote Similarity NPC222852
0.5865 Remote Similarity NPC122926
0.5865 Remote Similarity NPC113012
0.5862 Remote Similarity NPC477523
0.5859 Remote Similarity NPC474873
0.5854 Remote Similarity NPC469836
0.5854 Remote Similarity NPC477087
0.5854 Remote Similarity NPC474403
0.5854 Remote Similarity NPC477086
0.5844 Remote Similarity NPC68110
0.5844 Remote Similarity NPC477106
0.5843 Remote Similarity NPC228638
0.5833 Remote Similarity NPC476923
0.5833 Remote Similarity NPC167759
0.5833 Remote Similarity NPC56028
0.5833 Remote Similarity NPC269615
0.5833 Remote Similarity NPC305288
0.5833 Remote Similarity NPC476924
0.5833 Remote Similarity NPC163912
0.5821 Remote Similarity NPC140501
0.5821 Remote Similarity NPC160628
0.5811 Remote Similarity NPC283502
0.5811 Remote Similarity NPC245650
0.5811 Remote Similarity NPC472445
0.5811 Remote Similarity NPC471277
0.5811 Remote Similarity NPC48968
0.5811 Remote Similarity NPC471279

  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 NPC280065 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
0.6629 Remote Similarity NPD6095 Approved
0.6629 Remote Similarity NPD6094 Approved
0.6486 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6264 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6238 Remote Similarity NPD6413 Approved
0.6087 Remote Similarity NPD6927 Phase 3
0.5957 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5938 Remote Similarity NPD4228 Discovery
0.5926 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5865 Remote Similarity NPD6421 Discontinued
0.5821 Remote Similarity NPD4265 Approved
0.5797 Remote Similarity NPD4220 Pre-registration
0.5789 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5784 Remote Similarity NPD4211 Phase 1
0.5769 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5743 Remote Similarity NPD2258 Approved
0.5743 Remote Similarity NPD2259 Approved
0.5679 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5647 Remote Similarity NPD1452 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