Structure

Physi-Chem Properties

Molecular Weight:  325.3
Volume:  377.78
LogP:  6.146
LogD:  4.232
LogS:  -4.87
# Rotatable Bonds:  16
TPSA:  49.33
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.329
Synthetic Accessibility Score:  3.161
Fsp3:  0.85
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:  -4.669
MDCK Permeability:  1.7522212147014216e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.405
30% Bioavailability (F30%):  0.954

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.164
Plasma Protein Binding (PPB):  97.3670883178711%
Volume Distribution (VD):  0.776
Pgp-substrate:  2.4573142528533936%

ADMET: Metabolism

CYP1A2-inhibitor:  0.381
CYP1A2-substrate:  0.483
CYP2C19-inhibitor:  0.543
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.491
CYP2C9-substrate:  0.872
CYP2D6-inhibitor:  0.167
CYP2D6-substrate:  0.149
CYP3A4-inhibitor:  0.848
CYP3A4-substrate:  0.098

ADMET: Excretion

Clearance (CL):  4.55
Half-life (T1/2):  0.241

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.11
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.086
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.677
Carcinogencity:  0.049
Eye Corrosion:  0.044
Eye Irritation:  0.447
Respiratory Toxicity:  0.254

Download Data

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

  Natural Product: NPC29468

Natural Product ID:  NPC29468
Common Name*:   Semiplenamide C
IUPAC Name:   (E)-N-[(2S)-1-hydroxypropan-2-yl]-2-methylhexadec-2-enamide
Synonyms:   Semiplenamide C
Standard InCHIKey:  YATFRALIAPYFQO-YMIFCHIISA-N
Standard InCHI:  InChI=1S/C20H39NO2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-18(2)20(23)21-19(3)17-22/h16,19,22H,4-15,17H2,1-3H3,(H,21,23)/b18-16+/t19-/m0/s1
SMILES:  CCCCCCCCCCCCC/C=C(/C(=N[C@H](CO)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453231
PubChem CID:   11347939
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 = 1.5 uM PMID[565743]

☑ 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 NPC29468 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
0.9483 High Similarity NPC130807
0.8871 High Similarity NPC477525
0.8615 High Similarity NPC280065
0.8615 High Similarity NPC45060
0.8182 Intermediate Similarity NPC249713
0.806 Intermediate Similarity NPC103712
0.806 Intermediate Similarity NPC291196
0.7879 Intermediate Similarity NPC315141
0.7879 Intermediate Similarity NPC129995
0.7778 Intermediate Similarity NPC312826
0.7778 Intermediate Similarity NPC329003
0.7778 Intermediate Similarity NPC325550
0.7778 Intermediate Similarity NPC326524
0.7705 Intermediate Similarity NPC242930
0.7619 Intermediate Similarity NPC321030
0.7606 Intermediate Similarity NPC288086
0.7581 Intermediate Similarity NPC261158
0.7581 Intermediate Similarity NPC104138
0.7581 Intermediate Similarity NPC24216
0.7581 Intermediate Similarity NPC306420
0.7465 Intermediate Similarity NPC314678
0.7424 Intermediate Similarity NPC471023
0.7424 Intermediate Similarity NPC55068
0.7419 Intermediate Similarity NPC297020
0.7419 Intermediate Similarity NPC273023
0.7121 Intermediate Similarity NPC309877
0.7097 Intermediate Similarity NPC303672
0.7059 Intermediate Similarity NPC253468
0.7059 Intermediate Similarity NPC235311
0.7049 Intermediate Similarity NPC473672
0.7049 Intermediate Similarity NPC474495
0.7018 Intermediate Similarity NPC116934
0.6984 Remote Similarity NPC246519
0.6984 Remote Similarity NPC132669
0.6984 Remote Similarity NPC14234
0.6984 Remote Similarity NPC269800
0.6984 Remote Similarity NPC44193
0.6984 Remote Similarity NPC184014
0.697 Remote Similarity NPC74617
0.697 Remote Similarity NPC150505
0.6935 Remote Similarity NPC195986
0.6923 Remote Similarity NPC82799
0.6875 Remote Similarity NPC471992
0.6835 Remote Similarity NPC39966
0.6835 Remote Similarity NPC224072
0.6806 Remote Similarity NPC471022
0.68 Remote Similarity NPC264417
0.68 Remote Similarity NPC217095
0.678 Remote Similarity NPC160628
0.678 Remote Similarity NPC140501
0.6774 Remote Similarity NPC145032
0.6774 Remote Similarity NPC304223
0.6774 Remote Similarity NPC54542
0.6774 Remote Similarity NPC267340
0.6774 Remote Similarity NPC243539
0.6724 Remote Similarity NPC470439
0.6719 Remote Similarity NPC13011
0.6719 Remote Similarity NPC124382
0.6712 Remote Similarity NPC324638
0.6667 Remote Similarity NPC182758
0.6667 Remote Similarity NPC477106
0.6667 Remote Similarity NPC269823
0.6667 Remote Similarity NPC316674
0.662 Remote Similarity NPC187315
0.6618 Remote Similarity NPC6795
0.6615 Remote Similarity NPC471991
0.6613 Remote Similarity NPC267692
0.6613 Remote Similarity NPC26960
0.6613 Remote Similarity NPC307435
0.6613 Remote Similarity NPC182102
0.6579 Remote Similarity NPC476924
0.6567 Remote Similarity NPC325734
0.6562 Remote Similarity NPC474496
0.6562 Remote Similarity NPC119655
0.6552 Remote Similarity NPC213538
0.6552 Remote Similarity NPC256766
0.6548 Remote Similarity NPC34754
0.6462 Remote Similarity NPC167759
0.6462 Remote Similarity NPC163912
0.6462 Remote Similarity NPC56028
0.6462 Remote Similarity NPC305288
0.642 Remote Similarity NPC469833
0.642 Remote Similarity NPC469838
0.6389 Remote Similarity NPC113224
0.6364 Remote Similarity NPC262312
0.6364 Remote Similarity NPC70323
0.6364 Remote Similarity NPC3568
0.6364 Remote Similarity NPC256570
0.6364 Remote Similarity NPC192066
0.6364 Remote Similarity NPC17290
0.6364 Remote Similarity NPC35269
0.6364 Remote Similarity NPC23454
0.6353 Remote Similarity NPC316186
0.6349 Remote Similarity NPC474460
0.6349 Remote Similarity NPC72699
0.6341 Remote Similarity NPC228638
0.6333 Remote Similarity NPC138935
0.6324 Remote Similarity NPC210999
0.6316 Remote Similarity NPC182840
0.6316 Remote Similarity NPC103213
0.6316 Remote Similarity NPC29091
0.6316 Remote Similarity NPC255042
0.6286 Remote Similarity NPC273614
0.6269 Remote Similarity NPC477049
0.6269 Remote Similarity NPC4881
0.6267 Remote Similarity NPC97614
0.6265 Remote Similarity NPC477199
0.625 Remote Similarity NPC151782
0.625 Remote Similarity NPC261571
0.625 Remote Similarity NPC244038
0.6234 Remote Similarity NPC469835
0.6232 Remote Similarity NPC122239
0.623 Remote Similarity NPC269074
0.6222 Remote Similarity NPC183449
0.6222 Remote Similarity NPC45313
0.6222 Remote Similarity NPC197294
0.6222 Remote Similarity NPC8098
0.622 Remote Similarity NPC474312
0.6212 Remote Similarity NPC123669
0.6207 Remote Similarity NPC74672
0.6207 Remote Similarity NPC209047
0.6207 Remote Similarity NPC242503
0.6207 Remote Similarity NPC43074
0.6207 Remote Similarity NPC139782
0.619 Remote Similarity NPC85079
0.619 Remote Similarity NPC153538
0.619 Remote Similarity NPC31194
0.619 Remote Similarity NPC267110
0.619 Remote Similarity NPC248884
0.6154 Remote Similarity NPC188341
0.6154 Remote Similarity NPC49494
0.6136 Remote Similarity NPC473950
0.6136 Remote Similarity NPC111567
0.6136 Remote Similarity NPC309898
0.6136 Remote Similarity NPC473581
0.6136 Remote Similarity NPC282705
0.6136 Remote Similarity NPC15851
0.6136 Remote Similarity NPC186840
0.6136 Remote Similarity NPC263545
0.6136 Remote Similarity NPC182632
0.6136 Remote Similarity NPC475125
0.6136 Remote Similarity NPC473604
0.6129 Remote Similarity NPC319709
0.6129 Remote Similarity NPC289484
0.6119 Remote Similarity NPC329686
0.6118 Remote Similarity NPC166458
0.6094 Remote Similarity NPC199286
0.6094 Remote Similarity NPC477727
0.6094 Remote Similarity NPC474642
0.6094 Remote Similarity NPC473913
0.6094 Remote Similarity NPC249670
0.6094 Remote Similarity NPC471281
0.6087 Remote Similarity NPC181872
0.6087 Remote Similarity NPC226848
0.6064 Remote Similarity NPC471083
0.6064 Remote Similarity NPC50815
0.6064 Remote Similarity NPC247060
0.6061 Remote Similarity NPC217188
0.6056 Remote Similarity NPC324077
0.6056 Remote Similarity NPC47333
0.6034 Remote Similarity NPC15934
0.6 Remote Similarity NPC156782
0.6 Remote Similarity NPC165447
0.6 Remote Similarity NPC71053
0.6 Remote Similarity NPC9273
0.6 Remote Similarity NPC170776
0.6 Remote Similarity NPC76198
0.6 Remote Similarity NPC89824
0.6 Remote Similarity NPC54961
0.6 Remote Similarity NPC59408
0.6 Remote Similarity NPC129263
0.6 Remote Similarity NPC477723
0.6 Remote Similarity NPC475931
0.6 Remote Similarity NPC475477
0.6 Remote Similarity NPC329608
0.6 Remote Similarity NPC224148
0.6 Remote Similarity NPC93639
0.6 Remote Similarity NPC471959
0.6 Remote Similarity NPC294278
0.6 Remote Similarity NPC197272
0.6 Remote Similarity NPC157353
0.6 Remote Similarity NPC282088
0.6 Remote Similarity NPC256656
0.6 Remote Similarity NPC474812
0.6 Remote Similarity NPC158445
0.6 Remote Similarity NPC55383
0.5974 Remote Similarity NPC469836
0.5972 Remote Similarity NPC77891
0.597 Remote Similarity NPC256209
0.597 Remote Similarity NPC473532
0.597 Remote Similarity NPC49059
0.597 Remote Similarity NPC189677
0.5968 Remote Similarity NPC76976
0.5949 Remote Similarity NPC476923
0.5942 Remote Similarity NPC11130
0.5942 Remote Similarity NPC245650
0.5938 Remote Similarity NPC471280
0.5938 Remote Similarity NPC471275
0.5938 Remote Similarity NPC125122
0.5938 Remote Similarity NPC471276

  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 NPC29468 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
0.7424 Intermediate Similarity NPD3210 Clinical (unspecified phase)
0.678 Remote Similarity NPD4265 Approved
0.6712 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6207 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6129 Remote Similarity NPD3211 Approved
0.5833 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5797 Remote Similarity NPD4219 Approved
0.5714 Remote Similarity NPD860 Phase 2
0.5667 Remote Similarity NPD6094 Approved
0.5667 Remote Similarity NPD6095 Approved
0.5652 Remote Similarity NPD342 Phase 1

  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